praneet1988 / inferring-and-visualizing-rna-velocity-in-bulk-rna-seq Goto Github PK

Hi,

I use the pipeline you provide. But When I use Velocyto, error occurred.

2022-05-06 09:27:43,140 - INFO - No SAMPLEID specified, the sample will be called CD133_vesicle_from_PLC_1_S37_L002_Aligned_HDXSQ (last 5 digits are a random-id to avoid overwriting some other file by mistake)
2022-05-06 09:27:43,140 - DEBUG - Using logic: Default
2022-05-06 09:27:43,140 - DEBUG - Cell barcodes will be determined while reading the .bam file
2022-05-06 09:27:43,162 - WARNING - Your system does not support calling grep MemAvailable /proc/meminfo so the memory effort for the samtools command could not be chosen appropriately. 32Gb will be assumed
2022-05-06 09:27:43,162 - DEBUG - Peeking into /mnt/dell4/Kota/CD133_vesicle_from_PLC_1_S37_L002_Aligned.velocyto.sorted.bam
2022-05-06 09:27:43,267 - WARNING - The file /mnt/dell4/Kota/cellsorted_CD133_vesicle_from_PLC_1_S37_L002_Aligned.velocyto.sorted.bam already exists. The sorting step will be skipped and the existing file will be used.
2022-05-06 09:27:43,267 - INFO - Load the annotation from /mnt/dell4/Homo_sapiens/UCSC/hg19/Annotation/Archives/archive-2015-07-17-14-32-32/Genes/genes.gtf
2022-05-06 09:27:44,108 - WARNING - The entry exon_number was not present in the gtf file. It will be infferred from the position.
2022-05-06 09:27:53,719 - DEBUG - Parsing Chromosome 1 strand - [line 0]
2022-05-06 09:27:54,212 - DEBUG - Done with 1- [line 23050]
2022-05-06 09:27:54,212 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:54,224 - DEBUG - Seen 1305 genes until now
2022-05-06 09:27:54,225 - DEBUG - Parsing Chromosome 1 strand + [line 23051]
2022-05-06 09:27:54,754 - DEBUG - Done with 1+ [line 48458]
2022-05-06 09:27:54,754 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:54,770 - DEBUG - Seen 2631 genes until now
2022-05-06 09:27:54,770 - DEBUG - Parsing Chromosome 10 strand - [line 48459]
2022-05-06 09:27:55,313 - DEBUG - Done with 10- [line 59341]
2022-05-06 09:27:55,313 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:55,319 - DEBUG - Seen 3136 genes until now
2022-05-06 09:27:55,319 - DEBUG - Parsing Chromosome 10 strand + [line 59342]
2022-05-06 09:27:55,544 - DEBUG - Done with 10+ [line 69777]
2022-05-06 09:27:55,544 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:55,550 - DEBUG - Seen 3662 genes until now
2022-05-06 09:27:55,550 - DEBUG - Parsing Chromosome 11 strand - [line 69778]
2022-05-06 09:27:55,820 - DEBUG - Done with 11- [line 82401]
2022-05-06 09:27:55,820 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:55,828 - DEBUG - Seen 4446 genes until now
2022-05-06 09:27:55,828 - DEBUG - Parsing Chromosome 11 strand + [line 82402]
2022-05-06 09:27:56,133 - DEBUG - Done with 11+ [line 96727]
2022-05-06 09:27:56,134 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:56,142 - DEBUG - Seen 5254 genes until now
2022-05-06 09:27:56,142 - DEBUG - Parsing Chromosome 12 strand - [line 96728]
2022-05-06 09:27:56,803 - DEBUG - Done with 12- [line 109880]
2022-05-06 09:27:56,803 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:56,811 - DEBUG - Seen 5919 genes until now
2022-05-06 09:27:56,811 - DEBUG - Parsing Chromosome 12 strand + [line 109881]
2022-05-06 09:27:57,103 - DEBUG - Done with 12+ [line 123770]
2022-05-06 09:27:57,104 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:57,110 - DEBUG - Seen 6563 genes until now
2022-05-06 09:27:57,110 - DEBUG - Parsing Chromosome 13 strand - [line 123771]
2022-05-06 09:27:57,206 - DEBUG - Done with 13- [line 128367]
2022-05-06 09:27:57,207 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:57,209 - DEBUG - Seen 6857 genes until now
2022-05-06 09:27:57,209 - DEBUG - Parsing Chromosome 13 strand + [line 128368]
2022-05-06 09:27:57,297 - DEBUG - Done with 13+ [line 132480]
2022-05-06 09:27:57,297 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:57,299 - DEBUG - Seen 7149 genes until now
2022-05-06 09:27:57,300 - DEBUG - Parsing Chromosome 14 strand - [line 132481]
2022-05-06 09:27:57,444 - DEBUG - Done with 14- [line 139278]
2022-05-06 09:27:57,445 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:57,448 - DEBUG - Seen 7528 genes until now
2022-05-06 09:27:57,449 - DEBUG - Parsing Chromosome 14 strand + [line 139279]
2022-05-06 09:27:57,612 - DEBUG - Done with 14+ [line 147015]
2022-05-06 09:27:57,612 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:57,617 - DEBUG - Seen 8010 genes until now
2022-05-06 09:27:57,617 - DEBUG - Parsing Chromosome 15 strand - [line 147016]
2022-05-06 09:27:58,251 - DEBUG - Done with 15- [line 156162]
2022-05-06 09:27:58,251 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:58,255 - DEBUG - Seen 8426 genes until now
2022-05-06 09:27:58,255 - DEBUG - Parsing Chromosome 15 strand + [line 156163]
2022-05-06 09:27:58,421 - DEBUG - Done with 15+ [line 164141]
2022-05-06 09:27:58,422 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:58,426 - DEBUG - Seen 8925 genes until now
2022-05-06 09:27:58,426 - DEBUG - Parsing Chromosome 16 strand - [line 164142]
2022-05-06 09:27:58,604 - DEBUG - Done with 16- [line 172634]
2022-05-06 09:27:58,605 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:58,609 - DEBUG - Seen 9435 genes until now
2022-05-06 09:27:58,609 - DEBUG - Parsing Chromosome 16 strand + [line 172635]
2022-05-06 09:27:58,843 - DEBUG - Done with 16+ [line 183783]
2022-05-06 09:27:58,843 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:58,854 - DEBUG - Seen 9991 genes until now
2022-05-06 09:27:58,855 - DEBUG - Parsing Chromosome 17 strand - [line 183784]
2022-05-06 09:27:59,154 - DEBUG - Done with 17- [line 197972]
2022-05-06 09:27:59,154 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:59,161 - DEBUG - Seen 10784 genes until now
2022-05-06 09:27:59,162 - DEBUG - Parsing Chromosome 17 strand + [line 197973]
2022-05-06 09:27:59,438 - DEBUG - Done with 17+ [line 211354]
2022-05-06 09:27:59,439 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:59,446 - DEBUG - Seen 11471 genes until now
2022-05-06 09:27:59,446 - DEBUG - Parsing Chromosome 17_ctg5_hap1 strand - [line 211355]
2022-05-06 09:27:59,454 - DEBUG - Done with 17_ctg5_hap1- [line 211728]
2022-05-06 09:27:59,454 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:59,455 - DEBUG - Seen 11471 genes until now
2022-05-06 09:27:59,455 - DEBUG - Parsing Chromosome 17_ctg5_hap1 strand + [line 211729]
2022-05-06 09:27:59,457 - DEBUG - Done with 17_ctg5_hap1+ [line 211823]
2022-05-06 09:27:59,457 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:59,457 - DEBUG - Seen 11471 genes until now
2022-05-06 09:27:59,457 - DEBUG - Parsing Chromosome 17_gl000205_random strand + [line 211824]
2022-05-06 09:27:59,457 - DEBUG - Done with 17_gl000205_random+ [line 211824]
2022-05-06 09:27:59,457 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:59,458 - DEBUG - Seen 11472 genes until now
2022-05-06 09:27:59,458 - DEBUG - Parsing Chromosome 18 strand - [line 211825]
2022-05-06 09:27:59,531 - DEBUG - Done with 18- [line 215288]
2022-05-06 09:27:59,531 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:59,533 - DEBUG - Seen 11659 genes until now
2022-05-06 09:27:59,533 - DEBUG - Parsing Chromosome 18 strand + [line 215289]
2022-05-06 09:28:00,179 - DEBUG - Done with 18+ [line 219231]
2022-05-06 09:28:00,179 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:00,181 - DEBUG - Seen 11864 genes until now
2022-05-06 09:28:00,181 - DEBUG - Parsing Chromosome 19 strand - [line 219232]
2022-05-06 09:28:00,437 - DEBUG - Done with 19- [line 231523]
2022-05-06 09:28:00,437 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:00,444 - DEBUG - Seen 12678 genes until now
2022-05-06 09:28:00,445 - DEBUG - Parsing Chromosome 19 strand + [line 231524]
2022-05-06 09:28:00,720 - DEBUG - Done with 19+ [line 244758]
2022-05-06 09:28:00,720 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:00,728 - DEBUG - Seen 13577 genes until now
2022-05-06 09:28:00,728 - DEBUG - Parsing Chromosome 19_gl000209_random strand + [line 244759]
2022-05-06 09:28:00,731 - DEBUG - Done with 19_gl000209_random+ [line 244895]
2022-05-06 09:28:00,731 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:00,731 - DEBUG - Seen 13585 genes until now
2022-05-06 09:28:00,731 - DEBUG - Parsing Chromosome 1_gl000191_random strand - [line 244896]
2022-05-06 09:28:00,733 - DEBUG - Done with 1_gl000191_random- [line 244950]
2022-05-06 09:28:00,733 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:00,733 - DEBUG - Seen 13585 genes until now
2022-05-06 09:28:00,733 - DEBUG - Parsing Chromosome 1_gl000192_random strand - [line 244951]
2022-05-06 09:28:00,734 - DEBUG - Done with 1_gl000192_random- [line 245001]
2022-05-06 09:28:00,735 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:00,735 - DEBUG - Seen 13587 genes until now
2022-05-06 09:28:00,735 - DEBUG - Parsing Chromosome 2 strand - [line 245002]
2022-05-06 09:28:01,121 - DEBUG - Done with 2- [line 263870]
2022-05-06 09:28:01,122 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:01,131 - DEBUG - Seen 14417 genes until now
2022-05-06 09:28:01,131 - DEBUG - Parsing Chromosome 2 strand + [line 263871]
2022-05-06 09:28:01,502 - DEBUG - Done with 2+ [line 281952]
2022-05-06 09:28:01,502 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:01,510 - DEBUG - Seen 15266 genes until now
2022-05-06 09:28:01,510 - DEBUG - Parsing Chromosome 20 strand - [line 281953]
2022-05-06 09:28:01,630 - DEBUG - Done with 20- [line 287676]
2022-05-06 09:28:01,631 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:01,634 - DEBUG - Seen 15615 genes until now
2022-05-06 09:28:01,634 - DEBUG - Parsing Chromosome 20 strand + [line 287677]
2022-05-06 09:28:01,771 - DEBUG - Done with 20+ [line 294332]
2022-05-06 09:28:01,771 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:01,775 - DEBUG - Seen 16002 genes until now
2022-05-06 09:28:01,775 - DEBUG - Parsing Chromosome 21 strand - [line 294333]
2022-05-06 09:28:01,835 - DEBUG - Done with 21- [line 297176]
2022-05-06 09:28:01,836 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:01,837 - DEBUG - Seen 16185 genes until now
2022-05-06 09:28:01,838 - DEBUG - Parsing Chromosome 21 strand + [line 297177]
2022-05-06 09:28:02,541 - DEBUG - Done with 21+ [line 300102]
2022-05-06 09:28:02,541 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:02,543 - DEBUG - Seen 16341 genes until now
2022-05-06 09:28:02,543 - DEBUG - Parsing Chromosome 22 strand - [line 300103]
2022-05-06 09:28:02,641 - DEBUG - Done with 22- [line 304874]
2022-05-06 09:28:02,641 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:02,644 - DEBUG - Seen 16635 genes until now
2022-05-06 09:28:02,644 - DEBUG - Parsing Chromosome 22 strand + [line 304875]
2022-05-06 09:28:02,760 - DEBUG - Done with 22+ [line 310536]
2022-05-06 09:28:02,761 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:02,763 - DEBUG - Seen 16929 genes until now
2022-05-06 09:28:02,764 - DEBUG - Parsing Chromosome 3 strand - [line 310537]
2022-05-06 09:28:03,048 - DEBUG - Done with 3- [line 324266]
2022-05-06 09:28:03,049 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:03,055 - DEBUG - Seen 17642 genes until now
2022-05-06 09:28:03,055 - DEBUG - Parsing Chromosome 3 strand + [line 324267]
2022-05-06 09:28:03,344 - DEBUG - Done with 3+ [line 338415]
2022-05-06 09:28:03,344 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:03,353 - DEBUG - Seen 18372 genes until now
2022-05-06 09:28:03,354 - DEBUG - Parsing Chromosome 4 strand - [line 338416]
2022-05-06 09:28:03,544 - DEBUG - Done with 4- [line 347712]
2022-05-06 09:28:03,544 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:03,549 - DEBUG - Seen 18851 genes until now
2022-05-06 09:28:03,549 - DEBUG - Parsing Chromosome 4 strand + [line 347713]
2022-05-06 09:28:03,739 - DEBUG - Done with 4+ [line 356946]
2022-05-06 09:28:03,739 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:03,744 - DEBUG - Seen 19363 genes until now
2022-05-06 09:28:03,744 - DEBUG - Parsing Chromosome 4_ctg9_hap1 strand - [line 356947]
2022-05-06 09:28:03,746 - DEBUG - Done with 4_ctg9_hap1- [line 357014]
2022-05-06 09:28:03,746 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:03,746 - DEBUG - Seen 19363 genes until now
2022-05-06 09:28:03,746 - DEBUG - Parsing Chromosome 4_ctg9_hap1 strand + [line 357015]
2022-05-06 09:28:03,747 - DEBUG - Done with 4_ctg9_hap1+ [line 357042]
2022-05-06 09:28:03,747 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:03,747 - DEBUG - Seen 19363 genes until now
2022-05-06 09:28:03,747 - DEBUG - Parsing Chromosome 4_gl000193_random strand - [line 357043]
2022-05-06 09:28:03,747 - DEBUG - Done with 4_gl000193_random- [line 357048]
2022-05-06 09:28:03,747 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:03,747 - DEBUG - Seen 19364 genes until now
2022-05-06 09:28:03,747 - DEBUG - Parsing Chromosome 4_gl000194_random strand - [line 357049]
2022-05-06 09:28:03,748 - DEBUG - Done with 4_gl000194_random- [line 357067]
2022-05-06 09:28:03,748 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:03,748 - DEBUG - Seen 19365 genes until now
2022-05-06 09:28:03,748 - DEBUG - Parsing Chromosome 5 strand - [line 357068]
2022-05-06 09:28:03,955 - DEBUG - Done with 5- [line 367035]
2022-05-06 09:28:03,955 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:03,961 - DEBUG - Seen 19944 genes until now
2022-05-06 09:28:03,962 - DEBUG - Parsing Chromosome 5 strand + [line 367036]
2022-05-06 09:28:04,200 - DEBUG - Done with 5+ [line 378629]
2022-05-06 09:28:04,200 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:04,206 - DEBUG - Seen 20560 genes until now
2022-05-06 09:28:04,206 - DEBUG - Parsing Chromosome 6 strand - [line 378630]
2022-05-06 09:28:04,463 - DEBUG - Done with 6- [line 391139]
2022-05-06 09:28:04,464 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:04,470 - DEBUG - Seen 21237 genes until now
2022-05-06 09:28:04,470 - DEBUG - Parsing Chromosome 6 strand + [line 391140]
2022-05-06 09:28:05,438 - DEBUG - Done with 6+ [line 402242]
2022-05-06 09:28:05,439 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,447 - DEBUG - Seen 21905 genes until now
2022-05-06 09:28:05,447 - DEBUG - Parsing Chromosome 6_apd_hap1 strand - [line 402243]
2022-05-06 09:28:05,465 - DEBUG - Done with 6_apd_hap1- [line 403104]
2022-05-06 09:28:05,465 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,465 - DEBUG - Seen 21905 genes until now
2022-05-06 09:28:05,466 - DEBUG - Parsing Chromosome 6_apd_hap1 strand + [line 403105]
2022-05-06 09:28:05,477 - DEBUG - Done with 6_apd_hap1+ [line 403638]
2022-05-06 09:28:05,477 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,477 - DEBUG - Seen 21905 genes until now
2022-05-06 09:28:05,477 - DEBUG - Parsing Chromosome 6_cox_hap2 strand - [line 403639]
2022-05-06 09:28:05,521 - DEBUG - Done with 6_cox_hap2- [line 405640]
2022-05-06 09:28:05,521 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,522 - DEBUG - Seen 21906 genes until now
2022-05-06 09:28:05,522 - DEBUG - Parsing Chromosome 6_cox_hap2 strand + [line 405641]
2022-05-06 09:28:05,557 - DEBUG - Done with 6_cox_hap2+ [line 407389]
2022-05-06 09:28:05,557 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,558 - DEBUG - Seen 21906 genes until now
2022-05-06 09:28:05,558 - DEBUG - Parsing Chromosome 6_dbb_hap3 strand - [line 407390]
2022-05-06 09:28:05,597 - DEBUG - Done with 6_dbb_hap3- [line 409192]
2022-05-06 09:28:05,597 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,598 - DEBUG - Seen 21906 genes until now
2022-05-06 09:28:05,598 - DEBUG - Parsing Chromosome 6_dbb_hap3 strand + [line 409193]
2022-05-06 09:28:05,633 - DEBUG - Done with 6_dbb_hap3+ [line 410913]
2022-05-06 09:28:05,633 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,634 - DEBUG - Seen 21906 genes until now
2022-05-06 09:28:05,634 - DEBUG - Parsing Chromosome 6_mann_hap4 strand - [line 410914]
2022-05-06 09:28:05,663 - DEBUG - Done with 6_mann_hap4- [line 412381]
2022-05-06 09:28:05,663 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,664 - DEBUG - Seen 21906 genes until now
2022-05-06 09:28:05,664 - DEBUG - Parsing Chromosome 6_mann_hap4 strand + [line 412382]
2022-05-06 09:28:05,693 - DEBUG - Done with 6_mann_hap4+ [line 413693]
2022-05-06 09:28:05,694 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,694 - DEBUG - Seen 21906 genes until now
2022-05-06 09:28:05,695 - DEBUG - Parsing Chromosome 6_mcf_hap5 strand - [line 413694]
2022-05-06 09:28:05,734 - DEBUG - Done with 6_mcf_hap5- [line 415624]
2022-05-06 09:28:05,734 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,735 - DEBUG - Seen 21907 genes until now
2022-05-06 09:28:05,735 - DEBUG - Parsing Chromosome 6_mcf_hap5 strand + [line 415625]
2022-05-06 09:28:05,768 - DEBUG - Done with 6_mcf_hap5+ [line 417121]
2022-05-06 09:28:05,768 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,769 - DEBUG - Seen 21907 genes until now
2022-05-06 09:28:05,769 - DEBUG - Parsing Chromosome 6_qbl_hap6 strand - [line 417122]
2022-05-06 09:28:05,807 - DEBUG - Done with 6_qbl_hap6- [line 419021]
2022-05-06 09:28:05,807 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,808 - DEBUG - Seen 21907 genes until now
2022-05-06 09:28:05,808 - DEBUG - Parsing Chromosome 6_qbl_hap6 strand + [line 419022]
2022-05-06 09:28:05,845 - DEBUG - Done with 6_qbl_hap6+ [line 420751]
2022-05-06 09:28:05,845 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,846 - DEBUG - Seen 21907 genes until now
2022-05-06 09:28:05,846 - DEBUG - Parsing Chromosome 6_ssto_hap7 strand - [line 420752]
2022-05-06 09:28:05,879 - DEBUG - Done with 6_ssto_hap7- [line 422384]
2022-05-06 09:28:05,880 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,880 - DEBUG - Seen 21907 genes until now
2022-05-06 09:28:05,880 - DEBUG - Parsing Chromosome 6_ssto_hap7 strand + [line 422385]
2022-05-06 09:28:05,911 - DEBUG - Done with 6_ssto_hap7+ [line 423880]
2022-05-06 09:28:05,911 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,912 - DEBUG - Seen 21907 genes until now
2022-05-06 09:28:05,912 - DEBUG - Parsing Chromosome 7 strand - [line 423881]
2022-05-06 09:28:06,133 - DEBUG - Done with 7- [line 434605]
2022-05-06 09:28:06,133 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:06,138 - DEBUG - Seen 22517 genes until now
2022-05-06 09:28:06,139 - DEBUG - Parsing Chromosome 7 strand + [line 434606]
2022-05-06 09:28:06,391 - DEBUG - Done with 7+ [line 446945]
2022-05-06 09:28:06,392 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:06,397 - DEBUG - Seen 23150 genes until now
2022-05-06 09:28:06,398 - DEBUG - Parsing Chromosome 7_gl000195_random strand - [line 446946]
2022-05-06 09:28:06,398 - DEBUG - Done with 7_gl000195_random- [line 446949]
2022-05-06 09:28:06,398 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:06,398 - DEBUG - Seen 23151 genes until now
2022-05-06 09:28:06,398 - DEBUG - Parsing Chromosome 8 strand - [line 446950]
2022-05-06 09:28:06,572 - DEBUG - Done with 8- [line 455414]
2022-05-06 09:28:06,572 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:06,576 - DEBUG - Seen 23667 genes until now
2022-05-06 09:28:06,577 - DEBUG - Parsing Chromosome 8 strand + [line 455415]
2022-05-06 09:28:06,728 - DEBUG - Done with 8+ [line 462748]
2022-05-06 09:28:06,728 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:06,732 - DEBUG - Seen 24095 genes until now
2022-05-06 09:28:06,732 - DEBUG - Parsing Chromosome 9 strand - [line 462749]
2022-05-06 09:28:06,924 - DEBUG - Done with 9- [line 471970]
2022-05-06 09:28:06,925 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:06,929 - DEBUG - Seen 24659 genes until now
2022-05-06 09:28:06,930 - DEBUG - Parsing Chromosome 9 strand + [line 471971]
2022-05-06 09:28:07,141 - DEBUG - Done with 9+ [line 482378]
2022-05-06 09:28:07,142 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,146 - DEBUG - Seen 25145 genes until now
2022-05-06 09:28:07,146 - DEBUG - Parsing Chromosome Un_gl000211 strand + [line 482379]
2022-05-06 09:28:07,147 - DEBUG - Done with Un_gl000211+ [line 482385]
2022-05-06 09:28:07,147 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,147 - DEBUG - Seen 25146 genes until now
2022-05-06 09:28:07,147 - DEBUG - Parsing Chromosome Un_gl000212 strand + [line 482386]
2022-05-06 09:28:07,147 - DEBUG - Done with Un_gl000212+ [line 482393]
2022-05-06 09:28:07,147 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,147 - DEBUG - Seen 25147 genes until now
2022-05-06 09:28:07,147 - DEBUG - Parsing Chromosome Un_gl000213 strand - [line 482394]
2022-05-06 09:28:07,148 - DEBUG - Done with Un_gl000213- [line 482406]
2022-05-06 09:28:07,148 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,148 - DEBUG - Seen 25148 genes until now
2022-05-06 09:28:07,148 - DEBUG - Parsing Chromosome Un_gl000213 strand + [line 482407]
2022-05-06 09:28:07,148 - DEBUG - Done with Un_gl000213+ [line 482407]
2022-05-06 09:28:07,148 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,148 - DEBUG - Seen 25148 genes until now
2022-05-06 09:28:07,148 - DEBUG - Parsing Chromosome Un_gl000215 strand + [line 482408]
2022-05-06 09:28:07,148 - DEBUG - Done with Un_gl000215+ [line 482409]
2022-05-06 09:28:07,148 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,149 - DEBUG - Seen 25148 genes until now
2022-05-06 09:28:07,149 - DEBUG - Parsing Chromosome Un_gl000218 strand - [line 482410]
2022-05-06 09:28:07,149 - DEBUG - Done with Un_gl000218- [line 482419]
2022-05-06 09:28:07,149 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,149 - DEBUG - Seen 25150 genes until now
2022-05-06 09:28:07,149 - DEBUG - Parsing Chromosome Un_gl000219 strand - [line 482420]
2022-05-06 09:28:07,149 - DEBUG - Done with Un_gl000219- [line 482426]
2022-05-06 09:28:07,149 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,150 - DEBUG - Seen 25151 genes until now
2022-05-06 09:28:07,150 - DEBUG - Parsing Chromosome Un_gl000220 strand + [line 482427]
2022-05-06 09:28:07,150 - DEBUG - Done with Un_gl000220+ [line 482444]
2022-05-06 09:28:07,150 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,151 - DEBUG - Seen 25158 genes until now
2022-05-06 09:28:07,151 - DEBUG - Parsing Chromosome Un_gl000222 strand - [line 482445]
2022-05-06 09:28:07,151 - DEBUG - Done with Un_gl000222- [line 482464]
2022-05-06 09:28:07,151 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,151 - DEBUG - Seen 25158 genes until now
2022-05-06 09:28:07,151 - DEBUG - Parsing Chromosome Un_gl000223 strand - [line 482465]
2022-05-06 09:28:07,152 - DEBUG - Done with Un_gl000223- [line 482496]
2022-05-06 09:28:07,152 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,152 - DEBUG - Seen 25158 genes until now
2022-05-06 09:28:07,152 - DEBUG - Parsing Chromosome Un_gl000223 strand + [line 482497]
2022-05-06 09:28:07,153 - DEBUG - Done with Un_gl000223+ [line 482499]
2022-05-06 09:28:07,153 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,153 - DEBUG - Seen 25158 genes until now
2022-05-06 09:28:07,153 - DEBUG - Parsing Chromosome Un_gl000227 strand - [line 482500]
2022-05-06 09:28:07,153 - DEBUG - Done with Un_gl000227- [line 482502]
2022-05-06 09:28:07,153 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,153 - DEBUG - Seen 25158 genes until now
2022-05-06 09:28:07,153 - DEBUG - Parsing Chromosome Un_gl000228 strand - [line 482503]
2022-05-06 09:28:07,153 - DEBUG - Done with Un_gl000228- [line 482510]
2022-05-06 09:28:07,154 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,154 - DEBUG - Seen 25158 genes until now
2022-05-06 09:28:07,154 - DEBUG - Parsing Chromosome Un_gl000228 strand + [line 482511]
2022-05-06 09:28:07,154 - DEBUG - Done with Un_gl000228+ [line 482515]
2022-05-06 09:28:07,154 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,154 - DEBUG - Seen 25159 genes until now
2022-05-06 09:28:07,154 - DEBUG - Parsing Chromosome X strand - [line 482516]
2022-05-06 09:28:07,349 - DEBUG - Done with X- [line 491920]
2022-05-06 09:28:07,350 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,355 - DEBUG - Seen 25719 genes until now
2022-05-06 09:28:07,355 - DEBUG - Parsing Chromosome X strand + [line 491921]
2022-05-06 09:28:07,556 - DEBUG - Done with X+ [line 501736]
2022-05-06 09:28:07,556 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,561 - DEBUG - Seen 26258 genes until now
2022-05-06 09:28:07,562 - DEBUG - Parsing Chromosome Y strand - [line 501737]
2022-05-06 09:28:07,623 - DEBUG - Done with Y- [line 504685]
2022-05-06 09:28:07,624 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,625 - DEBUG - Seen 26337 genes until now
2022-05-06 09:28:07,625 - DEBUG - Parsing Chromosome Y strand + [line 504686]
2022-05-06 09:28:07,650 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,651 - DEBUG - Done with Y+ [line 505972]
2022-05-06 09:28:07,651 - DEBUG - Fixing corner cases of transcript models containg intron longer than 1000Kbp
2022-05-06 09:28:09,073 - DEBUG - Generated 957406 features corresponding to 54070 transcript models from /mnt/dell4/Homo_sapiens/UCSC/hg19/Annotation/Archives/archive-2015-07-17-14-32-32/Genes/genes.gtf
2022-05-06 09:28:09,095 - INFO - Load the repeat masking annotation from /mnt/dell4/Kota/GRCh38_rmsk.gtf
2022-05-06 09:28:09,095 - DEBUG - Reading /mnt/dell4/Kota/GRCh38_rmsk.gtf, the file will be sorted in memory
2022-05-06 09:29:23,793 - DEBUG - Processed masked annotation .gtf and generated 4545598 intervals to mask!
2022-05-06 09:29:24,686 - INFO - Scan /mnt/dell4/Kota/CD133_vesicle_from_PLC_1_S37_L002_Aligned.velocyto.sorted.bam to validate intron intervals
2022-05-06 09:29:27,456 - DEBUG - Reading /mnt/dell4/Kota/CD133_vesicle_from_PLC_1_S37_L002_Aligned.velocyto.sorted.bam
2022-05-06 09:29:27,472 - DEBUG - Read first 0 million reads
2022-05-06 09:29:27,473 - DEBUG - Marking up chromosome MT
2022-05-06 09:29:27,473 - WARNING - The .bam file refers to a chromosome 'MT+' not present in the annotation (.gtf) file
2022-05-06 09:29:27,473 - WARNING - The .bam file refers to a chromosome 'MT-' not present in the annotation (.gtf) file
2022-05-06 09:29:33,510 - DEBUG - Marking up chromosome 1
2022-05-06 09:36:27,453 - DEBUG - Marking up chromosome 2
2022-05-06 09:39:27,247 - DEBUG - Read first 10 million reads
2022-05-06 09:40:51,953 - DEBUG - Marking up chromosome 3
2022-05-06 09:44:08,252 - DEBUG - Marking up chromosome 4
2022-05-06 09:46:04,300 - DEBUG - Marking up chromosome 5
2022-05-06 09:48:35,946 - DEBUG - Read first 20 million reads
2022-05-06 09:49:34,299 - DEBUG - Marking up chromosome 6
2022-05-06 09:54:07,622 - DEBUG - Marking up chromosome 7
2022-05-06 09:58:27,385 - DEBUG - Read first 30 million reads
2022-05-06 09:59:16,124 - DEBUG - Marking up chromosome 8
2022-05-06 10:01:33,193 - DEBUG - Marking up chromosome 9
2022-05-06 10:04:11,369 - DEBUG - Marking up chromosome 10
2022-05-06 10:06:48,166 - DEBUG - Marking up chromosome 11
2022-05-06 10:08:17,138 - DEBUG - Read first 40 million reads
2022-05-06 10:11:10,313 - DEBUG - Marking up chromosome 12
2022-05-06 10:16:27,883 - DEBUG - Marking up chromosome 13
2022-05-06 10:17:36,592 - DEBUG - Marking up chromosome 14
2022-05-06 10:18:30,474 - DEBUG - Read first 50 million reads
2022-05-06 10:22:20,385 - DEBUG - Marking up chromosome 15
2022-05-06 10:24:48,630 - DEBUG - Marking up chromosome 16
2022-05-06 10:25:57,510 - DEBUG - Read first 60 million reads
2022-05-06 10:27:21,617 - DEBUG - Marking up chromosome 17
2022-05-06 10:32:39,165 - DEBUG - Marking up chromosome 18
2022-05-06 10:33:38,379 - DEBUG - Marking up chromosome 19
2022-05-06 10:36:17,952 - DEBUG - Read first 70 million reads
2022-05-06 10:38:55,659 - DEBUG - Marking up chromosome 20
2022-05-06 10:40:43,239 - DEBUG - Marking up chromosome 21
2022-05-06 10:41:52,243 - DEBUG - Marking up chromosome 22
2022-05-06 10:43:20,304 - DEBUG - Marking up chromosome X
2022-05-06 10:45:34,489 - DEBUG - Marking up chromosome Y
2022-05-06 10:45:41,570 - DEBUG - End of file. Reset index: start scanning from initial position.
2022-05-06 10:45:41,571 - DEBUG - 0 reads were skipped because no apropiate cell or umi barcode was found
2022-05-06 10:45:41,572 - DEBUG - Start molecule counting!
2022-05-06 10:45:48,024 - DEBUG - Features available for chromosomes : ['1-', '1+', '10-', '10+', '11-', '11+', '12-', '12+', '13-', '13+', '14-', '14+', '15-', '15+', '16-', '16+', '17-', '17+', '17_ctg5_hap1-', '17_ctg5_hap1+', '17_gl000205_random+', '18-', '18+', '19-', '19+', '19_gl000209_random+', '1_gl000191_random-', '1_gl000192_random-', '2-', '2+', '20-', '20+', '21-', '21+', '22-', '22+', '3-', '3+', '4-', '4+', '4_ctg9_hap1-', '4_ctg9_hap1+', '4_gl000193_random-', '4_gl000194_random-', '5-', '5+', '6-', '6+', '6_apd_hap1-', '6_apd_hap1+', '6_cox_hap2-', '6_cox_hap2+', '6_dbb_hap3-', '6_dbb_hap3+', '6_mann_hap4-', '6_mann_hap4+', '6_mcf_hap5-', '6_mcf_hap5+', '6_qbl_hap6-', '6_qbl_hap6+', '6_ssto_hap7-', '6_ssto_hap7+', '7-', '7+', '7_gl000195_random-', '8-', '8+', '9-', '9+', 'Un_gl000211+', 'Un_gl000212+', 'Un_gl000213-', 'Un_gl000213+', 'Un_gl000215+', 'Un_gl000218-', 'Un_gl000219-', 'Un_gl000220+', 'Un_gl000222-', 'Un_gl000223-', 'Un_gl000223+', 'Un_gl000227-', 'Un_gl000228-', 'Un_gl000228+', 'X-', 'X+', 'Y-', 'Y+']
2022-05-06 10:45:48,025 - DEBUG - Mask available for chromosomes : ['1-', '1+', '10-', '10+', '10_GL383545v1_alt-', '10_GL383545v1_alt+', '10_GL383546v1_alt-', '10_GL383546v1_alt+', '10_KI270824v1_alt-', '10_KI270824v1_alt+', '10_KI270825v1_alt-', '10_KI270825v1_alt+', '10_KN196480v1_fix-', '10_KN196480v1_fix+', '10_KN538365v1_fix-', '10_KN538365v1_fix+', '10_KN538366v1_fix-', '10_KN538366v1_fix+', '10_KN538367v1_fix-', '10_KN538367v1_fix+', '10_KQ090020v1_alt-', '10_KQ090020v1_alt+', '10_KQ090021v1_fix-', '10_KQ090021v1_fix+', '10_ML143354v1_fix-', '10_ML143354v1_fix+', '10_ML143355v1_fix-', '10_ML143355v1_fix+', '11-', '11+', '11_GL383547v1_alt-', '11_GL383547v1_alt+', '11_JH159136v1_alt-', '11_JH159136v1_alt+', '11_JH159137v1_alt-', '11_JH159137v1_alt+', '11_KI270721v1_random-', '11_KI270721v1_random+', '11_KI270826v1_alt-', '11_KI270826v1_alt+', '11_KI270827v1_alt-', '11_KI270827v1_alt+', '11_KI270829v1_alt-', '11_KI270829v1_alt+', '11_KI270830v1_alt-', '11_KI270830v1_alt+', '11_KI270831v1_alt-', '11_KI270831v1_alt+', '11_KI270832v1_alt-', '11_KI270832v1_alt+', '11_KI270902v1_alt-', '11_KI270902v1_alt+', '11_KI270903v1_alt-', '11_KI270903v1_alt+', '11_KI270927v1_alt-', '11_KI270927v1_alt+', '11_KN196481v1_fix-', '11_KN196481v1_fix+', '11_KN538368v1_alt-', '11_KN538368v1_alt+', '11_KQ090022v1_fix-', '11_KQ090022v1_fix+', '11_KQ759759v1_fix-', '11_KQ759759v1_fix+', '11_KV766195v1_fix-', '11_KV766195v1_fix+', '11_KZ559108v1_fix-', '11_KZ559108v1_fix+', '11_KZ559109v1_fix-', '11_KZ559109v1_fix+', '11_KZ559110v1_alt-', '11_KZ559110v1_alt+', '11_KZ559111v1_alt-', '11_KZ559111v1_alt+', '11_ML143356v1_fix-', '11_ML143356v1_fix+', '11_ML143357v1_fix-', '11_ML143357v1_fix+', '11_ML143358v1_fix-', '11_ML143358v1_fix+', '11_ML143359v1_fix-', '11_ML143359v1_fix+', '11_ML143360v1_fix-', '11_ML143360v1_fix+', '12-', '12+', '12_GL383549v1_alt-', '12_GL383549v1_alt+', '12_GL383550v2_alt-', '12_GL383550v2_alt+', '12_GL383551v1_alt-', '12_GL383551v1_alt+', '12_GL383552v1_alt-', '12_GL383552v1_alt+', '12_GL383553v2_alt-', '12_GL383553v2_alt+', '12_GL877875v1_alt-', '12_GL877875v1_alt+', '12_GL877876v1_alt-', '12_GL877876v1_alt+', '12_KI270833v1_alt-', '12_KI270833v1_alt+', '12_KI270834v1_alt-', '12_KI270834v1_alt+', '12_KI270835v1_alt-', '12_KI270835v1_alt+', '12_KI270836v1_alt-', '12_KI270836v1_alt+', '12_KI270837v1_alt-', '12_KI270837v1_alt+', '12_KI270904v1_alt-', '12_KI270904v1_alt+', '12_KN196482v1_fix-', '12_KN196482v1_fix+', '12_KN538369v1_fix-', '12_KN538369v1_fix+', '12_KN538370v1_fix-', '12_KN538370v1_fix+', '12_KQ090023v1_alt-', '12_KQ090023v1_alt+', '12_KQ759760v1_fix-', '12_KQ759760v1_fix+', '12_KZ208916v1_fix-', '12_KZ208916v1_fix+', '12_KZ208917v1_fix-', '12_KZ208917v1_fix+', '12_KZ208918v1_alt-', '12_KZ208918v1_alt+', '12_KZ559112v1_alt-', '12_KZ559112v1_alt+', '12_ML143361v1_fix-', '12_ML143361v1_fix+', '12_ML143362v1_fix-', '12_ML143362v1_fix+', '13-', '13+', '13_KI270838v1_alt-', '13_KI270838v1_alt+', '13_KI270839v1_alt-', '13_KI270839v1_alt+', '13_KI270840v1_alt-', '13_KI270840v1_alt+', '13_KI270841v1_alt-', '13_KI270841v1_alt+', '13_KI270842v1_alt-', '13_KI270842v1_alt+', '13_KI270843v1_alt-', '13_KI270843v1_alt+', '13_KN196483v1_fix-', '13_KN196483v1_fix+', '13_KN538371v1_fix-', '13_KN538371v1_fix+', '13_KN538372v1_fix-', '13_KN538372v1_fix+', '13_KN538373v1_fix-', '13_KN538373v1_fix+', '13_KQ090024v1_alt-', '13_KQ090024v1_alt+', '13_KQ090025v1_alt-', '13_KQ090025v1_alt+', '13_ML143363v1_fix+', '13_ML143364v1_fix-', '13_ML143364v1_fix+', '13_ML143365v1_fix-', '13_ML143365v1_fix+', '13_ML143366v1_fix-', '13_ML143366v1_fix+', '14-', '14+', '14_GL000009v2_random-', '14_GL000009v2_random+', '14_GL000194v1_random-', '14_GL000194v1_random+', '14_GL000225v1_random-', '14_GL000225v1_random+', '14_KI270722v1_random-', '14_KI270722v1_random+', '14_KI270723v1_random-', '14_KI270723v1_random+', '14_KI270724v1_random-', '14_KI270724v1_random+', '14_KI270725v1_random-', '14_KI270725v1_random+', '14_KI270726v1_random-', '14_KI270726v1_random+', '14_KI270844v1_alt-', '14_KI270844v1_alt+', '14_KI270845v1_alt-', '14_KI270845v1_alt+', '14_KI270846v1_alt-', '14_KI270846v1_alt+', '14_KI270847v1_alt-', '14_KI270847v1_alt+', '14_KZ208919v1_alt-', '14_KZ208919v1_alt+', '14_KZ208920v1_fix-', '14_KZ208920v1_fix+', '14_ML143367v1_fix-', '14_ML143367v1_fix+', '14_ML143368v1_alt-', '14_ML143368v1_alt+', '15-', '15+', '15_GL383554v1_alt-', '15_GL383554v1_alt+', '15_GL383555v2_alt-', '15_GL383555v2_alt+', '15_KI270727v1_random-', '15_KI270727v1_random+', '15_KI270848v1_alt-', '15_KI270848v1_alt+', '15_KI270849v1_alt-', '15_KI270849v1_alt+', '15_KI270850v1_alt-', '15_KI270850v1_alt+', '15_KI270851v1_alt-', '15_KI270851v1_alt+', '15_KI270852v1_alt-', '15_KI270852v1_alt+', '15_KI270905v1_alt-', '15_KI270905v1_alt+', '15_KI270906v1_alt-', '15_KI270906v1_alt+', '15_KN538374v1_fix-', '15_KN538374v1_fix+', '15_KQ031389v1_alt-', '15_KQ031389v1_alt+', '15_ML143369v1_fix-', '15_ML143369v1_fix+', '15_ML143370v1_fix-', '15_ML143370v1_fix+', '15_ML143371v1_fix-', '15_ML143371v1_fix+', '15_ML143372v1_fix-', '15_ML143372v1_fix+', '16-', '16+', '16_GL383556v1_alt-', '16_GL383556v1_alt+', '16_GL383557v1_alt-', '16_GL383557v1_alt+', '16_KI270728v1_random-', '16_KI270728v1_random+', '16_KI270853v1_alt-', '16_KI270853v1_alt+', '16_KI270854v1_alt-', '16_KI270854v1_alt+', '16_KI270855v1_alt-', '16_KI270855v1_alt+', '16_KI270856v1_alt-', '16_KI270856v1_alt+', '16_KQ031390v1_alt-', '16_KQ031390v1_alt+', '16_KQ090026v1_alt-', '16_KQ090026v1_alt+', '16_KQ090027v1_alt-', '16_KQ090027v1_alt+', '16_KV880768v1_fix-', '16_KV880768v1_fix+', '16_KZ208921v1_alt-', '16_KZ208921v1_alt+', '16_KZ559113v1_fix-', '16_KZ559113v1_fix+', '16_ML143373v1_fix-', '16_ML143373v1_fix+', '17-', '17+', '17_GL000205v2_random-', '17_GL000205v2_random+', '17_GL000258v2_alt-', '17_GL000258v2_alt+', '17_GL383563v3_alt-', '17_GL383563v3_alt+', '17_GL383564v2_alt-', '17_GL383564v2_alt+', '17_GL383565v1_alt-', '17_GL383565v1_alt+', '17_GL383566v1_alt-', '17_GL383566v1_alt+', '17_JH159146v1_alt-', '17_JH159146v1_alt+', '17_JH159147v1_alt-', '17_JH159147v1_alt+', '17_JH159148v1_alt-', '17_JH159148v1_alt+', '17_KI270729v1_random-', '17_KI270729v1_random+', '17_KI270730v1_random-', '17_KI270730v1_random+', '17_KI270857v1_alt-', '17_KI270857v1_alt+', '17_KI270858v1_alt-', '17_KI270858v1_alt+', '17_KI270859v1_alt-', '17_KI270859v1_alt+', '17_KI270860v1_alt-', '17_KI270860v1_alt+', '17_KI270861v1_alt-', '17_KI270861v1_alt+', '17_KI270862v1_alt-', '17_KI270862v1_alt+', '17_KI270907v1_alt-', '17_KI270907v1_alt+', '17_KI270908v1_alt-', '17_KI270908v1_alt+', '17_KI270909v1_alt-', '17_KI270909v1_alt+', '17_KI270910v1_alt-', '17_KI270910v1_alt+', '17_KV575245v1_fix-', '17_KV575245v1_fix+', '17_KV766196v1_fix-', '17_KV766196v1_fix+', '17_KV766197v1_alt-', '17_KV766197v1_alt+', '17_KV766198v1_alt-', '17_KV766198v1_alt+', '17_KZ559114v1_alt-', '17_KZ559114v1_alt+', '17_ML143374v1_fix-', '17_ML143374v1_fix+', '17_ML143375v1_fix-', '17_ML143375v1_fix+', '18-', '18+', '18_GL383567v1_alt-', '18_GL383567v1_alt+', '18_GL383568v1_alt-', '18_GL383568v1_alt+', '18_GL383569v1_alt-', '18_GL383569v1_alt+', '18_GL383570v1_alt-', '18_GL383570v1_alt+', '18_GL383571v1_alt-', '18_GL383571v1_alt+', '18_GL383572v1_alt-', '18_GL383572v1_alt+', '18_KI270863v1_alt-', '18_KI270863v1_alt+', '18_KI270864v1_alt-', '18_KI270864v1_alt+', '18_KI270911v1_alt-', '18_KI270911v1_alt+', '18_KI270912v1_alt-', '18_KI270912v1_alt+', '18_KQ090028v1_fix-', '18_KQ090028v1_fix+', '18_KQ458385v1_alt-', '18_KQ458385v1_alt+', '18_KZ208922v1_fix-', '18_KZ208922v1_fix+', '18_KZ559115v1_fix-', '18_KZ559115v1_fix+', '18_KZ559116v1_alt-', '18_KZ559116v1_alt+', '19-', '19+', '19_GL000209v2_alt-', '19_GL000209v2_alt+', '19_GL383573v1_alt-', '19_GL383573v1_alt+', '19_GL383574v1_alt-', '19_GL383574v1_alt+', '19_GL383575v2_alt-', '19_GL383575v2_alt+', '19_GL383576v1_alt-', '19_GL383576v1_alt+', '19_GL949746v1_alt-', '19_GL949746v1_alt+', '19_GL949747v2_alt-', '19_GL949747v2_alt+', '19_GL949748v2_alt-', '19_GL949748v2_alt+', '19_GL949749v2_alt-', '19_GL949749v2_alt+', '19_GL949750v2_alt-', '19_GL949750v2_alt+', '19_GL949751v2_alt-', '19_GL949751v2_alt+', '19_GL949752v1_alt-', '19_GL949752v1_alt+', '19_GL949753v2_alt-', '19_GL949753v2_alt+', '19_KI270865v1_alt-', '19_KI270865v1_alt+', '19_KI270866v1_alt-', '19_KI270866v1_alt+', '19_KI270867v1_alt-', '19_KI270867v1_alt+', '19_KI270868v1_alt-', '19_KI270868v1_alt+', '19_KI270882v1_alt-', '19_KI270882v1_alt+', '19_KI270883v1_alt-', '19_KI270883v1_alt+', '19_KI270884v1_alt-', '19_KI270884v1_alt+', '19_KI270885v1_alt-', '19_KI270885v1_alt+', '19_KI270886v1_alt-', '19_KI270886v1_alt+', '19_KI270887v1_alt-', '19_KI270887v1_alt+', '19_KI270888v1_alt-', '19_KI270888v1_alt+', '19_KI270889v1_alt-', '19_KI270889v1_alt+', '19_KI270890v1_alt-', '19_KI270890v1_alt+', '19_KI270891v1_alt-', '19_KI270891v1_alt+', '19_KI270914v1_alt-', '19_KI270914v1_alt+', '19_KI270915v1_alt-', '19_KI270915v1_alt+', '19_KI270916v1_alt-', '19_KI270916v1_alt+', '19_KI270917v1_alt-', '19_KI270917v1_alt+', '19_KI270918v1_alt-', '19_KI270918v1_alt+', '19_KI270919v1_alt-', '19_KI270919v1_alt+', '19_KI270920v1_alt-', '19_KI270920v1_alt+', '19_KI270921v1_alt-', '19_KI270921v1_alt+', '19_KI270922v1_alt-', '19_KI270922v1_alt+', '19_KI270923v1_alt-', '19_KI270923v1_alt+', '19_KI270929v1_alt-', '19_KI270929v1_alt+', '19_KI270930v1_alt-', '19_KI270930v1_alt+', '19_KI270931v1_alt-', '19_KI270931v1_alt+', '19_KI270932v1_alt-', '19_KI270932v1_alt+', '19_KI270933v1_alt-', '19_KI270933v1_alt+', '19_KI270938v1_alt-', '19_KI270938v1_alt+', '19_KN196484v1_fix-', '19_KN196484v1_fix+', '19_KQ458386v1_fix-', '19_KQ458386v1_fix+', '19_KV575246v1_alt-', '19_KV575246v1_alt+', '19_KV575247v1_alt-', '19_KV575247v1_alt+', '19_KV575248v1_alt-', '19_KV575248v1_alt+', '19_KV575249v1_alt-', '19_KV575249v1_alt+', '19_KV575250v1_alt-', '19_KV575250v1_alt+', '19_KV575251v1_alt-', '19_KV575251v1_alt+', '19_KV575252v1_alt-', '19_KV575252v1_alt+', '19_KV575253v1_alt-', '19_KV575253v1_alt+', '19_KV575254v1_alt-', '19_KV575254v1_alt+', '19_KV575255v1_alt-', '19_KV575255v1_alt+', '19_KV575256v1_alt-', '19_KV575256v1_alt+', '19_KV575257v1_alt-', '19_KV575257v1_alt+', '19_KV575258v1_alt-', '19_KV575258v1_alt+', '19_KV575259v1_alt-', '19_KV575259v1_alt+', '19_KV575260v1_alt-', '19_KV575260v1_alt+', '19_ML143376v1_fix-', '19_ML143376v1_fix+', '1_GL383518v1_alt-', '1_GL383518v1_alt+', '1_GL383519v1_alt-', '1_GL383519v1_alt+', '1_GL383520v2_alt-', '1_GL383520v2_alt+', '1_KI270706v1_random-', '1_KI270706v1_random+', '1_KI270707v1_random-', '1_KI270707v1_random+', '1_KI270708v1_random-', '1_KI270708v1_random+', '1_KI270709v1_random-', '1_KI270709v1_random+', '1_KI270710v1_random-', '1_KI270710v1_random+', '1_KI270711v1_random-', '1_KI270711v1_random+', '1_KI270712v1_random-', '1_KI270712v1_random+', '1_KI270713v1_random-', '1_KI270713v1_random+', '1_KI270714v1_random-', '1_KI270714v1_random+', '1_KI270759v1_alt-', '1_KI270759v1_alt+', '1_KI270760v1_alt-', '1_KI270760v1_alt+', '1_KI270761v1_alt-', '1_KI270761v1_alt+', '1_KI270762v1_alt-', '1_KI270762v1_alt+', '1_KI270763v1_alt-', '1_KI270763v1_alt+', '1_KI270764v1_alt-', '1_KI270764v1_alt+', '1_KI270765v1_alt-', '1_KI270765v1_alt+', '1_KI270766v1_alt-', '1_KI270766v1_alt+', '1_KI270892v1_alt-', '1_KI270892v1_alt+', '1_KN196472v1_fix-', '1_KN196472v1_fix+', '1_KN196473v1_fix-', '1_KN196473v1_fix+', '1_KN196474v1_fix-', '1_KN196474v1_fix+', '1_KN538360v1_fix-', '1_KN538360v1_fix+', '1_KN538361v1_fix-', '1_KN538361v1_fix+', '1_KQ031383v1_fix-', '1_KQ031383v1_fix+', '1_KQ458382v1_alt-', '1_KQ458382v1_alt+', '1_KQ458383v1_alt-', '1_KQ458383v1_alt+', '1_KQ458384v1_alt-', '1_KQ458384v1_alt+', '1_KQ983255v1_alt-', '1_KQ983255v1_alt+', '1_KV880763v1_alt-', '1_KV880763v1_alt+', '1_KZ208904v1_alt-', '1_KZ208904v1_alt+', '1_KZ208905v1_alt-', '1_KZ208905v1_alt+', '1_KZ208906v1_fix-', '1_KZ208906v1_fix+', '1_KZ559100v1_fix-', '1_KZ559100v1_fix+', '2-', '2+', '20-', '20+', '20_GL383577v2_alt-', '20_GL383577v2_alt+', '20_KI270869v1_alt-', '20_KI270869v1_alt+', '20_KI270870v1_alt-', '20_KI270870v1_alt+', '20_KI270871v1_alt-', '20_KI270871v1_alt+', '21-', '21+', '21_GL383578v2_alt-', '21_GL383578v2_alt+', '21_GL383579v2_alt-', '21_GL383579v2_alt+', '21_GL383580v2_alt-', '21_GL383580v2_alt+', '21_GL383581v2_alt-', '21_GL383581v2_alt+', '21_KI270872v1_alt-', '21_KI270872v1_alt+', '21_KI270873v1_alt-', '21_KI270873v1_alt+', '21_KI270874v1_alt-', '21_KI270874v1_alt+', '21_ML143377v1_fix-', '21_ML143377v1_fix+', '22-', '22+', '22_GL383582v2_alt-', '22_GL383582v2_alt+', '22_GL383583v2_alt-', '22_GL383583v2_alt+', '22_KB663609v1_alt-', '22_KB663609v1_alt+', '22_KI270731v1_random-', '22_KI270731v1_random+', '22_KI270732v1_random-', '22_KI270732v1_random+', '22_KI270733v1_random-', '22_KI270733v1_random+', '22_KI270734v1_random-', '22_KI270734v1_random+', '22_KI270735v1_random-', '22_KI270735v1_random+', '22_KI270736v1_random-', '22_KI270736v1_random+', '22_KI270737v1_random-', '22_KI270737v1_random+', '22_KI270738v1_random-', '22_KI270738v1_random+', '22_KI270739v1_random-', '22_KI270739v1_random+', '22_KI270875v1_alt-', '22_KI270875v1_alt+', '22_KI270876v1_alt-', '22_KI270876v1_alt+', '22_KI270877v1_alt-', '22_KI270877v1_alt+', '22_KI270878v1_alt-', '22_KI270878v1_alt+', '22_KI270879v1_alt-', '22_KI270879v1_alt+', '22_KI270928v1_alt-', '22_KI270928v1_alt+', '22_KN196485v1_alt-', '22_KN196485v1_alt+', '22_KN196486v1_alt-', '22_KN196486v1_alt+', '22_KQ458387v1_alt-', '22_KQ458387v1_alt+', '22_KQ458388v1_alt-', '22_KQ458388v1_alt+', '22_KQ759761v1_alt-', '22_KQ759761v1_alt+', '22_KQ759762v1_fix-', '22_KQ759762v1_fix+', '22_ML143378v1_fix-', '22_ML143378v1_fix+', '22_ML143379v1_fix-', '22_ML143379v1_fix+', '22_ML143380v1_fix-', '22_ML143380v1_fix+', '2_GL383521v1_alt-', '2_GL383521v1_alt+', '2_GL383522v1_alt-', '2_GL383522v1_alt+', '2_GL582966v2_alt-', '2_GL582966v2_alt+', '2_KI270715v1_random+', '2_KI270716v1_random+', '2_KI270767v1_alt-', '2_KI270767v1_alt+', '2_KI270768v1_alt-', '2_KI270768v1_alt+', '2_KI270769v1_alt-', '2_KI270769v1_alt+', '2_KI270770v1_alt-', '2_KI270770v1_alt+', '2_KI270771v1_alt-', '2_KI270771v1_alt+', '2_KI270772v1_alt-', '2_KI270772v1_alt+', '2_KI270773v1_alt-', '2_KI270773v1_alt+', '2_KI270774v1_alt-', '2_KI270774v1_alt+', '2_KI270775v1_alt-', '2_KI270775v1_alt+', '2_KI270776v1_alt-', '2_KI270776v1_alt+', '2_KI270893v1_alt-', '2_KI270893v1_alt+', '2_KI270894v1_alt-', '2_KI270894v1_alt+', '2_KN538362v1_fix-', '2_KN538362v1_fix+', '2_KN538363v1_fix-', '2_KN538363v1_fix+', '2_KQ031384v1_fix-', '2_KQ031384v1_fix+', '2_KQ983256v1_alt-', '2_KQ983256v1_alt+', '2_KZ208907v1_alt-', '2_KZ208907v1_alt+', '2_KZ208908v1_alt-', '2_KZ208908v1_alt+', '2_ML143341v1_fix-', '2_ML143341v1_fix+', '2_ML143342v1_fix-', '2_ML143342v1_fix+', '3-', '3+', '3_GL000221v1_random-', '3_GL000221v1_random+', '3_GL383526v1_alt-', '3_GL383526v1_alt+', '3_JH636055v2_alt-', '3_JH636055v2_alt+', '3_KI270777v1_alt-', '3_KI270777v1_alt+', '3_KI270778v1_alt-', '3_KI270778v1_alt+', '3_KI270779v1_alt-', '3_KI270779v1_alt+', '3_KI270780v1_alt-', '3_KI270780v1_alt+', '3_KI270781v1_alt-', '3_KI270781v1_alt+', '3_KI270782v1_alt-', '3_KI270782v1_alt+', '3_KI270783v1_alt-', '3_KI270783v1_alt+', '3_KI270784v1_alt-', '3_KI270784v1_alt+', '3_KI270895v1_alt-', '3_KI270895v1_alt+', '3_KI270924v1_alt-', '3_KI270924v1_alt+', '3_KI270934v1_alt-', '3_KI270934v1_alt+', '3_KI270935v1_alt-', '3_KI270935v1_alt+', '3_KI270936v1_alt-', '3_KI270936v1_alt+', '3_KI270937v1_alt-', '3_KI270937v1_alt+', '3_KN196475v1_fix-', '3_KN196475v1_fix+', '3_KN196476v1_fix-', '3_KN196476v1_fix+', '3_KN538364v1_fix-', '3_KN538364v1_fix+', '3_KQ031385v1_fix-', '3_KQ031385v1_fix+', '3_KQ031386v1_fix-', '3_KQ031386v1_fix+', '3_KV766192v1_fix-', '3_KV766192v1_fix+', '3_KZ208909v1_alt-', '3_KZ208909v1_alt+', '3_KZ559101v1_alt-', '3_KZ559101v1_alt+', '3_KZ559102v1_alt-', '3_KZ559102v1_alt+', '3_KZ559103v1_alt-', '3_KZ559103v1_alt+', '3_KZ559104v1_fix-', '3_KZ559104v1_fix+', '3_KZ559105v1_alt-', '3_KZ559105v1_alt+', '3_ML143343v1_alt-', '3_ML143343v1_alt+', '4-', '4+', '4_GL000008v2_random-', '4_GL000008v2_random+', '4_GL000257v2_alt-', '4_GL000257v2_alt+', '4_GL383527v1_alt-', '4_GL383527v1_alt+', '4_GL383528v1_alt-', '4_GL383528v1_alt+', '4_KI270785v1_alt-', '4_KI270785v1_alt+', '4_KI270786v1_alt-', '4_KI270786v1_alt+', '4_KI270787v1_alt-', '4_KI270787v1_alt+', '4_KI270788v1_alt-', '4_KI270788v1_alt+', '4_KI270789v1_alt-', '4_KI270789v1_alt+', '4_KI270790v1_alt-', '4_KI270790v1_alt+', '4_KI270896v1_alt-', '4_KI270896v1_alt+', '4_KI270925v1_alt-', '4_KI270925v1_alt+', '4_KQ090013v1_alt-', '4_KQ090013v1_alt+', '4_KQ090014v1_alt-', '4_KQ090014v1_alt+', '4_KQ090015v1_alt-', '4_KQ090015v1_alt+', '4_KQ983257v1_fix-', '4_KQ983257v1_fix+', '4_KQ983258v1_alt-', '4_KQ983258v1_alt+', '4_KV766193v1_alt-', '4_KV766193v1_alt+', '4_ML143344v1_fix-', '4_ML143344v1_fix+', '4_ML143345v1_fix-', '4_ML143345v1_fix+', '4_ML143346v1_fix-', '4_ML143346v1_fix+', '4_ML143347v1_fix-', '4_ML143347v1_fix+', '4_ML143348v1_fix-', '4_ML143348v1_fix+', '4_ML143349v1_fix-', '4_ML143349v1_fix+', '5-', '5+', '5_GL000208v1_random-', '5_GL000208v1_random+', '5_GL339449v2_alt-', '5_GL339449v2_alt+', '5_GL383530v1_alt-', '5_GL383530v1_alt+', '5_GL383531v1_alt-', '5_GL383531v1_alt+', '5_GL383532v1_alt-', '5_GL383532v1_alt+', '5_GL949742v1_alt-', '5_GL949742v1_alt+', '5_KI270791v1_alt-', '5_KI270791v1_alt+', '5_KI270792v1_alt-', '5_KI270792v1_alt+', '5_KI270793v1_alt-', '5_KI270793v1_alt+', '5_KI270794v1_alt-', '5_KI270794v1_alt+', '5_KI270795v1_alt-', '5_KI270795v1_alt+', '5_KI270796v1_alt-', '5_KI270796v1_alt+', '5_KI270897v1_alt-', '5_KI270897v1_alt+', '5_KI270898v1_alt-', '5_KI270898v1_alt+', '5_KN196477v1_alt-', '5_KN196477v1_alt+', '5_KV575243v1_alt-', '5_KV575243v1_alt+', '5_KV575244v1_fix-', '5_KV575244v1_fix+', '5_KZ208910v1_alt-', '5_KZ208910v1_alt+', '5_ML143350v1_fix-', '5_ML143350v1_fix+', '6-', '6+', '6_GL000250v2_alt-', '6_GL000250v2_alt+', '6_GL000251v2_alt-', '6_GL000251v2_alt+', '6_GL000252v2_alt-', '6_GL000252v2_alt+', '6_GL000253v2_alt-', '6_GL000253v2_alt+', '6_GL000254v2_alt-', '6_GL000254v2_alt+', '6_GL000255v2_alt-', '6_GL000255v2_alt+', '6_GL000256v2_alt-', '6_GL000256v2_alt+', '6_GL383533v1_alt-', '6_GL383533v1_alt+', '6_KB021644v2_alt-', '6_KB021644v2_alt+', '6_KI270758v1_alt-', '6_KI270758v1_alt+', '6_KI270797v1_alt-', '6_KI270797v1_alt+', '6_KI270798v1_alt-', '6_KI270798v1_alt+', '6_KI270799v1_alt-', '6_KI270799v1_alt+', '6_KI270800v1_alt-', '6_KI270800v1_alt+', '6_KI270801v1_alt-', '6_KI270801v1_alt+', '6_KI270802v1_alt-', '6_KI270802v1_alt+', '6_KN196478v1_fix-', '6_KN196478v1_fix+', '6_KQ031387v1_fix-', '6_KQ031387v1_fix+', '6_KQ090016v1_fix-', '6_KQ090016v1_fix+', '6_KQ090017v1_alt-', '6_KQ090017v1_alt+', '6_KV766194v1_fix-', '6_KV766194v1_fix+', '6_KZ208911v1_fix-', '6_KZ208911v1_fix+', '6_ML143351v1_fix-', '6_ML143351v1_fix+', '7-', '7+', '7_GL383534v2_alt-', '7_GL383534v2_alt+', '7_KI270803v1_alt-', '7_KI270803v1_alt+', '7_KI270804v1_alt-', '7_KI270804v1_alt+', '7_KI270805v1_alt-', '7_KI270805v1_alt+', '7_KI270806v1_alt-', '7_KI270806v1_alt+', '7_KI270807v1_alt-', '7_KI270807v1_alt+', '7_KI270808v1_alt-', '7_KI270808v1_alt+', '7_KI270809v1_alt-', '7_KI270809v1_alt+', '7_KI270899v1_alt-', '7_KI270899v1_alt+', '7_KQ031388v1_fix-', '7_KQ031388v1_fix+', '7_KV880764v1_fix-', '7_KV880764v1_fix+', '7_KV880765v1_fix-', '7_KV880765v1_fix+', '7_KZ208912v1_fix-', '7_KZ208912v1_fix+', '7_KZ208913v1_alt-', '7_KZ208913v1_alt+', '7_KZ559106v1_alt-', '7_KZ559106v1_alt+', '7_ML143352v1_fix-', '7_ML143352v1_fix+', '8-', '8+', '8_KI270810v1_alt-', '8_KI270810v1_alt+', '8_KI270811v1_alt-', '8_KI270811v1_alt+', '8_KI270812v1_alt-', '8_KI270812v1_alt+', '8_KI270813v1_alt-', '8_KI270813v1_alt+', '8_KI270814v1_alt-', '8_KI270814v1_alt+', '8_KI270815v1_alt-', '8_KI270815v1_alt+', '8_KI270816v1_alt-', '8_KI270816v1_alt+', '8_KI270817v1_alt-', '8_KI270817v1_alt+', '8_KI270818v1_alt-', '8_KI270818v1_alt+', '8_KI270819v1_alt-', '8_KI270819v1_alt+', '8_KI270820v1_alt-', '8_KI270820v1_alt+', '8_KI270821v1_alt-', '8_KI270821v1_alt+', '8_KI270822v1_alt-', '8_KI270822v1_alt+', '8_KI270900v1_alt-', '8_KI270900v1_alt+', '8_KI270901v1_alt-', '8_KI270901v1_alt+', '8_KI270926v1_alt-', '8_KI270926v1_alt+', '8_KV880766v1_fix-', '8_KV880766v1_fix+', '8_KV880767v1_fix-', '8_KV880767v1_fix+', '8_KZ208914v1_fix-', '8_KZ208914v1_fix+', '8_KZ208915v1_fix-', '8_KZ208915v1_fix+', '8_KZ559107v1_alt-', '8_KZ559107v1_alt+', '9-', '9+', '9_GL383539v1_alt-', '9_GL383539v1_alt+', '9_GL383540v1_alt-', '9_GL383540v1_alt+', '9_GL383541v1_alt-', '9_GL383541v1_alt+', '9_GL383542v1_alt-', '9_GL383542v1_alt+', '9_KI270717v1_random-', '9_KI270717v1_random+', '9_KI270718v1_random-', '9_KI270718v1_random+', '9_KI270719v1_random-', '9_KI270719v1_random+', '9_KI270720v1_random-', '9_KI270720v1_random+', '9_KI270823v1_alt-', '9_KI270823v1_alt+', '9_KN196479v1_fix-', '9_KN196479v1_fix+', '9_KQ090018v1_alt-', '9_KQ090018v1_alt+', '9_KQ090019v1_alt-', '9_KQ090019v1_alt+', '9_ML143353v1_fix-', '9_ML143353v1_fix+', 'M-', 'M+', 'Un_GL000195v1-', 'Un_GL000195v1+', 'Un_GL000213v1-', 'Un_GL000213v1+', 'Un_GL000214v1-', 'Un_GL000214v1+', 'Un_GL000216v2-', 'Un_GL000216v2+', 'Un_GL000218v1-', 'Un_GL000218v1+', 'Un_GL000219v1-', 'Un_GL000219v1+', 'Un_GL000220v1-', 'Un_GL000220v1+', 'Un_GL000224v1-', 'Un_GL000224v1+', 'Un_GL000226v1+', 'Un_KI270302v1+', 'Un_KI270303v1-', 'Un_KI270304v1-', 'Un_KI270305v1+', 'Un_KI270310v1-', 'Un_KI270311v1+', 'Un_KI270312v1-', 'Un_KI270315v1+', 'Un_KI270316v1+', 'Un_KI270317v1-', 'Un_KI270320v1+', 'Un_KI270322v1-', 'Un_KI270329v1-', 'Un_KI270330v1-', 'Un_KI270330v1+', 'Un_KI270333v1-', 'Un_KI270334v1+', 'Un_KI270335v1+', 'Un_KI270336v1-', 'Un_KI270337v1-', 'Un_KI270338v1+', 'Un_KI270340v1+', 'Un_KI270362v1-', 'Un_KI270363v1-', 'Un_KI270364v1-', 'Un_KI270364v1+', 'Un_KI270366v1-', 'Un_KI270371v1+', 'Un_KI270372v1-', 'Un_KI270372v1+', 'Un_KI270373v1-', 'Un_KI270373v1+', 'Un_KI270374v1-', 'Un_KI270374v1+', 'Un_KI270375v1-', 'Un_KI270376v1-', 'Un_KI270378v1+', 'Un_KI270379v1+', 'Un_KI270381v1-', 'Un_KI270382v1+', 'Un_KI270383v1-', 'Un_KI270384v1-', 'Un_KI270385v1+', 'Un_KI270386v1-', 'Un_KI270387v1+', 'Un_KI270388v1+', 'Un_KI270389v1+', 'Un_KI270390v1+', 'Un_KI270391v1-', 'Un_KI270392v1+', 'Un_KI270393v1-', 'Un_KI270394v1+', 'Un_KI270395v1-', 'Un_KI270396v1-', 'Un_KI270411v1-', 'Un_KI270412v1-', 'Un_KI270414v1+', 'Un_KI270417v1+', 'Un_KI270418v1-', 'Un_KI270419v1+', 'Un_KI270420v1-', 'Un_KI270422v1-', 'Un_KI270423v1+', 'Un_KI270424v1+', 'Un_KI270425v1+', 'Un_KI270429v1+', 'Un_KI270435v1-', 'Un_KI270435v1+', 'Un_KI270438v1-', 'Un_KI270438v1+', 'Un_KI270442v1-', 'Un_KI270442v1+', 'Un_KI270448v1-', 'Un_KI270448v1+', 'Un_KI270465v1-', 'Un_KI270466v1+', 'Un_KI270467v1+', 'Un_KI270468v1+', 'Un_KI270507v1+', 'Un_KI270508v1-', 'Un_KI270509v1-', 'Un_KI270510v1+', 'Un_KI270511v1-', 'Un_KI270512v1-', 'Un_KI270512v1+', 'Un_KI270515v1+', 'Un_KI270516v1+', 'Un_KI270517v1-', 'Un_KI270518v1+', 'Un_KI270519v1-', 'Un_KI270519v1+', 'Un_KI270521v1-', 'Un_KI270521v1+', 'Un_KI270522v1-', 'Un_KI270528v1+', 'Un_KI270529v1-', 'Un_KI270530v1+', 'Un_KI270538v1-', 'Un_KI270538v1+', 'Un_KI270539v1+', 'Un_KI270544v1-', 'Un_KI270548v1+', 'Un_KI270579v1-', 'Un_KI270579v1+', 'Un_KI270580v1-', 'Un_KI270581v1-', 'Un_KI270581v1+', 'Un_KI270582v1-', 'Un_KI270582v1+', 'Un_KI270583v1+', 'Un_KI270584v1-', 'Un_KI270587v1-', 'Un_KI270588v1+', 'Un_KI270589v1-', 'Un_KI270589v1+', 'Un_KI270590v1-', 'Un_KI270591v1-', 'Un_KI270591v1+', 'Un_KI270593v1+', 'Un_KI270741v1-', 'Un_KI270741v1+', 'Un_KI270742v1-', 'Un_KI270742v1+', 'Un_KI270743v1-', 'Un_KI270743v1+', 'Un_KI270744v1-', 'Un_KI270744v1+', 'Un_KI270745v1-', 'Un_KI270745v1+', 'Un_KI270746v1-', 'Un_KI270746v1+', 'Un_KI270747v1-', 'Un_KI270747v1+', 'Un_KI270748v1-', 'Un_KI270748v1+', 'Un_KI270749v1-', 'Un_KI270749v1+', 'Un_KI270750v1-', 'Un_KI270750v1+', 'Un_KI270751v1-', 'Un_KI270751v1+', 'Un_KI270752v1-', 'Un_KI270752v1+', 'Un_KI270753v1-', 'Un_KI270753v1+', 'Un_KI270754v1-', 'Un_KI270754v1+', 'Un_KI270755v1-', 'Un_KI270755v1+', 'Un_KI270756v1+', 'Un_KI270757v1-', 'Un_KI270757v1+', 'X-', 'X+', 'X_KI270880v1_alt-', 'X_KI270880v1_alt+', 'X_KI270881v1_alt-', 'X_KI270881v1_alt+', 'X_KI270913v1_alt-', 'X_KI270913v1_alt+', 'X_KV766199v1_alt-', 'X_KV766199v1_alt+', 'X_ML143381v1_fix-', 'X_ML143381v1_fix+', 'X_ML143382v1_fix-', 'X_ML143382v1_fix+', 'X_ML143383v1_fix-', 'X_ML143383v1_fix+', 'X_ML143384v1_fix-', 'X_ML143384v1_fix+', 'X_ML143385v1_fix-', 'X_ML143385v1_fix+', 'Y-', 'Y+', 'Y_KI270740v1_random-', 'Y_KN196487v1_fix-', 'Y_KN196487v1_fix+', 'Y_KZ208923v1_fix-', 'Y_KZ208923v1_fix+', 'Y_KZ208924v1_fix-']
2022-05-06 10:45:48,025 - DEBUG - Summarizing the results of intron validation.
2022-05-06 10:45:48,613 - DEBUG - Validated 111700 introns (of which unique intervals 58817) out of 451668 total possible introns (considering each possible transcript models).
2022-05-06 10:45:48,614 - DEBUG - Reading /mnt/dell4/Kota/cellsorted_CD133_vesicle_from_PLC_1_S37_L002_Aligned.velocyto.sorted.bam
[E::idx_find_and_load] Could not retrieve index file for '/mnt/dell4/Kota/cellsorted_CD133_vesicle_from_PLC_1_S37_L002_Aligned.velocyto.sorted.bam'
2022-05-06 10:45:48,654 - DEBUG - Read first 0 million reads
2022-05-06 10:56:30,919 - DEBUG - Read first 10 million reads
2022-05-06 11:06:51,637 - DEBUG - Read first 20 million reads
2022-05-06 11:17:12,822 - DEBUG - Read first 30 million reads
2022-05-06 11:28:59,452 - DEBUG - Read first 40 million reads
2022-05-06 11:40:39,679 - DEBUG - Read first 50 million reads
2022-05-06 11:48:04,312 - DEBUG - Read first 60 million reads
2022-05-06 12:00:34,207 - DEBUG - Read first 70 million reads
2022-05-06 12:10:03,753 - DEBUG - Counting for batch 1, containing 1 cells and 71075728 reads
velocyto.sh: line 5: 43000 Killed velocyto run -U -m /mnt/dell4/Kota/GRCh38_rmsk.gtf --outputfolder VELOCYTO_OUT ${id}_Aligned.velocyto.sorted.bam /mnt/dell4/Homo_sapiens/UCSC/hg19/Annotation/Archives/archive-2015-07-17-14-32-32/Genes/genes.gtf

Could you tell me how to solve it?

Hello! I'm trying to run Velocyto on bulk RNA-seq from multiple samples, and while all of the upstream processing from your README file has worked beautifully, the cellsorted intermediate file is not populated, and therefore a loom file is not generated for any samples. Here is the bam file for input:

(RNAVelocity) [eed13@compute-a-16-60 CA1_0.25h_EE_rep1.dir]$ samtools view CA1_0.25h_EE_rep1Aligned.velocyto.sorted.bam | head
A00354:959:HKL37DSX5:4:1472:19551:16125 99 chr1 3069478 255 1S149M = 3069486 155 TGGGGCATGTATGGTGTGTTATGTTAGCTTTAAATATTGGCATTCCATGATACAGAAAAAAAATAAATCATGGTACTTTTGGCAGTGTTGCTTTAATTTAGGGATTAAGTTATACTAGAAAATATTAGGTTCCCACAGAGAGTAATAACT F:F,,F:FF:FFF:,FFF:FF::FFFFFFFF:FFFFFFF:F:FFFFFFFF,FFFFF:FFFFFFFF:FFFFFFFFFFF,:,FFFF,FFFFFFF:FFFFFFF:,,F::F:F:::FFF:F,FFFF:FF,F,:FF:,FFF:,FFFFFF:,FF,, AS:i:294 CB:Z:959 HI:i:1 NH:i:1 UB:Z:HKL37DSX5 nM:i:0
A00354:959:HKL37DSX5:4:1472:19551:16125 147 chr1 3069486 255 147M3S = 3069478 -155 TATGGTGTGTTATGTTAGCTTTAAATATTGGCATTCCATGATACAGAAAAAAAATAAATCATGGTACTTTTGGCAGTGTTGCTTTAATTTAGGGATTAAGTTATACTAGAAAATATTAGGTTCCCACAGAGAGTAATAACTGTCTTCCCC FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,FFF,FFFFFFFFFFF,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF,: AS:i:294 CB:Z:959 HI:i:1 NH:i:1 UB:Z:HKL37DSX5 nM:i:0
A00354:959:HKL37DSX5:4:1620:32750:30217 99 chr1 3072876 255 150M = 3073020 1241 GGCCAGAGTACTCTCTACAGGCAAGCTCTCCTCTTGCAGGGAAGGTGCACAGATATCTGGCATTCAGACCTGCCTCCTTGCTGAATATGAAGACCTGAAACAGGGCCTGTCCCAGAAGATGGGTTGCTTCTGCAATTTGCGCACTCATCT FFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:295 CB:Z:959 HI:i:1 NH:i:1 UB:Z:HKL37DSX5 XS:Z:- nM:i:0
A00354:959:HKL37DSX5:4:1620:32750:30217 147 chr1 3073020 255 94M949N54M2S = 3072876 -1241 TCATCTGCACAGACTGGTCTCCTGTTGTGGCCACCAGCTGCTCGCAACATGAACGGTTCGACTGAGAAGGCTACTCGAGCTGTAAGAGAGGAATCTGCTCTGGGGGTCAAAGCCCTCCTTGGCAGCCACCTTTTTCAGGCGGAGAAGGCC FF:FFFFFFF,FFFFFFFFF::FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FF,:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFF:FFFF:FFFFFFF,:FFFFFFFFFFFFFFFFFF:FFFFFFFFFF, AS:i:295 CB:Z:959 HI:i:1 NH:i:1 UB:Z:HKL37DSX5 XS:Z:- nM:i:0
A00354:959:HKL37DSX5:4:2374:26594:10786 99 chr1 3088616 0 137M13S = 3088616 137 TGTGGCTTCATTTTCATTAAACTCTAGAAAGTCCTTAATTTCTTTCTTTATTCCTTCCTTGACCAAGGTATCATTGAGAAGAGTGTTGTTCAGTTTCCACGTGAATGTTGGCTTTCTATTATTTATGTTGTTATTGACCCAGATCGGAAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFF AS:i:264 CB:Z:959 HI:i:1 NH:i:5 UB:Z:HKL37DSX5 nM:i:4
A00354:959:HKL37DSX5:4:2374:26594:10786 147 chr1 3088616 0 10S137M3S = 3088616 -137 CTTCCGATCTTGTGGCTTCATTTTCATTAAACTCTAGAAAGTCCTTAATTTCTTTCTTTATTCCTTCCTTGACCAAGGTATCATTGAGAAGAGTGTTGTTCAGTTTCCACGTGAATGTTGGCTTTCTATTATTTATGTTGTTATTGACCC FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFF,FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, AS:i:264 CB:Z:959 HI:i:1 NH:i:5 UB:Z:HKL37DSX5 nM:i:4
A00354:959:HKL37DSX5:4:1535:11776:6793 355 chr1 3113090 3 150M = 3378315 265321 CCCTGAGATTCCACCTCACACCAGTCAGAATGGCTAAGATCAAAAATTCAGGTGACAGCAGATGCTGGCGTGGATGTGGAGAAAGAGGAACACTCCTCCATTGTTGGTGGGATTGCAGGCTTGTACAAACACTATGGAAATCAGTCTGGC ,FF,:F:F,FFFF,FF,FFFF:F,,:FFFFFF:,FFF:FFFFFFF,F:FFFFFFFFF,FF:F,FFF,FFF:FFFF,:FFFFFFFFFFFFFFFFFF,FFFFF,,,::FFFF:FF:F:FFF,F,FFFFF:,FFFFF,F,:FF,FFFFFF:,: AS:i:223 CB:Z:959 HI:i:2 NH:i:2 UB:Z:HKL37DSX5 nM:i:9
A00354:959:HKL37DSX5:4:2565:20925:2660 99 chr1 3116985 255 8M104457N142M = 3221608 104767 TAATAGAGGTGTGAGAAAAGAAAGGGTATATTAAAAGGAATAGGCGGATTGCCCCAGTTAATACAAAATGCATCAAAAGGGAGGAAAATGTCCCAAAAAGCAGAGAGTACTCACTCTCTGGGCCTTATAGCAGGAGTACTCTGTTACCTT F,FF,:FFFF:FFF:FFFFFFFFF::F,:F,F,F:FFF::FFF:FF,F:F::FF,F:F,FF,FF:,FF,F,F,FF,FF::FFF:FFFFF,FFFFFFFFFFFFFFFF:,,,F,,FF,,FF,F,::F,FF:,FF::FFF:FFFFFFFF,F:, AS:i:270 CB:Z:959 HI:i:1 NH:i:1 UB:Z:HKL37DSX5 XS:Z:+ nM:i:10
A00354:959:HKL37DSX5:4:1133:19651:24940 99 chr1 3145199 255 150M = 3171237 26185 CCTCCAAAGTAGCCGATCACTTCTTTACTTTTCTGACATTTTGACAATATTTTTTTTCTTTCTCTTACTTTGCCACTGTTGTAATTGTGCATTTCCTGATGCACGTGGGACGGCTCAGGATGTTGGTATGATGAATTACTAACTCAAGAT FFFFFFFFFFFFFFF:FFFF:,,:,FFF,::FFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFFFF,:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:293 CB:Z:959 HI:i:1 NH:i:1 UB:Z:HKL37DSX5 nM:i:0
A00354:959:HKL37DSX5:4:2457:18801:13041 99 chr1 3147361 3 150M = 3245963 98734 GTCCTTATATTGTCTCCAGCAGAAGGTGGAGCCCAGATTAAAGGTGTGATCCACCACACCTTTAATCCCAGATGAAAGGCGTAGCCCAGATTAAAGGTGTGTTCCTTAAACTCGGAGATTCAATCTTCTGGAATCCATAGCCACTATGGC FFFFF:FFFFFFFFFFFFFFFFFFFFFF:F,FFFFFFFFFFF::FFFF,FFFFF,FFF:FFFFFFF,FFFFFFFFFF::F,FFF:FFF:FFFFFF::,FFFFFFFFFFFFFFF:FFFFFFFFFF:FF,F,,FFFFFF:F:F:FFFFFF:F AS:i:230 CB:Z:959 HI:i:1 NH:i:2 UB:Z:HKL37DSX5 nM:i:6

And the command along with the log/error:
(RNAVelocity) [eed13@compute-a-16-60 CA1_0.25h_EE_rep1.dir]$ velocyto run -U -vvv --outputfolder . CA1_0.25h_EE_rep1Aligned.velocyto.sorted.bam /n/groups/neuroduo/Erin/reference_files.dir/GRCm39.dir/Mus_musculus.GRCm39.111.chr.gtf
2024-05-31 16:26:27,915 - INFO - No SAMPLEID specified, the sample will be called CA1_0_PBMV3 (last 5 digits are a random-id to avoid overwriting some other file by mistake)
2024-05-31 16:26:27,915 - DEBUG - Using logic: Default
2024-05-31 16:26:27,916 - DEBUG - Cell barcodes will be determined while reading the .bam file
2024-05-31 16:26:27,952 - DEBUG - Peeking into /n/scratch/users/e/eed13/RNAVelocity/CA1_0.25h_EE_rep1.dir/CA1_0.25h_EE_rep1Aligned.velocyto.sorted.bam
2024-05-31 16:26:27,970 - WARNING - The file /n/scratch/users/e/eed13/RNAVelocity/CA1_0.25h_EE_rep1.dir/cellsorted_CA1_0.25h_EE_rep1Aligned.velocyto.sorted.bam already exists. The sorting step will be skipped and the existing file will be used.
2024-05-31 16:26:27,970 - INFO - Load the annotation from /n/groups/neuroduo/Erin/reference_files.dir/GRCm39.dir/Mus_musculus.GRCm39.111.chr.gtf
2024-05-31 16:26:33,710 - DEBUG - Parsing Chromosome 1 strand - [line 0]
2024-05-31 16:26:34,185 - DEBUG - Done with 1- [line 59575]
2024-05-31 16:26:34,185 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:34,195 - DEBUG - Seen 1747 genes until now
2024-05-31 16:26:34,195 - DEBUG - Parsing Chromosome 1 strand + [line 59576]
2024-05-31 16:26:34,659 - DEBUG - Done with 1+ [line 118661]
2024-05-31 16:26:34,660 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:34,670 - DEBUG - Seen 3557 genes until now
2024-05-31 16:26:34,670 - DEBUG - Parsing Chromosome 10 strand - [line 118662]
2024-05-31 16:26:34,858 - DEBUG - Done with 10- [line 160609]
2024-05-31 16:26:34,858 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:34,866 - DEBUG - Seen 4860 genes until now
2024-05-31 16:26:34,866 - DEBUG - Parsing Chromosome 10 strand + [line 160610]
2024-05-31 16:26:35,371 - DEBUG - Done with 10+ [line 205967]
2024-05-31 16:26:35,372 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:35,380 - DEBUG - Seen 6264 genes until now
2024-05-31 16:26:35,380 - DEBUG - Parsing Chromosome 11 strand - [line 205968]
2024-05-31 16:26:35,668 - DEBUG - Done with 11- [line 270664]
2024-05-31 16:26:35,668 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:35,680 - DEBUG - Seen 7870 genes until now
2024-05-31 16:26:35,680 - DEBUG - Parsing Chromosome 11 strand + [line 270665]
2024-05-31 16:26:36,222 - DEBUG - Done with 11+ [line 335655]
2024-05-31 16:26:36,222 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:36,233 - DEBUG - Seen 9385 genes until now
2024-05-31 16:26:36,233 - DEBUG - Parsing Chromosome 12 strand - [line 335656]
2024-05-31 16:26:36,357 - DEBUG - Done with 12- [line 363365]
2024-05-31 16:26:36,357 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:36,364 - DEBUG - Seen 10739 genes until now
2024-05-31 16:26:36,365 - DEBUG - Parsing Chromosome 12 strand + [line 363366]
2024-05-31 16:26:36,534 - DEBUG - Done with 12+ [line 401151]
2024-05-31 16:26:36,534 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:36,542 - DEBUG - Seen 11949 genes until now
2024-05-31 16:26:36,542 - DEBUG - Parsing Chromosome 13 strand - [line 401152]
2024-05-31 16:26:36,708 - DEBUG - Done with 13- [line 438444]
2024-05-31 16:26:36,708 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:36,716 - DEBUG - Seen 13251 genes until now
2024-05-31 16:26:36,716 - DEBUG - Parsing Chromosome 13 strand + [line 438445]
2024-05-31 16:26:37,138 - DEBUG - Done with 13+ [line 467860]
2024-05-31 16:26:37,138 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:37,145 - DEBUG - Seen 14528 genes until now
2024-05-31 16:26:37,145 - DEBUG - Parsing Chromosome 14 strand - [line 467861]
2024-05-31 16:26:37,323 - DEBUG - Done with 14- [line 507798]
2024-05-31 16:26:37,323 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:37,331 - DEBUG - Seen 15755 genes until now
2024-05-31 16:26:37,331 - DEBUG - Parsing Chromosome 14 strand + [line 507799]
2024-05-31 16:26:37,480 - DEBUG - Done with 14+ [line 542074]
2024-05-31 16:26:37,481 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:37,488 - DEBUG - Seen 17117 genes until now
2024-05-31 16:26:37,488 - DEBUG - Parsing Chromosome 15 strand - [line 542075]
2024-05-31 16:26:37,660 - DEBUG - Done with 15- [line 580501]
2024-05-31 16:26:37,660 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:37,668 - DEBUG - Seen 18096 genes until now
2024-05-31 16:26:37,668 - DEBUG - Parsing Chromosome 15 strand + [line 580502]
2024-05-31 16:26:37,820 - DEBUG - Done with 15+ [line 614251]
2024-05-31 16:26:37,820 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:37,827 - DEBUG - Seen 19059 genes until now
2024-05-31 16:26:37,827 - DEBUG - Parsing Chromosome 16 strand - [line 614252]
2024-05-31 16:26:37,956 - DEBUG - Done with 16- [line 643286]
2024-05-31 16:26:37,956 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:37,962 - DEBUG - Seen 19879 genes until now
2024-05-31 16:26:37,962 - DEBUG - Parsing Chromosome 16 strand + [line 643287]
2024-05-31 16:26:38,439 - DEBUG - Done with 16+ [line 675700]
2024-05-31 16:26:38,439 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:38,445 - DEBUG - Seen 20711 genes until now
2024-05-31 16:26:38,445 - DEBUG - Parsing Chromosome 17 strand - [line 675701]
2024-05-31 16:26:38,658 - DEBUG - Done with 17- [line 723378]
2024-05-31 16:26:38,658 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:38,668 - DEBUG - Seen 21938 genes until now
2024-05-31 16:26:38,669 - DEBUG - Parsing Chromosome 17 strand + [line 723379]
2024-05-31 16:26:38,889 - DEBUG - Done with 17+ [line 773931]
2024-05-31 16:26:38,889 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:38,898 - DEBUG - Seen 23126 genes until now
2024-05-31 16:26:38,898 - DEBUG - Parsing Chromosome 18 strand - [line 773932]
2024-05-31 16:26:38,991 - DEBUG - Done with 18- [line 794411]
2024-05-31 16:26:38,992 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:38,996 - DEBUG - Seen 23786 genes until now
2024-05-31 16:26:38,996 - DEBUG - Parsing Chromosome 18 strand + [line 794412]
2024-05-31 16:26:39,112 - DEBUG - Done with 18+ [line 821511]
2024-05-31 16:26:39,113 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:39,118 - DEBUG - Seen 24565 genes until now
2024-05-31 16:26:39,118 - DEBUG - Parsing Chromosome 19 strand - [line 821512]
2024-05-31 16:26:39,266 - DEBUG - Done with 19- [line 854981]
2024-05-31 16:26:39,267 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:39,272 - DEBUG - Seen 25279 genes until now
2024-05-31 16:26:39,272 - DEBUG - Parsing Chromosome 19 strand + [line 854982]
2024-05-31 16:26:39,789 - DEBUG - Done with 19+ [line 884581]
2024-05-31 16:26:39,789 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:39,794 - DEBUG - Seen 26023 genes until now
2024-05-31 16:26:39,795 - DEBUG - Parsing Chromosome 2 strand - [line 884582]
2024-05-31 16:26:40,149 - DEBUG - Done with 2- [line 964481]
2024-05-31 16:26:40,149 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:40,162 - DEBUG - Seen 27882 genes until now
2024-05-31 16:26:40,163 - DEBUG - Parsing Chromosome 2 strand + [line 964482]
2024-05-31 16:26:40,491 - DEBUG - Done with 2+ [line 1039751]
2024-05-31 16:26:40,491 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:40,505 - DEBUG - Seen 29899 genes until now
2024-05-31 16:26:40,506 - DEBUG - Parsing Chromosome 3 strand - [line 1039752]
2024-05-31 16:26:40,685 - DEBUG - Done with 3- [line 1081512]
2024-05-31 16:26:40,686 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:40,695 - DEBUG - Seen 31394 genes until now
2024-05-31 16:26:40,696 - DEBUG - Parsing Chromosome 3 strand + [line 1081513]
2024-05-31 16:26:40,899 - DEBUG - Done with 3+ [line 1127702]
2024-05-31 16:26:40,900 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:40,909 - DEBUG - Seen 32855 genes until now
2024-05-31 16:26:40,909 - DEBUG - Parsing Chromosome 4 strand - [line 1127703]
2024-05-31 16:26:41,595 - DEBUG - Done with 4- [line 1181103]
2024-05-31 16:26:41,595 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:41,605 - DEBUG - Seen 34286 genes until now
2024-05-31 16:26:41,606 - DEBUG - Parsing Chromosome 4 strand + [line 1181104]
2024-05-31 16:26:41,837 - DEBUG - Done with 4+ [line 1233607]
2024-05-31 16:26:41,837 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:41,848 - DEBUG - Seen 35795 genes until now
2024-05-31 16:26:41,849 - DEBUG - Parsing Chromosome 5 strand - [line 1233608]
2024-05-31 16:26:42,123 - DEBUG - Done with 5- [line 1294653]
2024-05-31 16:26:42,124 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:42,135 - DEBUG - Seen 37429 genes until now
2024-05-31 16:26:42,135 - DEBUG - Parsing Chromosome 5 strand + [line 1294654]
2024-05-31 16:26:42,406 - DEBUG - Done with 5+ [line 1356593]
2024-05-31 16:26:42,406 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:42,418 - DEBUG - Seen 39151 genes until now
2024-05-31 16:26:42,418 - DEBUG - Parsing Chromosome 6 strand - [line 1356594]
2024-05-31 16:26:42,625 - DEBUG - Done with 6- [line 1404907]
2024-05-31 16:26:42,626 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:42,637 - DEBUG - Seen 40734 genes until now
2024-05-31 16:26:42,637 - DEBUG - Parsing Chromosome 6 strand + [line 1404908]
2024-05-31 16:26:42,859 - DEBUG - Done with 6+ [line 1456670]
2024-05-31 16:26:42,859 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:42,870 - DEBUG - Seen 42381 genes until now
2024-05-31 16:26:42,870 - DEBUG - Parsing Chromosome 7 strand - [line 1456671]
2024-05-31 16:26:43,834 - DEBUG - Done with 7- [line 1534606]
2024-05-31 16:26:43,834 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:43,856 - DEBUG - Seen 44966 genes until now
2024-05-31 16:26:43,856 - DEBUG - Parsing Chromosome 7 strand + [line 1534607]
2024-05-31 16:26:44,175 - DEBUG - Done with 7+ [line 1610002]
2024-05-31 16:26:44,176 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:44,190 - DEBUG - Seen 47216 genes until now
2024-05-31 16:26:44,190 - DEBUG - Parsing Chromosome 8 strand - [line 1610003]
2024-05-31 16:26:44,362 - DEBUG - Done with 8- [line 1648479]
2024-05-31 16:26:44,362 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:44,370 - DEBUG - Seen 48489 genes until now
2024-05-31 16:26:44,370 - DEBUG - Parsing Chromosome 8 strand + [line 1648480]
2024-05-31 16:26:44,588 - DEBUG - Done with 8+ [line 1698120]
2024-05-31 16:26:44,588 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:44,597 - DEBUG - Seen 49842 genes until now
2024-05-31 16:26:44,597 - DEBUG - Parsing Chromosome 9 strand - [line 1698121]
2024-05-31 16:26:44,835 - DEBUG - Done with 9- [line 1752034]
2024-05-31 16:26:44,835 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:44,844 - DEBUG - Seen 51248 genes until now
2024-05-31 16:26:44,845 - DEBUG - Parsing Chromosome 9 strand + [line 1752035]
2024-05-31 16:26:45,087 - DEBUG - Done with 9+ [line 1807833]
2024-05-31 16:26:45,087 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:45,097 - DEBUG - Seen 52764 genes until now
2024-05-31 16:26:45,098 - DEBUG - Parsing Chromosome MT strand - [line 1807834]
2024-05-31 16:26:45,098 - DEBUG - Done with MT- [line 1807863]
2024-05-31 16:26:45,098 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:45,098 - DEBUG - Seen 52773 genes until now
2024-05-31 16:26:45,098 - DEBUG - Parsing Chromosome MT strand + [line 1807864]
2024-05-31 16:26:45,099 - DEBUG - Done with MT+ [line 1807980]
2024-05-31 16:26:45,099 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:45,099 - DEBUG - Seen 52801 genes until now
2024-05-31 16:26:45,099 - DEBUG - Parsing Chromosome X strand - [line 1807981]
2024-05-31 16:26:45,232 - DEBUG - Done with X- [line 1838889]
2024-05-31 16:26:45,233 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:45,239 - DEBUG - Seen 54099 genes until now
2024-05-31 16:26:45,239 - DEBUG - Parsing Chromosome X strand + [line 1838890]
2024-05-31 16:26:45,384 - DEBUG - Done with X+ [line 1872954]
2024-05-31 16:26:45,385 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:45,392 - DEBUG - Seen 55489 genes until now
2024-05-31 16:26:45,392 - DEBUG - Parsing Chromosome Y strand - [line 1872955]
2024-05-31 16:26:45,426 - DEBUG - Done with Y- [line 1880111]
2024-05-31 16:26:45,426 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:45,430 - DEBUG - Seen 56412 genes until now
2024-05-31 16:26:45,430 - DEBUG - Parsing Chromosome Y strand + [line 1880112]
2024-05-31 16:26:45,462 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:45,465 - DEBUG - Done with Y+ [line 1887001]
2024-05-31 16:26:45,466 - DEBUG - Fixing corner cases of transcript models containg intron longer than 1000Kbp
2024-05-31 16:26:46,738 - DEBUG - Generated 1577210 features corresponding to 149076 transcript models from /n/groups/neuroduo/Erin/reference_files.dir/GRCm39.dir/Mus_musculus.GRCm39.111.chr.gtf
2024-05-31 16:26:46,766 - INFO - Scan /n/scratch/users/e/eed13/RNAVelocity/CA1_0.25h_EE_rep1.dir/CA1_0.25h_EE_rep1Aligned.velocyto.sorted.bam to validate intron intervals
2024-05-31 16:26:48,527 - DEBUG - Reading /n/scratch/users/e/eed13/RNAVelocity/CA1_0.25h_EE_rep1.dir/CA1_0.25h_EE_rep1Aligned.velocyto.sorted.bam
2024-05-31 16:26:48,538 - DEBUG - Read first 0 million reads
2024-05-31 16:26:48,538 - DEBUG - Marking up chromosome 1
2024-05-31 16:28:12,824 - DEBUG - Marking up chromosome 2
2024-05-31 16:30:05,801 - DEBUG - Marking up chromosome 3
2024-05-31 16:30:12,449 - DEBUG - Read first 10 million reads
2024-05-31 16:31:09,175 - DEBUG - Marking up chromosome 4
2024-05-31 16:32:16,762 - DEBUG - Marking up chromosome 5
2024-05-31 16:33:39,411 - DEBUG - Marking up chromosome 6
2024-05-31 16:33:44,662 - DEBUG - Read first 20 million reads
2024-05-31 16:34:48,414 - DEBUG - Marking up chromosome 7
2024-05-31 16:36:07,371 - DEBUG - Marking up chromosome 8
2024-05-31 16:37:07,164 - DEBUG - Marking up chromosome 9
2024-05-31 16:37:16,758 - DEBUG - Read first 30 million reads
2024-05-31 16:38:23,534 - DEBUG - Marking up chromosome 10
2024-05-31 16:39:28,547 - DEBUG - Marking up chromosome 11
2024-05-31 16:40:51,023 - DEBUG - Read first 40 million reads
2024-05-31 16:41:04,040 - DEBUG - Marking up chromosome 12
2024-05-31 16:42:15,777 - DEBUG - Marking up chromosome 13
2024-05-31 16:43:04,504 - DEBUG - Marking up chromosome 14
2024-05-31 16:43:42,807 - DEBUG - Read first 50 million reads
2024-05-31 16:43:56,867 - DEBUG - Marking up chromosome 15
2024-05-31 16:44:47,074 - DEBUG - Marking up chromosome 16
2024-05-31 16:45:54,381 - DEBUG - Marking up chromosome 17
2024-05-31 16:46:31,659 - DEBUG - Read first 60 million reads
2024-05-31 16:46:55,002 - DEBUG - Marking up chromosome 18
2024-05-31 16:47:37,391 - DEBUG - Marking up chromosome 19
2024-05-31 16:48:38,023 - DEBUG - Marking up chromosome X
2024-05-31 16:49:17,595 - DEBUG - Marking up chromosome Y
2024-05-31 16:49:18,225 - DEBUG - Marking up chromosome MT
2024-05-31 16:50:17,496 - DEBUG - Read first 70 million reads
2024-05-31 16:52:10,803 - DEBUG - End of file. Reset index: start scanning from initial position.
2024-05-31 16:52:10,804 - DEBUG - 0 reads were skipped because no apropiate cell or umi barcode was found
2024-05-31 16:52:10,804 - DEBUG - Start molecule counting!
2024-05-31 16:52:12,650 - DEBUG - Features available for chromosomes : ['1-', '1+', '10-', '10+', '11-', '11+', '12-', '12+', '13-', '13+', '14-', '14+', '15-', '15+', '16-', '16+', '17-', '17+', '18-', '18+', '19-', '19+', '2-', '2+', '3-', '3+', '4-', '4+', '5-', '5+', '6-', '6+', '7-', '7+', '8-', '8+', '9-', '9+', 'MT-', 'MT+', 'X-', 'X+', 'Y-', 'Y+']
2024-05-31 16:52:12,650 - DEBUG - Mask available for chromosomes : []
2024-05-31 16:52:12,650 - DEBUG - Summarizing the results of intron validation.
2024-05-31 16:52:13,231 - DEBUG - Validated 391425 introns (of which unique intervals 141734) out of 714067 total possible introns (considering each possible transcript models).
2024-05-31 16:52:13,232 - DEBUG - Reading /n/scratch/users/e/eed13/RNAVelocity/CA1_0.25h_EE_rep1.dir/cellsorted_CA1_0.25h_EE_rep1Aligned.velocyto.sorted.bam
2024-05-31 16:52:13,236 - DEBUG - Counting for batch 1, containing 0 cells and 0 reads
2024-05-31 16:52:13,236 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
2024-05-31 16:52:13,236 - WARNING - The barcode selection mode is off, no cell events will be identified by <80 counts
2024-05-31 16:52:13,237 - WARNING - 0 of the barcodes where without cell
2024-05-31 16:52:13,237 - DEBUG - 0 reads were skipped because no apropiate cell or umi barcode was found
2024-05-31 16:52:13,237 - DEBUG - Counting done!
2024-05-31 16:52:13,274 - DEBUG - Example of barcode: 959 and cell_id: CA1_0_PBMV3:959
2024-05-31 16:52:13,274 - DEBUG - Generating output file ./CA1_0_PBMV3.loom
2024-05-31 16:52:13,274 - DEBUG - Collecting row attributes
2024-05-31 16:52:13,606 - DEBUG - Generating data table
2024-05-31 16:52:13,607 - DEBUG - Writing loom file
Traceback (most recent call last):
File "/n/groups/neuroduo/Erin/runscripts/RNAVelocity/bin/velocyto", line 8, in
sys.exit(cli())
File "/n/groups/neuroduo/Erin/runscripts/RNAVelocity/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/n/groups/neuroduo/Erin/runscripts/RNAVelocity/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/n/groups/neuroduo/Erin/runscripts/RNAVelocity/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/n/groups/neuroduo/Erin/runscripts/RNAVelocity/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/n/groups/neuroduo/Erin/runscripts/RNAVelocity/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/n/groups/neuroduo/Erin/runscripts/RNAVelocity/lib/python3.10/site-packages/velocyto/commands/run.py", line 113, in run
return _run(bamfile=bamfile, gtffile=gtffile, bcfile=bcfile, outputfolder=outputfolder,
File "/n/groups/neuroduo/Erin/runscripts/RNAVelocity/lib/python3.10/site-packages/velocyto/commands/_run.py", line 287, in _run
ds = loompy.create(filename=outfile, layers=total, row_attrs=ra, col_attrs=ca)
File "/n/groups/neuroduo/Erin/runscripts/RNAVelocity/lib/python3.10/site-packages/loompy/loompy.py", line 1053, in create
raise ValueError("Main matrix cannot be empty")
ValueError: Main matrix cannot be empty