Comments (10)
jma1991
commented on July 19, 2024
Fixed in #87
Please try with the latest dev branch, and let us know if it solved your issue.
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amizeranschi
commented on July 19, 2024
Hi, thanks a lot for looking into this issue. I tested again now with the latest dev:
N E X T F L O W ~ version 23.04.2
Pulling nf-core/rnasplice ...
Fast-forward
Launching `https://github.com/nf-core/rnasplice` [evil_keller] DSL2 - revision: 317076b2c3 [dev]
Unfortunately, the outcome was the same as the one reported above.
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:RMATS:RMATS_POST (K562_HNRNPK_TRT-K562_HNRNPK_CTL)'
Caused by:
Process `NFCORE_RNASPLICE:RNASPLICE:RMATS:RMATS_POST (K562_HNRNPK_TRT-K562_HNRNPK_CTL)` terminated with an error exit status (1)
Command executed:
mkdir -p K562_HNRNPK_TRT-K562_HNRNPK_CTL/rmats_post
rmats.py \
--gtf gencode_v44_spike-ins.gtf \
--b1 K562_HNRNPK_TRT_bamlist.txt \
--b2 K562_HNRNPK_CTL_bamlist.txt \
--od K562_HNRNPK_TRT-K562_HNRNPK_CTL/rmats_post \
--tmp K562_HNRNPK_TRT-K562_HNRNPK_CTL/rmats_temp \
-t paired \
--libType fr-unstranded \
--readLength 100 \
--variable-read-length \
--nthread 12 \
--tstat 12 \
--cstat 0.0001 \
--task post \
--paired-stats \
\
\
\
--allow-clipping \
1> K562_HNRNPK_TRT-K562_HNRNPK_CTL/rmats_post.log
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:RMATS:RMATS_POST":
rmats: $(echo $(rmats.py --version) | sed -e "s/v//g")
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
K562_HNRNPK_TRT_REP1_sorted.bam not found in .rmats files
K562_HNRNPK_TRT_REP2_sorted.bam not found in .rmats files
K562_HNRNPK_CTL_REP1_sorted.bam not found in .rmats files
K562_HNRNPK_CTL_REP2_sorted.bam not found in .rmats files
Work dir:
/data/share/santina-cutrupi/work/95/3c889e4ab5c9b8c8e00c1a39902cf9
This is what the work dir looks like. Please let me know if I can do any further digging in there, in case it helps with identifying the issue.
$ ls -lhat /data/share/santina-cutrupi/work/95/3c889e4ab5c9b8c8e00c1a39902cf9
total 40K
-rw-r--r-- 1 ubuntu ubuntu 1.1K Aug 2 13:22 .command.log
-rw-r--r-- 1 ubuntu ubuntu 1 Aug 2 13:22 .exitcode
drwxrwxr-x 3 ubuntu ubuntu 4.0K Aug 2 13:22 .
-rw-r--r-- 1 ubuntu ubuntu 232 Aug 2 13:22 .command.err
drwxr-xr-x 4 ubuntu ubuntu 80 Aug 2 13:22 K562_HNRNPK_TRT-K562_HNRNPK_CTL
-rw-r--r-- 1 ubuntu root 0 Aug 2 13:22 .command.trace
-rw-r--r-- 1 ubuntu ubuntu 0 Aug 2 13:22 .command.out
lrwxrwxrwx 1 ubuntu ubuntu 98 Aug 2 13:22 K562_HNRNPK_CTL_REP2_sorted.bam -> /data/share/santina-cutrupi/work/82/f300060e385abd4ed924bdba6646e5/K562_HNRNPK_CTL_REP2_sorted.bam
lrwxrwxrwx 1 ubuntu ubuntu 98 Aug 2 13:22 K562_HNRNPK_CTL_REP1_sorted.bam -> /data/share/santina-cutrupi/work/52/d7c6630f2bd54bec077a772e534260/K562_HNRNPK_CTL_REP1_sorted.bam
lrwxrwxrwx 1 ubuntu ubuntu 98 Aug 2 13:22 K562_HNRNPK_TRT_REP2_sorted.bam -> /data/share/santina-cutrupi/work/ce/3e2653945b846206b2e4c37dc6bde0/K562_HNRNPK_TRT_REP2_sorted.bam
lrwxrwxrwx 1 ubuntu ubuntu 98 Aug 2 13:22 K562_HNRNPK_TRT_REP1_sorted.bam -> /data/share/santina-cutrupi/work/64/19c0a94b1ed0224e24cb9f8aa88c85/K562_HNRNPK_TRT_REP1_sorted.bam
lrwxrwxrwx 1 ubuntu ubuntu 94 Aug 2 13:22 K562_HNRNPK_CTL_bamlist.txt -> /data/share/santina-cutrupi/work/e2/5a11b96da70ad1762e7a7c430e9a06/K562_HNRNPK_CTL_bamlist.txt
lrwxrwxrwx 1 ubuntu ubuntu 94 Aug 2 13:22 K562_HNRNPK_TRT_bamlist.txt -> /data/share/santina-cutrupi/work/e2/5a11b96da70ad1762e7a7c430e9a06/K562_HNRNPK_TRT_bamlist.txt
lrwxrwxrwx 1 ubuntu ubuntu 60 Aug 2 13:22 gencode_v44_spike-ins.gtf -> /data/share/santina-cutrupi/genome/gencode_v44_spike-ins.gtf
-rw-r--r-- 1 ubuntu ubuntu 0 Aug 2 13:22 .command.begin
-rw-rw-r-- 1 ubuntu ubuntu 218 Aug 2 13:21 .command.condor
-rw-rw-r-- 1 ubuntu ubuntu 762 Aug 2 13:21 .command.sh
-rwxrw-r-- 1 ubuntu ubuntu 14K Aug 2 13:21 .command.run
drwxrwxr-x 3 ubuntu ubuntu 52 Aug 2 13:21 ..
I'm guessing that these are the *.rmats files referred to in the error:
$ find /data/share/santina-cutrupi/work/95/3c889e4ab5c9b8c8e00c1a39902cf9 -name "*.rmats"
/data/share/santina-cutrupi/work/95/3c889e4ab5c9b8c8e00c1a39902cf9/K562_HNRNPK_TRT-K562_HNRNPK_CTL/rmats_temp/2023-08-02-10_16_03_793196_0.rmats
/data/share/santina-cutrupi/work/95/3c889e4ab5c9b8c8e00c1a39902cf9/K562_HNRNPK_TRT-K562_HNRNPK_CTL/rmats_temp/2023-08-02-10_16_03_793196_1.rmats
/data/share/santina-cutrupi/work/95/3c889e4ab5c9b8c8e00c1a39902cf9/K562_HNRNPK_TRT-K562_HNRNPK_CTL/rmats_temp/2023-08-02-10_16_03_793196_2.rmats
/data/share/santina-cutrupi/work/95/3c889e4ab5c9b8c8e00c1a39902cf9/K562_HNRNPK_TRT-K562_HNRNPK_CTL/rmats_temp/2023-08-02-10_16_03_793196_3.rmats
And these are the entries containing .bam in the above files.
$ grep ".bam" /data/share/santina-cutrupi/work/95/3c889e4ab5c9b8c8e00c1a39902cf9/K562_HNRNPK_TRT-K562_HNRNPK_CTL/rmats_temp/*.rmats
/data/share/santina-cutrupi/work/95/3c889e4ab5c9b8c8e00c1a39902cf9/K562_HNRNPK_TRT-K562_HNRNPK_CTL/rmats_temp/2023-08-02-10_16_03_793196_0.rmats:K562_TARDBP_TRT_REP1_sorted.bam
/data/share/santina-cutrupi/work/95/3c889e4ab5c9b8c8e00c1a39902cf9/K562_HNRNPK_TRT-K562_HNRNPK_CTL/rmats_temp/2023-08-02-10_16_03_793196_1.rmats:K562_TARDBP_TRT_REP2_sorted.bam
/data/share/santina-cutrupi/work/95/3c889e4ab5c9b8c8e00c1a39902cf9/K562_HNRNPK_TRT-K562_HNRNPK_CTL/rmats_temp/2023-08-02-10_16_03_793196_2.rmats:K562_TARDBP_CTL_REP1_sorted.bam
/data/share/santina-cutrupi/work/95/3c889e4ab5c9b8c8e00c1a39902cf9/K562_HNRNPK_TRT-K562_HNRNPK_CTL/rmats_temp/2023-08-02-10_16_03_793196_3.rmats:K562_TARDBP_CTL_REP2_sorted.bam
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amizeranschi
commented on July 19, 2024
Looks like the .rmats files contain the BAM files for the wrong experimental condition, i.e. the K562_TARDBP BAM files appear to be mentioned for the K562_HNRNPK_TRT-K562_HNRNPK_CTL contrast, judging from the names of the directories above.
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jma1991
commented on July 19, 2024
Can you post your sample and contrast sheet? I'll make a dummy copy for further testing.
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amizeranschi
commented on July 19, 2024
The sample and contrast sheet are linked in the first post, above.
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jma1991
commented on July 19, 2024
Can you pull the code from #88 and run with your data? I've refactored the code and tested it on some dummy data which mimics the experimental design of your data, but would be good to have you test before I merge the PR.
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amizeranschi
commented on July 19, 2024
Thanks again for working on this. I tested again with the zifornd/rnasplice -r dev -latest and the issue with RMATS_POST seems to be solved now. However, the pipeline now crashed due to a new issue with MISO_SASHIMI (which didn't occur before when I tested with only a single contrast at a time):
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI (3)'
Caused by:
Process `NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI (3)` terminated with an error exit status (1)
Command executed:
sashimi_plot --plot-event ENSG00000147403.18 index miso_settings.txt --output-dir sashimi
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI":
python: $(python --version | sed "s/Python //g")
misopy: $(python -c "import pkg_resources; print(pkg_resources.get_distribution('misopy').version)")
END_VERSIONS
Command exit status:
1
Command output:
- Looking for chromosome chrX directories
Error: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_HNRNPK_CTL_REP2_sorted not a directory.
Error: Could not find MISO output files for sample HepG2_HNRNPK_CTL_REP2_sorted (after searching in /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_HNRNPK_CTL_REP2_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Searching for MISO files in: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/K562_HNRNPK_TRT_REP1_sorted
- Looking for chromosome chrX directories
Error: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/K562_HNRNPK_TRT_REP1_sorted not a directory.
Error: Could not find MISO output files for sample K562_HNRNPK_TRT_REP1_sorted (after searching in /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/K562_HNRNPK_TRT_REP1_sorted and its subdirectories). Are you sure MISO output files are present in that do_data/K562_HNRNPK_TRT_REP1_sorted not a directory.
Error: Could not find MISO output files for sample K562_HNRNPK_TRT_REP1_sorted (after searching in /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/K562_HNRNPK_TRT_REP1_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Searching for MISO files in: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_TARDBP_CTL_REP1_sorted
- Looking for chromosome chrX directories
Error: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_TARDBP_CTL_REP1_sorted not a directory.
Error: Could not find MISO output files for sample HepG2_TARDBP_CTL_REP1_sorted (after searching in /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_TARDBP_CTL_REP1_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Searching for MISO files in: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/K562_HNRNPK_CTL_REP1_sorted
- Looking for chromosome chrX directories
Error: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/K562_HNRNPK_CTL_REP1_sorted not a directory.
Error: Could not find MISO output files for sample K562_HNRNPK_CTL_REP1_sorted (after searching in /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/K562_HNRNPK_CTL_REP1_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Searching for MISO files in: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/K562_HNRNPK_TRT_REP2_sorted
- Looking for chromosome chrX directories
Error: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/K562_HNRNPK_TRT_REP2_sorted not a directory.
Error: Could not find MISO output files for sample K562_HNRNPK_TRT_REP2_sorted (after searching in /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/K562_HNRNPK_TRT_REP2_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Searching for MISO files in: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_HNRNPK_TRT_REP2_sorted
- Looking for chromosome chrX directories
Error: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_HNRNPK_TRT_REP2_sorted not a directory.
Error: Could not find MISO output files for sample HepG2_HNRNPK_TRT_REP2_sorted (after searching in /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_HNRNPK_TRT_REP2_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Searching for MISO files in: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/K562_HNRNPK_CTL_REP2_sorted
- Looking for chromosome chrX directories
Error: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/K562_HNRNPK_CTL_REP2_sorted not a directory.
Error: Could not find MISO output files for sample K562_HNRNPK_CTL_REP2_sorted (after searching in /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/K562_HNRNPK_CTL_REP2_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Searching for MISO files in: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_HNRNPK_CTL_REP1_sorted
- Looking for chromosome chrX directories
Error: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_HNRNPK_CTL_REP1_sorted not a directory.
Error: Could not find MISO output files for sample HepG2_HNRNPK_CTL_REP1_sorted (after searching in /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_HNRNPK_CTL_REP1_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Searching for MISO files in: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_HNRNPK_TRT_REP1_sorted
- Looking for chromosome chrX directories
Error: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_HNRNPK_TRT_REP1_sorted not a directory.
Error: Could not find MISO output files for sample HepG2_HNRNPK_TRT_REP1_sorted (after searching in /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_HNRNPK_TRT_REP1_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Searching for MISO files in: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_TARDBP_TRT_REP2_sorted
- Looking for chromosome chrX directories
Error: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_TARDBP_TRT_REP2_sorted not a directory.
Error: Could not find MISO output files for sample HepG2_TARDBP_TRT_REP2_sorted (after searching in /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_TARDBP_TRT_REP2_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Reading dimensions from settings...
- Height: 7.00
- Width: 7.00
Plotting read densities and MISO estimates along event...
- Event: ENSG00000147403.18
Setting up plot using dimensions: [7.0, 7.0]
Using intron scale 30.0
Using exon scale 4.0
Reading sample label: K562_TARDBP_TRT_REP1_sorted.bam
Processing BAM: /data/share/santina-cutrupi/test-rnasplice/star/K562_TARDBP_TRT_REP1_sorted.bam
Command error:
- Looking for chromosome chrX directories
Error: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/K562_HNRNPK_TRT_REP2_sorted not a directory.
Error: Could not find MISO output files for sample K562_HNRNPK_TRT_REP2_sorted (after searching in /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/K562_HNRNPK_TRT_REP2_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Searching for MISO files in: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_HNRNPK_TRT_REP2_sorted
- Looking for chromosome chrX directories
Error: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_HNRNPK_TRT_REP2_sorted not a directory.
Error: Could not find MISO output files for sample HepG2_HNRNPK_TRT_REP2_sorted (after searching in /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_HNRNPK_TRT_REP2_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Searching for MISO files in: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/K562_HNRNPK_CTL_REP2_sorted
- Looking for chromosome chrX directories
Error: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/K562_HNRNPK_CTL_REP2_sorted not a directory.
Error: Could not find MISO output files for sample K562_HNRNPK_CTL_REP2_sorted (after searching in /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/K562_HNRNPK_CTL_REP2_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Searching for MISO files in: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_HNRNPK_CTL_REP1_sorted
- Looking for chromosome chrX directories
Error: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_HNRNPK_CTL_REP1_sorted not a directory.
Error: Could not find MISO output files for sample HepG2_HNRNPK_CTL_REP1_sorted (after searching in /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_HNRNPK_CTL_REP1_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Searching for MISO files in: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_HNRNPK_TRT_REP1_sorted
- Looking for chromosome chrX directories
Error: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_HNRNPK_TRT_REP1_sorted not a directory.
Error: Could not find MISO output files for sample HepG2_HNRNPK_TRT_REP1_sorted (after searching in /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_HNRNPK_TRT_REP1_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Searching for MISO files in: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_TARDBP_TRT_REP2_sorted
- Looking for chromosome chrX directories
Error: /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_TARDBP_TRT_REP2_sorted not a directory.
Error: Could not find MISO output files for sample HepG2_TARDBP_TRT_REP2_sorted (after searching in /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/HepG2_TARDBP_TRT_REP2_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Reading dimensions from settings...
- Height: 7.00
- Width: 7.00
Plotting read densities and MISO estimates along event...
- Event: ENSG00000147403.18
Setting up plot using dimensions: [7.0, 7.0]
Using intron scale 30.0
Using exon scale 4.0
Reading sample label: K562_TARDBP_TRT_REP1_sorted.bam
Processing BAM: /data/share/santina-cutrupi/test-rnasplice/star/K562_TARDBP_TRT_REP1_sorted.bam
[E::hts_open_format] Failed to open file "/data/share/santina-cutrupi/test-rnasplice/star/K562_TARDBP_TRT_REP1_sorted.bam" : No such file or directory
Traceback (most recent call last):
File "/usr/local/bin/sashimi_plot", line 11, in <module>
sys.exit(main())
File "/usr/local/lib/python2.7/site-packages/misopy/sashimi_plot/sashimi_plot.py", line 276, in main
plot_label=plot_label)
File "/usr/local/lib/python2.7/site-packages/misopy/sashimi_plot/sashimi_plot.py", line 153, in plot_event
plot_label=plot_label)
File "/usr/local/lib/python2.7/site-packages/misopy/sashimi_plot/plot_utils/plot_gene.py", line 698, in plot_density_from_file
plot_title=plot_title)
File "/usr/local/lib/python2.7/site-packages/misopy/sashimi_plot/plot_utils/plot_gene.py", line 260, in plot_density
junction_log_base=junction_log_base)
File "/usr/local/lib/python2.7/site-packages/misopy/sashimi_plot/plot_utils/plot_gene.py", line 48, in plot_density_single
bamfile = pysam.Samfile(bam_filename, 'rb')
File "pysam/libcalignmentfile.pyx", line 751, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 950, in pysam.libcalignmentfile.AlignmentFile._open
IOError: [Errno 2] could not open alignment file `/data/share/santina-cutrupi/test-rnasplice/star/K562_TARDBP_TRT_REP1_sorted.bam`: No such file or directory
Work dir:
/data/share/santina-cutrupi/work/b2/cc51deec0ce0205e0a7c0da3f1d60b
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amizeranschi
commented on July 19, 2024
There seems to be a problem with the directory naming convention. MISO expects directories ending with _sorted (such as K562_HNRNPK_TRT_REP2_sorted), but the actual directories in miso_data do not have this ending:
$ ls -lhat /data/share/santina-cutrupi/test-rnasplice/misopy/miso_data/
total 68K
drwxrwxr-x 4 ubuntu ubuntu 121 Aug 4 08:57 ..
drwxrwxr-x 44 ubuntu ubuntu 4.0K Aug 4 07:36 K562_TARDBP_TRT_REP1
drwxrwxr-x 18 ubuntu ubuntu 4.0K Aug 4 07:36 .
drwxrwxr-x 39 ubuntu ubuntu 4.0K Aug 4 07:32 HepG2_TARDBP_TRT_REP2
drwxrwxr-x 47 ubuntu ubuntu 4.0K Aug 4 07:30 K562_TARDBP_TRT_REP2
drwxrwxr-x 49 ubuntu ubuntu 4.0K Aug 4 07:29 K562_HNRNPK_CTL_REP2
drwxrwxr-x 37 ubuntu ubuntu 4.0K Aug 4 07:28 HepG2_TARDBP_TRT_REP1
drwxrwxr-x 40 ubuntu ubuntu 4.0K Aug 4 07:25 HepG2_HNRNPK_TRT_REP1
drwxrwxr-x 48 ubuntu ubuntu 4.0K Aug 4 07:24 K562_HNRNPK_TRT_REP2
drwxrwxr-x 35 ubuntu ubuntu 4.0K Aug 4 07:23 HepG2_TARDBP_CTL_REP2
drwxrwxr-x 46 ubuntu ubuntu 4.0K Aug 4 07:21 K562_TARDBP_CTL_REP1
drwxrwxr-x 49 ubuntu ubuntu 4.0K Aug 4 07:20 K562_TARDBP_CTL_REP2
drwxrwxr-x 46 ubuntu ubuntu 4.0K Aug 4 07:19 K562_HNRNPK_CTL_REP1
drwxrwxr-x 35 ubuntu ubuntu 4.0K Aug 4 07:16 HepG2_HNRNPK_CTL_REP2
drwxrwxr-x 38 ubuntu ubuntu 4.0K Aug 4 07:15 HepG2_TARDBP_CTL_REP1
drwxrwxr-x 47 ubuntu ubuntu 4.0K Aug 4 07:13 K562_HNRNPK_TRT_REP1
drwxrwxr-x 37 ubuntu ubuntu 4.0K Aug 4 07:09 HepG2_HNRNPK_TRT_REP2
drwxrwxr-x 41 ubuntu ubuntu 4.0K Aug 4 07:08 HepG2_HNRNPK_CTL_REP1
As for the last error:
[E::hts_open_format] Failed to open file "/data/share/santina-cutrupi/test-rnasplice/star/K562_TARDBP_TRT_REP1_sorted.bam" : No such file or directory
This one is strange, because that file is definitely present there, at least it is at this moment in time.
$ ls -lhat /data/share/santina-cutrupi/test-rnasplice/star/K562_TARDBP_TRT_REP1_sorted.bam
-rw-r--r-- 1 ubuntu ubuntu 2.5G Aug 4 06:50 /data/share/santina-cutrupi/test-rnasplice/star/K562_TARDBP_TRT_REP1_sorted.bam
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amizeranschi
commented on July 19, 2024
The same MISO issue also happened now when running a previous test with only one contrast, which previously worked fine.
from rnasplice.
jma1991
commented on July 19, 2024
Closing this issue as the rMATS bug has been fixed. Please open a new issue to discuss the MISO bug.
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Related Issues (20)
- link to example contrastsheet.csv is not working HOT 1
- Empty output for BAM+rMats HOT 2
- make contrasts file names consistent with those of the differentialabundance pipeline HOT 1
- Missing rMATS arguments HOT 2
- DEXSeq-DTU Stager pScreenAdjusted HOT 1
- sashimi_plot error HOT 2
- contrast file problem? HOT 7
- EXITING because of FATAL ERROR: Genome version: 20201 is INCOMPATIBLE with running STAR version: 2.7.9a HOT 2
- MISO error HOT 3
- The processes for splitting files are running very slowly with large numbers of input samples HOT 5
- Error: suppa_split_file.R Input_file must contain samplesheet samples. HOT 2
- ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1)' HOT 11
- Error in DRIMSeq::dmDSdata(counts = counts, samples = samps) HOT 3
- Error single-end execution HOT 1
- Error in SUPPA: Clustergroups are assigned incorrectly HOT 4
- Miso error HOT 8
- `NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DEXSEQ_DTU (1)` HOT 7
- RNA splice output
- Merged genes output HOT 3
- STAGER error: subscript out of bounds HOT 4
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