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Hi,

Is there way to extract reads that were successfully assembled by vdjer from the original bam file?

I mean the following. I supposed that vdjer.sam contains reads that were assembled by vdjer. But, when I try to extract fastq reads from vdjer.sam and re-analyse them, vdjer produces empty result.

Steps to reproduce:

./STAR --readFilesIn demo_R1.fastq demo_R2.fastq ... > demo.sort.bam
./samtools index demo.sort.bam
./vdjer --in demo.sort.bam ... > vdjer.sam

At this point all ok, vdjer.sam contains a lot of alignments and vdj_contigs.fa a lot of records.

Then I do:

./SamToFastq I=vdjer.sam F=demo2_R1.fastq F2=demo2_R2.fastq
./STAR --readFilesIn demo2_R1.fastq demo2_R2.fastq ... > demo2.sort.bam
./samtools index demo2.sort.bam
./vdjer --in demo2.sort.bam ... > vdjer2.sam

and now vdjer2.sam is empty and vdj_contigs.fa is empty too. Why?

Thanks!

Hello,

I am testing VDJer on a transcriptomic sample. I aligned sequences with STAR (obtaining median read depth of the IGH region of 178, and up to 3000).

I was surprised to only get 52 alignments in the standard SAM file and 120 in sensitive mode.

Is this to be expected given the read coverage? I would be very grateful for your advice and can share further details as required.

Thanks!

Hi,

I'm trying to run vdjer on bam files obtained with STAR and get zero clones even on the sample data which is in the demo folder. For example, for the file star.sort.bam from demo/ folder I do the following:

samtools fastq star.sort.bam > data.fastq
STAR --runThreadN 42 --genomeDir gencode_hg38/ --readFilesIn data.fastq --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outStd BAM_SortedByCoordinate > data.sort.bam
samtools index data.sort.bam
vdjer --in data.sort.bam --rl 50 --ins 175 --chain IGH --ref-dir ~/local/vdjer/reference/igh > vdjer.sam 2>log 

As result vdjer returns zero clones, but with the original bam file vdjer works fine and produces a lot of clones as expected. In the log produced by vdjer there are lines:

Extracting reads...
primary_reads size1: [74341]
secondary_reads size1: [50130]
primary_output1: [0] primary_output2: [0] secondary_output1: [0] secondary_output2: [0]

It seems that all zeros in the last line is not good.

I use STAR version 2.4.2a (but I also tried 2.5.2b) and reference downloaded from http://www.gencodegenes.org/releases/current.html (GRCh38.p7 ALL and Comprehensive gene annotation GTF) which I build with:

STAR --runMode genomeGenerate --runThreadN 52 --genomeDir gencode_hg38/ --genomeFastaFiles GRCh38.p7.genome.fa --sjdbGTFfile gencode.v25.chr_patch_hapl_scaff.annotation.gtf

What I'm doing wrong? Maybe vdjer requires another STAR reference?

Upon running on sorted bam file (113.9 mb file, on which I can run samtools flagstat), I always get a segmentation fault error.

$VDJER --in in.bam --rl 50 --t 8 --ins 216 --chain IGH --ref-dir $VDJER_REF_DIR > vdjer.sam 2> vdjer.log

Last line on vdjer.log is "Extracting reads..."

If you need any more details, please let me know.

Hi, I am trying to use VDJer to pull out BCR-seq data from sorted and indexed BAM files created by HISAT2 (alignment with hg38 ucsc). However, when I run it, it stops at PRE_PRE_GRAPH1 stage with the following error:

input_len: 7333, record_len: 151
Initial char in input invalid: J
ERROR! INVALID INPUT:
===========================0TCATTCTTCTTTCAATCAGCAGGGACCGTGCACTCTCTTGGAGCCACCATAGAAAACAGAGGTGCATCCAGCACCACAGAAAACAGAGCCACCACAGAAAACAGAGGGTGACTAAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJF-FJJFJJJJJJJAFJJAJAJFAJAJJFJJFJJJJJJJJJJ<JJJJJJFJFJJJJF<<FAAF-FA0GCTGCAGCTGGGAGTGTGCAGAGACTGGAGGGGATGACAGTCACCCTCTGTTTTCTGTGGTGGCTCTGTTTTCTGTGGTGCTGGATGCACCTCTGTTTTCTATGGTGGCTCCAAF7F<--A)JJF-JJJJ<<<FFFFAFJJFAJJAFAJFAAF-FAAF<<FJJJJFJFJJJJJJ<JJJJJJJJJJFJJFJJAJAFJAJAJJFAJJJJJJJFJJF-FJJJJFFJJJJ0GTGACTGTCATCCCCTCCAGTCTCTGCACACTCCCAGCTGC ....

Does anyone know if VDJer accepts BAMs from aligners other than STAR? Could this error be because of the use of HISAT2 instead of STAR? Many thanks for any comments or help! Ondrej

Is there someplace where mouse references and indices compatible with VDJer can be obtained or do I need to just do my best to mimic what you did with the human set?

Thanks,
Dante

We hard time running the tool for bam file from GTEx project. We use bam files produced by GTEx consortium. Reads were mapped to hg19 using Tophap. Bam files contain both mapped and unmapped reads:

This is how we run it

vdjer --in ../G18051.GTEX-OHPM-0526-SM-2YUMJ.1.bam --ins 175 --chain IGH --ref-dir igh

And we are getting this error

Increasing read_name bufIncreasing read_name bufIncreasing read_name bufSegmentation fault

The full log file is the end of the message.

Do you have any idea why we are getting this error
Thanks,
Serghei

ELAPSED_SECS START 0 0
PROC_STATUS START Name: vdjer
PROC_STATUS START State: R (running)
PROC_STATUS START Tgid: 14054
PROC_STATUS START Pid: 14054
PROC_STATUS START PPid: 12870
PROC_STATUS START TracerPid: 0
PROC_STATUS START Uid: 9872 9872 9872 9872
PROC_STATUS START Gid: 8164 8164 8164 8164
PROC_STATUS START Utrace: 0
PROC_STATUS START FDSize: 256
PROC_STATUS START Groups: 8164 11539 12325
PROC_STATUS START VmPeak: 19092 kB
PROC_STATUS START VmSize: 19092 kB
PROC_STATUS START VmLck: 0 kB
PROC_STATUS START VmHWM: 1468 kB
PROC_STATUS START VmRSS: 1468 kB
PROC_STATUS START VmData: 2260 kB
PROC_STATUS START VmStk: 92 kB
PROC_STATUS START VmExe: 944 kB
PROC_STATUS START VmLib: 3420 kB
PROC_STATUS START VmPTE: 56 kB
PROC_STATUS START VmSwap: 0 kB
PROC_STATUS START Threads: 1
PROC_STATUS START SigQ: 2/96529
PROC_STATUS START SigPnd: 0000000000000000
PROC_STATUS START ShdPnd: 0000000000000000
PROC_STATUS START SigBlk: 0000000000000000
PROC_STATUS START SigIgn: 0000000000000000
PROC_STATUS START SigCgt: 0000000180000000
PROC_STATUS START CapInh: 0000000000000000
PROC_STATUS START CapPrm: 0000000000000000
PROC_STATUS START CapEff: 0000000000000000
PROC_STATUS START CapBnd: ffffffffffffffff
PROC_STATUS START Cpus_allowed: fff
PROC_STATUS START Cpus_allowed_list: 0-11
PROC_STATUS START Mems_allowed: 00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000003
PROC_STATUS START Mems_allowed_list: 0-1
PROC_STATUS START voluntary_ctxt_switches: 47
PROC_STATUS START nonvoluntary_ctxt_switches: 1
BUDDY_INFO START Node 0, zone DMA 1 1 2 1 2 0 0 0 1 1 3
BUDDY_INFO START Node 0, zone DMA32 94266 38488 6900 980 66 9 1 1 0 1 0
BUDDY_INFO START Node 0, zone Normal 484059 45546 19 0 1 2 2 0 1 0 0
BUDDY_INFO START Node 1, zone Normal 285971 247761 167789 80793 19026 1751 180 58 16 1 0
STAT:1488256353 START 14054 (vdjer) R 12870 14054 12870 34843 14054 4202496 460 0 3 0 0 0 0 0 20 0 1 0 11708590 19550208 369 1073741824 4194304 5160262 140722877782336 140722877776104 140603237045872 0 0 0 0 0 0 0 17 2 0 0 0 0 0
input ../G18051.GTEX-OHPM-0526-SM-2YUMJ.1.bam
min node freq 3
min base qual 90
min contig score (log scaled) -5.000000
num threads 1
v anchor file /u/home/n/ngcrawfo/project-zarlab/igor/imrep_revision/tools/vdjer/igh//v_index
j anchor file /u/home/n/ngcrawfo/project-zarlab/igor/imrep_revision/tools/vdjer/igh//j_index
max anchor mismatches: 4
min V/J window 10
max V/J window 90
conserved J AA 87
total untrimmed contig length 486
extension beyond conserved J AA 162
fasta file containing functional V/D/J sequences /u/home/n/ngcrawfo/project-zarlab/igor/imrep_revision/tools/vdjer/igh//ig_vdj.fa
variable region locus chr14:105566277-106879844
constant region locus chr14:105566277-105939754
median insert length 175
read coverage floor for contig filtering 1
kmer 35
source node similarity file /u/home/n/ngcrawfo/project-zarlab/igor/imrep_revision/tools/vdjer/igh//v_region.fa
vregion kmer size 15
minimum homology score for source nodes 30
span for read base filtering 35
span for mate base filtering 48
start point for contig filtering 52
stop point for contig filtering 411
window overlap check size 320
read length: 76Loading vmers
Loading jmers
ELAPSED_SECS POST_VJF_INIT 228 228
PROC_STATUS POST_VJF_INIT Name: vdjer
PROC_STATUS POST_VJF_INIT State: R (running)
PROC_STATUS POST_VJF_INIT Tgid: 14054
PROC_STATUS POST_VJF_INIT Pid: 14054
PROC_STATUS POST_VJF_INIT PPid: 12870
PROC_STATUS POST_VJF_INIT TracerPid: 0
PROC_STATUS POST_VJF_INIT Uid: 9872 9872 9872 9872
PROC_STATUS POST_VJF_INIT Gid: 8164 8164 8164 8164
PROC_STATUS POST_VJF_INIT Utrace: 0
PROC_STATUS POST_VJF_INIT FDSize: 256
PROC_STATUS POST_VJF_INIT Groups: 8164 11539 12325
PROC_STATUS POST_VJF_INIT VmPeak: 289504 kB
PROC_STATUS POST_VJF_INIT VmSize: 256732 kB
PROC_STATUS POST_VJF_INIT VmLck: 0 kB
PROC_STATUS POST_VJF_INIT VmHWM: 243432 kB
PROC_STATUS POST_VJF_INIT VmRSS: 210784 kB
PROC_STATUS POST_VJF_INIT VmData: 239900 kB
PROC_STATUS POST_VJF_INIT VmStk: 92 kB
PROC_STATUS POST_VJF_INIT VmExe: 944 kB
PROC_STATUS POST_VJF_INIT VmLib: 3420 kB
PROC_STATUS POST_VJF_INIT VmPTE: 480 kB
PROC_STATUS POST_VJF_INIT VmSwap: 0 kB
PROC_STATUS POST_VJF_INIT Threads: 1
PROC_STATUS POST_VJF_INIT SigQ: 2/96529
PROC_STATUS POST_VJF_INIT SigPnd: 0000000000000000
PROC_STATUS POST_VJF_INIT ShdPnd: 0000000000000000
PROC_STATUS POST_VJF_INIT SigBlk: 0000000000000000
PROC_STATUS POST_VJF_INIT SigIgn: 0000000000000000
PROC_STATUS POST_VJF_INIT SigCgt: 0000000180000000
PROC_STATUS POST_VJF_INIT CapInh: 0000000000000000
PROC_STATUS POST_VJF_INIT CapPrm: 0000000000000000
PROC_STATUS POST_VJF_INIT CapEff: 0000000000000000
PROC_STATUS POST_VJF_INIT CapBnd: ffffffffffffffff
PROC_STATUS POST_VJF_INIT Cpus_allowed: fff
PROC_STATUS POST_VJF_INIT Cpus_allowed_list: 0-11
PROC_STATUS POST_VJF_INIT Mems_allowed: 00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000003
PROC_STATUS POST_VJF_INIT Mems_allowed_list: 0-1
PROC_STATUS POST_VJF_INIT voluntary_ctxt_switches: 137691
PROC_STATUS POST_VJF_INIT nonvoluntary_ctxt_switches: 11958
BUDDY_INFO POST_VJF_INIT Node 0, zone DMA 1 1 2 1 2 0 0 0 1 1 3
BUDDY_INFO POST_VJF_INIT Node 0, zone DMA32 94271 38488 6871 981 66 9 1 1 0 1 0
BUDDY_INFO POST_VJF_INIT Node 0, zone Normal 70236 22773 0 1 0 0 0 0 1 0 0
BUDDY_INFO POST_VJF_INIT Node 1, zone Normal 75966 223104 151832 73709 17664 2288 809 512 238 15 0
STAT:1488256581 POST_VJF_INIT 14054 (vdjer) R 12870 14054 12870 34843 14054 4202496 22385 0 3 0 11576 704 0 0 20 0 1 0 11708590 262893568 52696 1073741824 4194304 5160262 140722877782336 140722877780248 140603237045872 0 0 0 0 0 0 0 17 2 0 0 183 0 0
Extracting reads...
primary_reads size1: [0]
secondary_reads size1: [0]
Increasing read_name bufIncreasing read_name bufIncreasing read_name bufSegmentation fault

Hi, I am not sure how to set the ins parameter and what does it mean, could you please help on this?

Here is a simulated IGH sample (using simNGS):

igh.fa.txt - simulated IGH transcripts
r1.fastq.txt - simulated reads (left pairs)
r2.fastq.txt - simulated reads (right pairs)

The .txt suffix is appended to each filename to be able to upload it here to GitHub.

The read length is 100, inferred coverage is 16.

I ran all the commands as described in VDJer Usage and the resulting output is empty. 38 assembly of human was used (alt contigs were removed).

The tools from the same categories: TRUST, mixcr (rna-seq workflow) produce a high number of contigs.

Please, help identify what is the issue with VDJer.

Hello,

can vdjer work on whole-exome sequencing data? or how to adjust the parameters to make it work for whole-exome sequencing data?

Thanks much!

Hello! Thank you for this tool. I attempted post-processing using the scripts and was met the following error when I set the argument to "no" for light chains:

read_count_file = sys.argv[7]
IndexError: list index out of range

I did not have this issue when I performed post-processing on the heavy chain. Might you be able to help me sort our this error, please?

Many thanks!

Hi everyone,

I'm trying to use vdjer on my data. I perform the tutorial, with the data provided in the package and It's working. Problems appears when I tried with my data.
I have a bam file (median ins 175, 2X75PE, aligned with star with --outSAMtype BAM SortedByCoordinate option).

I tried:

vdjer --in /bam_test/sample1_Aligned.sortedByCoord.out.bam --t 8 --ins 175 --chain IGH --ref-dir /home/igh > //bam_test/sample1_Aligned.sortedByCoord.out.bam/vdjer_STAR.sam 2> /bam_test/sample1_Aligned.sortedByCoord.out.bam/vdjer_samtools.log

Problems occurs when I looked at the output, I get an empty vdi_contig.fa, and when I looked to vdjer_STAR.sam It returns me
(my_root) -bash-4.2$ more vdjer_STAR.sam
@hd VN:1.4 SO:unsorted

Does anyone get this and have a solution ?

Thanks a lot !
nicolas

Now that I have a better understanding of the tool, I have tested VDJer on 200 samples. It runs as I expect for IGK and IGL, producing contigs in some, but not all samples, and more in cases than controls (where one may expect more circulating B cells). Usually, a sample gives both light chain contigs or none at all. However, I never get any IGH contigs, and I am puzzled.

I have confirmed that the IGH region is no worse covered than the IGK/IGL regions.

Do you have any suggestions? I will gladly share log files or other materials as needed.

Many thanks for your advice,

Andrew

Hi,

Is it important which STAR pipeline (1-pass or 2-pass) to use for further processing with VDJer?

Thanks!

When trying to compile under Mac OS 10.12 I get the following error (repeatedly, and in different places)

In file included from src/main/c/assembler2_vdj.c:15:
src/main/c/sparsehash/sparse_hash_map:94:10: fatal error: 'tr1/functional' file not found

What am I missing?

Hello

I was trying to use vdjer but I kept getting into error.

Below is the core dump error and log files.

/work/UGE/8.0.1/hoffman2/spool/n6261/job_scripts/929296: line 1: 17148 Aborted (core dumped) ./vdjer --in /u/home/h/harryyan/project-eeskin/utilities/vdjer-0.12/G19324.GTEX-S341-0326-SM-2XCAU.1.bam --t 4 --ins 175 --chain IGH --ref-dir /u/home/h/harryyan/project-eeskin/utilities/vdjer-0.12/db/igh > test.sam 2> test.log

[harryyan@login3 vdjer-0.12]$ cat test.log ELAPSED_SECS START 0 0 PROC_STATUS START Name: vdjer PROC_STATUS START State: R (running) PROC_STATUS START Tgid: 17148 PROC_STATUS START Pid: 17148 PROC_STATUS START PPid: 17147 PROC_STATUS START TracerPid: 0 PROC_STATUS START Uid: 11493 11493 11493 11493 PROC_STATUS START Gid: 8164 8164 8164 8164 PROC_STATUS START Utrace: 0 PROC_STATUS START FDSize: 256 PROC_STATUS START Groups: 8164 62342 PROC_STATUS START VmPeak: 19096 kB PROC_STATUS START VmSize: 19096 kB PROC_STATUS START VmLck: 0 kB PROC_STATUS START VmHWM: 1472 kB PROC_STATUS START VmRSS: 1472 kB PROC_STATUS START VmData: 2264 kB PROC_STATUS START VmStk: 96 kB PROC_STATUS START VmExe: 944 kB PROC_STATUS START VmLib: 3420 kB PROC_STATUS START VmPTE: 56 kB PROC_STATUS START VmSwap: 0 kB PROC_STATUS START Threads: 1 PROC_STATUS START SigQ: 0/193442 PROC_STATUS START SigPnd: 0000000000000000 PROC_STATUS START ShdPnd: 0000000000000000 PROC_STATUS START SigBlk: 0000000000000000 PROC_STATUS START SigIgn: 0000000000000000 PROC_STATUS START SigCgt: 0000000180000000 PROC_STATUS START CapInh: 0000000000000000 PROC_STATUS START CapPrm: 0000000000000000 PROC_STATUS START CapEff: 0000000000000000 PROC_STATUS START CapBnd: ffffffffffffffff PROC_STATUS START Cpus_allowed: ffffffff PROC_STATUS START Cpus_allowed_list: 0-31 PROC_STATUS START Mems_allowed: 00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000003 PROC_STATUS START Mems_allowed_list: 0-1 PROC_STATUS START voluntary_ctxt_switches: 22 PROC_STATUS START nonvoluntary_ctxt_switches: 2 BUDDY_INFO START Node 0, zone DMA 3 2 2 1 2 1 0 0 1 1 3 BUDDY_INFO START Node 0, zone DMA32 681 632 506 304 186 120 134 64 43 60 733 BUDDY_INFO START Node 0, zone Normal 9658 10031 5043 5620 5978 4392 2999 2068 1541 1648 426 BUDDY_INFO START Node 1, zone Normal 9695 21256 17926 11515 20274 10822 8944 4658 3728 1323 190 STAT:1478159295 START 17148 (vdjer) R 17147 17147 17147 0 -1 4202496 508 0 2 0 0 0 0 0 20 0 1 0 512859146 19554304 370 18446744073709551615 4194304 5160238 140729453823936 140729453812664 48002282497280 0 0 0 0 0 0 0 17 5 0 0 0 0 0 input /u/home/h/harryyan/project-eeskin/utilities/vdjer-0.12/G19324.GTEX-S341-0326-SM-2XCAU.1.bam min node freq 3 min base qual 90 min contig score (log scaled) -5.000000 num threads 4 v anchor file /u/home/h/harryyan/project-eeskin/utilities/vdjer-0.12/db/igh/v_index j anchor file /u/home/h/harryyan/project-eeskin/utilities/vdjer-0.12/db/igh/j_index max anchor mismatches: 4 min V/J window 10 max V/J window 90 conserved J AA 87 total untrimmed contig length 486 extension beyond conserved J AA 162 fasta file containing functional V/D/J sequences /u/home/h/harryyan/project-eeskin/utilities/vdjer-0.12/db/igh/ig_vdj.fa variable region locus chr14:105566277-106879844 constant region locus chr14:105566277-105939754 median insert length 175 read coverage floor for contig filtering 1 kmer 35 source node similarity file /u/home/h/harryyan/project-eeskin/utilities/vdjer-0.12/db/igh/v_region.fa vregion kmer size 15 minimum homology score for source nodes 30 span for read base filtering 35 span for mate base filtering 48 start point for contig filtering 52 stop point for contig filtering 411 window overlap check size 320 read length: 76Loading vmers Loading jmers ELAPSED_SECS POST_VJF_INIT 13 13 PROC_STATUS POST_VJF_INIT Name: vdjer PROC_STATUS POST_VJF_INIT State: R (running) PROC_STATUS POST_VJF_INIT Tgid: 17148 PROC_STATUS POST_VJF_INIT Pid: 17148 PROC_STATUS POST_VJF_INIT PPid: 17147 PROC_STATUS POST_VJF_INIT TracerPid: 0 PROC_STATUS POST_VJF_INIT Uid: 11493 11493 11493 11493 PROC_STATUS POST_VJF_INIT Gid: 8164 8164 8164 8164 PROC_STATUS POST_VJF_INIT Utrace: 0 PROC_STATUS POST_VJF_INIT FDSize: 256 PROC_STATUS POST_VJF_INIT Groups: 8164 62342 PROC_STATUS POST_VJF_INIT VmPeak: 289180 kB PROC_STATUS POST_VJF_INIT VmSize: 256408 kB PROC_STATUS POST_VJF_INIT VmLck: 0 kB PROC_STATUS POST_VJF_INIT VmHWM: 245144 kB PROC_STATUS POST_VJF_INIT VmRSS: 212496 kB PROC_STATUS POST_VJF_INIT VmData: 239576 kB PROC_STATUS POST_VJF_INIT VmStk: 96 kB PROC_STATUS POST_VJF_INIT VmExe: 944 kB PROC_STATUS POST_VJF_INIT VmLib: 3420 kB PROC_STATUS POST_VJF_INIT VmPTE: 480 kB PROC_STATUS POST_VJF_INIT VmSwap: 0 kB PROC_STATUS POST_VJF_INIT Threads: 1 PROC_STATUS POST_VJF_INIT SigQ: 0/193442 PROC_STATUS POST_VJF_INIT SigPnd: 0000000000000000 PROC_STATUS POST_VJF_INIT ShdPnd: 0000000000000000 PROC_STATUS POST_VJF_INIT SigBlk: 0000000000000000 PROC_STATUS POST_VJF_INIT SigIgn: 0000000000000000 PROC_STATUS POST_VJF_INIT SigCgt: 0000000180000000 PROC_STATUS POST_VJF_INIT CapInh: 0000000000000000 PROC_STATUS POST_VJF_INIT CapPrm: 0000000000000000 PROC_STATUS POST_VJF_INIT CapEff: 0000000000000000 PROC_STATUS POST_VJF_INIT CapBnd: ffffffffffffffff PROC_STATUS POST_VJF_INIT Cpus_allowed: ffffffff PROC_STATUS POST_VJF_INIT Cpus_allowed_list: 0-31 PROC_STATUS POST_VJF_INIT Mems_allowed: 00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000003 PROC_STATUS POST_VJF_INIT Mems_allowed_list: 0-1 PROC_STATUS POST_VJF_INIT voluntary_ctxt_switches: 53 PROC_STATUS POST_VJF_INIT nonvoluntary_ctxt_switches: 1320 BUDDY_INFO POST_VJF_INIT Node 0, zone DMA 3 2 2 1 2 1 0 0 1 1 3 BUDDY_INFO POST_VJF_INIT Node 0, zone DMA32 681 632 506 304 186 120 134 64 43 60 733 BUDDY_INFO POST_VJF_INIT Node 0, zone Normal 745 9655 5054 1493 2178 4400 3008 2076 1544 1563 426 BUDDY_INFO POST_VJF_INIT Node 1, zone Normal 6323 21296 17943 11521 20041 10823 8944 4658 3728 1322 190 STAT:1478159308 POST_VJF_INIT 17148 (vdjer) R 17147 17147 17147 0 -1 4202496 22341 0 2 0 1218 32 0 0 20 0 1 0 512859146 262561792 53124 18446744073709551615 4194304 5160238 140729453823936 140729453821848 48002282497280 0 0 0 0 0 0 0 17 0 0 0 36 0 0 Extracting reads... primary_reads size1: [0] secondary_reads size1: [0] Increasing read_name bufIncreasing read_name bufIncreasing read_name bufIncreasing read_name bufprimary_output1: [254182] primary_output2: [254182] secondary_output1: [12595706] secondary_output2: [12595706] Read extract done... ELAPSED_SECS POST_READ_EXTRACT 2220 2207 PROC_STATUS POST_READ_EXTRACT Name: vdjer PROC_STATUS POST_READ_EXTRACT State: R (running) PROC_STATUS POST_READ_EXTRACT Tgid: 17148 PROC_STATUS POST_READ_EXTRACT Pid: 17148 PROC_STATUS POST_READ_EXTRACT PPid: 17147 PROC_STATUS POST_READ_EXTRACT TracerPid: 0 PROC_STATUS POST_READ_EXTRACT Uid: 11493 11493 11493 11493 PROC_STATUS POST_READ_EXTRACT Gid: 8164 8164 8164 8164 PROC_STATUS POST_READ_EXTRACT Utrace: 0 PROC_STATUS POST_READ_EXTRACT FDSize: 256 PROC_STATUS POST_READ_EXTRACT Groups: 8164 62342 PROC_STATUS POST_READ_EXTRACT VmPeak: 16536692 kB PROC_STATUS POST_READ_EXTRACT VmSize: 15749272 kB PROC_STATUS POST_READ_EXTRACT VmLck: 0 kB PROC_STATUS POST_READ_EXTRACT VmHWM: 16390668 kB PROC_STATUS POST_READ_EXTRACT VmRSS: 15603908 kB PROC_STATUS POST_READ_EXTRACT VmData: 15732440 kB PROC_STATUS POST_READ_EXTRACT VmStk: 96 kB PROC_STATUS POST_READ_EXTRACT VmExe: 944 kB PROC_STATUS POST_READ_EXTRACT VmLib: 3420 kB PROC_STATUS POST_READ_EXTRACT VmPTE: 30552 kB PROC_STATUS POST_READ_EXTRACT VmSwap: 0 kB PROC_STATUS POST_READ_EXTRACT Threads: 1 PROC_STATUS POST_READ_EXTRACT SigQ: 0/193442 PROC_STATUS POST_READ_EXTRACT SigPnd: 0000000000000000 PROC_STATUS POST_READ_EXTRACT ShdPnd: 0000000000000000 PROC_STATUS POST_READ_EXTRACT SigBlk: 0000000000000000 PROC_STATUS POST_READ_EXTRACT SigIgn: 0000000000000000 PROC_STATUS POST_READ_EXTRACT SigCgt: 0000000180000000 PROC_STATUS POST_READ_EXTRACT CapInh: 0000000000000000 PROC_STATUS POST_READ_EXTRACT CapPrm: 0000000000000000 PROC_STATUS POST_READ_EXTRACT CapEff: 0000000000000000 PROC_STATUS POST_READ_EXTRACT CapBnd: ffffffffffffffff PROC_STATUS POST_READ_EXTRACT Cpus_allowed: ffffffff PROC_STATUS POST_READ_EXTRACT Cpus_allowed_list: 0-31 PROC_STATUS POST_READ_EXTRACT Mems_allowed: 00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000003 PROC_STATUS POST_READ_EXTRACT Mems_allowed_list: 0-1 PROC_STATUS POST_READ_EXTRACT voluntary_ctxt_switches: 71 PROC_STATUS POST_READ_EXTRACT nonvoluntary_ctxt_switches: 225040 BUDDY_INFO POST_READ_EXTRACT Node 0, zone DMA 3 2 2 1 2 1 0 0 1 1 3 BUDDY_INFO POST_READ_EXTRACT Node 0, zone DMA32 681 632 508 302 184 118 134 63 42 1 0 BUDDY_INFO POST_READ_EXTRACT Node 0, zone Normal 14391 10954 4339 1305 436 173 1411 2056 1544 39 111 BUDDY_INFO POST_READ_EXTRACT Node 1, zone Normal 410 238 414 151 111 67 101 54 1898 127 0 STAT:1478161515 POST_READ_EXTRACT 17148 (vdjer) R 17147 17147 17147 0 -1 4202496 1832231 0 2 0 220254 1632 0 0 20 0 1 0 512859146 16127254528 3900977 18446744073709551615 4194304 5160238 140729453823936 140729453823432 48002282497280 0 0 0 0 0 0 0 17 5 0 0 36 0 0 Assembling... Assembling: -> ELAPSED_SECS PRE_PRE_GRAPH1 2220 0 PROC_STATUS PRE_PRE_GRAPH1 Name: vdjer PROC_STATUS PRE_PRE_GRAPH1 State: R (running) PROC_STATUS PRE_PRE_GRAPH1 Tgid: 17148 PROC_STATUS PRE_PRE_GRAPH1 Pid: 17148 PROC_STATUS PRE_PRE_GRAPH1 PPid: 17147 PROC_STATUS PRE_PRE_GRAPH1 TracerPid: 0 PROC_STATUS PRE_PRE_GRAPH1 Uid: 11493 11493 11493 11493 PROC_STATUS PRE_PRE_GRAPH1 Gid: 8164 8164 8164 8164 PROC_STATUS PRE_PRE_GRAPH1 Utrace: 0 PROC_STATUS PRE_PRE_GRAPH1 FDSize: 256 PROC_STATUS PRE_PRE_GRAPH1 Groups: 8164 62342 PROC_STATUS PRE_PRE_GRAPH1 VmPeak: 16536692 kB PROC_STATUS PRE_PRE_GRAPH1 VmSize: 15749272 kB PROC_STATUS PRE_PRE_GRAPH1 VmLck: 0 kB PROC_STATUS PRE_PRE_GRAPH1 VmHWM: 16390668 kB PROC_STATUS PRE_PRE_GRAPH1 VmRSS: 15603916 kB PROC_STATUS PRE_PRE_GRAPH1 VmData: 15732440 kB PROC_STATUS PRE_PRE_GRAPH1 VmStk: 96 kB PROC_STATUS PRE_PRE_GRAPH1 VmExe: 944 kB PROC_STATUS PRE_PRE_GRAPH1 VmLib: 3420 kB PROC_STATUS PRE_PRE_GRAPH1 VmPTE: 30552 kB PROC_STATUS PRE_PRE_GRAPH1 VmSwap: 0 kB PROC_STATUS PRE_PRE_GRAPH1 Threads: 1 PROC_STATUS PRE_PRE_GRAPH1 SigQ: 0/193442 PROC_STATUS PRE_PRE_GRAPH1 SigPnd: 0000000000000000 PROC_STATUS PRE_PRE_GRAPH1 ShdPnd: 0000000000000000 PROC_STATUS PRE_PRE_GRAPH1 SigBlk: 0000000000000000 PROC_STATUS PRE_PRE_GRAPH1 SigIgn: 0000000000000000 PROC_STATUS PRE_PRE_GRAPH1 SigCgt: 0000000180000000 PROC_STATUS PRE_PRE_GRAPH1 CapInh: 0000000000000000 PROC_STATUS PRE_PRE_GRAPH1 CapPrm: 0000000000000000 PROC_STATUS PRE_PRE_GRAPH1 CapEff: 0000000000000000 PROC_STATUS PRE_PRE_GRAPH1 CapBnd: ffffffffffffffff PROC_STATUS PRE_PRE_GRAPH1 Cpus_allowed: ffffffff PROC_STATUS PRE_PRE_GRAPH1 Cpus_allowed_list: 0-31 PROC_STATUS PRE_PRE_GRAPH1 Mems_allowed: 00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000003 PROC_STATUS PRE_PRE_GRAPH1 Mems_allowed_list: 0-1 PROC_STATUS PRE_PRE_GRAPH1 voluntary_ctxt_switches: 71 PROC_STATUS PRE_PRE_GRAPH1 nonvoluntary_ctxt_switches: 225040 BUDDY_INFO PRE_PRE_GRAPH1 Node 0, zone DMA 3 2 2 1 2 1 0 0 1 1 3 BUDDY_INFO PRE_PRE_GRAPH1 Node 0, zone DMA32 681 632 508 302 184 118 134 63 42 1 0 BUDDY_INFO PRE_PRE_GRAPH1 Node 0, zone Normal 14391 10954 4339 1305 436 173 1411 2056 1544 39 111 BUDDY_INFO PRE_PRE_GRAPH1 Node 1, zone Normal 410 238 414 151 111 67 101 54 1898 127 0 STAT:1478161515 PRE_PRE_GRAPH1 17148 (vdjer) R 17147 17147 17147 0 -1 4202496 1832237 0 2 0 220254 1632 0 0 20 0 1 0 512859146 16127254528 3900980 18446744073709551615 4194304 5160238 140729453823936 140729453823432 48002282497280 0 0 0 0 0 0 0 17 5 0 0 36 0 0 input_len: 155559384, record_len: 153 pre_record_count: 1000000 Pre Num reads: 1016728 Pre Num nodes: 5275986 ELAPSED_SECS PRE_PRE_GRAPH2 2261 41 PROC_STATUS PRE_PRE_GRAPH2 Name: vdjer PROC_STATUS PRE_PRE_GRAPH2 State: R (running) PROC_STATUS PRE_PRE_GRAPH2 Tgid: 17148 PROC_STATUS PRE_PRE_GRAPH2 Pid: 17148 PROC_STATUS PRE_PRE_GRAPH2 PPid: 17147 PROC_STATUS PRE_PRE_GRAPH2 TracerPid: 0 PROC_STATUS PRE_PRE_GRAPH2 Uid: 11493 11493 11493 11493 PROC_STATUS PRE_PRE_GRAPH2 Gid: 8164 8164 8164 8164 PROC_STATUS PRE_PRE_GRAPH2 Utrace: 0 PROC_STATUS PRE_PRE_GRAPH2 FDSize: 256 PROC_STATUS PRE_PRE_GRAPH2 Groups: 8164 62342 PROC_STATUS PRE_PRE_GRAPH2 VmPeak: 17528048 kB PROC_STATUS PRE_PRE_GRAPH2 VmSize: 16938224 kB PROC_STATUS PRE_PRE_GRAPH2 VmLck: 0 kB PROC_STATUS PRE_PRE_GRAPH2 VmHWM: 17382612 kB PROC_STATUS PRE_PRE_GRAPH2 VmRSS: 16792784 kB PROC_STATUS PRE_PRE_GRAPH2 VmData: 16921392 kB PROC_STATUS PRE_PRE_GRAPH2 VmStk: 96 kB PROC_STATUS PRE_PRE_GRAPH2 VmExe: 944 kB PROC_STATUS PRE_PRE_GRAPH2 VmLib: 3420 kB PROC_STATUS PRE_PRE_GRAPH2 VmPTE: 32876 kB PROC_STATUS PRE_PRE_GRAPH2 VmSwap: 0 kB PROC_STATUS PRE_PRE_GRAPH2 Threads: 1 PROC_STATUS PRE_PRE_GRAPH2 SigQ: 0/193442 PROC_STATUS PRE_PRE_GRAPH2 SigPnd: 0000000000000000 PROC_STATUS PRE_PRE_GRAPH2 ShdPnd: 0000000000000000 PROC_STATUS PRE_PRE_GRAPH2 SigBlk: 0000000000000000 PROC_STATUS PRE_PRE_GRAPH2 SigIgn: 0000000000000000 PROC_STATUS PRE_PRE_GRAPH2 SigCgt: 0000000180000000 PROC_STATUS PRE_PRE_GRAPH2 CapInh: 0000000000000000 PROC_STATUS PRE_PRE_GRAPH2 CapPrm: 0000000000000000 PROC_STATUS PRE_PRE_GRAPH2 CapEff: 0000000000000000 PROC_STATUS PRE_PRE_GRAPH2 CapBnd: ffffffffffffffff PROC_STATUS PRE_PRE_GRAPH2 Cpus_allowed: ffffffff PROC_STATUS PRE_PRE_GRAPH2 Cpus_allowed_list: 0-31 PROC_STATUS PRE_PRE_GRAPH2 Mems_allowed: 00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000003 PROC_STATUS PRE_PRE_GRAPH2 Mems_allowed_list: 0-1 PROC_STATUS PRE_PRE_GRAPH2 voluntary_ctxt_switches: 71 PROC_STATUS PRE_PRE_GRAPH2 nonvoluntary_ctxt_switches: 229176 BUDDY_INFO PRE_PRE_GRAPH2 Node 0, zone DMA 3 2 2 1 2 1 0 0 1 1 3 BUDDY_INFO PRE_PRE_GRAPH2 Node 0, zone DMA32 656 566 430 266 157 105 124 59 44 1 0 BUDDY_INFO PRE_PRE_GRAPH2 Node 0, zone Normal 1874 1148 758 482 329 211 1390 1993 1492 41 87 BUDDY_INFO PRE_PRE_GRAPH2 Node 1, zone Normal 262 356 434 119 89 67 103 52 1254 72 0 STAT:1478161556 PRE_PRE_GRAPH2 17148 (vdjer) R 17147 17147 17147 0 -1 4202496 2001768 0 2 0 224119 1830 0 0 20 0 1 0 512859146 17344741376 4198196 18446744073709551615 4194304 5160238 140729453823936 140729453812488 48002282497280 0 0 0 0 0 0 0 17 3 0 0 36 0 0 input_len: 7708572072, record_len: 153 pre_record_count: 1000000 pre_record_count: 2000000 pre_record_count: 3000000 pre_record_count: 4000000 pre_record_count: 5000000 pre_record_count: 6000000 pre_record_count: 7000000 pre_record_count: 8000000 pre_record_count: 9000000 pre_record_count: 10000000 vdjer: src/main/c/sparsehash/internal/densehashtable.h:782: void google::dense_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::clear_to_size(typename Alloc::rebind<Value>::other::size_type) [with Value = std::pair<const char* const, pre_node>, Key = const char*, HashFcn = my_hash, ExtractKey = google::dense_hash_map<const char*, pre_node, my_hash, eqstr, google::libc_allocator_with_realloc<std::pair<const char* const, pre_node> > >::SelectKey, SetKey = google::dense_hash_map<const char*, pre_node, my_hash, eqstr, google::libc_allocator_with_realloc<std::pair<const char* const, pre_node> > >::SetKey, EqualKey = eqstr, Alloc = google::libc_allocator_with_realloc<std::pair<const char* const, pre_node> >]: Assertion table' failed.`

Thank you for your help!

Harry

Hello,

I'm just getting started with VDJer, running on a CentOS terminal. I ran the exact same command given in the readme, only with my own indexed and sorted BAM from STAR. All went well until the assembly, when I received this error:

Initial char in input invalid: T
ERROR!  INVALID INPUT:
===========================0CTTATTATCAGTGAATTTATCATCATCCCCTATTTTACATAAGGAAATGGGGTTAGAAAGACCAAATAACATTTTTTCAACATCAAAACACTAGCTTT
===========================

I glanced at the source code and saw that sequences are tested for a zero or one at the beginning to identify whether they are forward or reverse. However, in the error dump, there is clearly a zero in the first position, not a T!

Do you have any idea why this might have happened?

Thanks,

Andrew