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ATAC example miss /bamCoverage/*.filtered.seq_depth_norm.bw files #910
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Thank you for your message. I am on a conference till July 28, 2023. I will answer your email once I am back in my office.
In urgent cases, please, contact genomics-core(at)rcii.de
Kind Regards,
Nicholas Strieder
--
Dr. rer. nat. Nicholas Strieder
~~
Leibniz-Institut für Immuntherapie - LIT
NGS Core - Bininformatics
Universitätsklinikum Regensburg
Franz-Josef-Strauß-Allee 11
93053 Regensburg
Germany
Phone: ++49 (0)941 944 18188
E-mail: ***@***.***
>> HamletShaoE ***@***.***> 27.7.23 07:20 >>>
I have installed snakepipes and downloaded ATACseq example for test run. However, the example does not run as I expected.
I first run following the suggestion from command.sh and get this:
-----
(snakePipes) ***@***.*** ~/DATA/snakePipe/testData/ATAC $ATAC-seq -d . --sampleSheet sampleSheet.tsv --DAG dm6_ensembl_release94
Sample sheet found and header is ok!
…---- This analysis has been done using snakePipes version 2.7.3 ----
Sample sheet found and header is ok!
SystemExit in line 33 of /GPFS/zhangli_lab_permanent/shaoyi/software/mambaforge/envs/snakePipes/lib/python3.11/site-packages/snakePipes/workflows/ATAC-seq/internals.snakefile:
1
File "/GPFS/zhangli_lab_permanent/shaoyi/software/mambaforge/envs/snakePipes/lib/python3.11/site-packages/snakePipes/workflows/ATAC-seq/Snakefile", line 26, in <module>
File "/GPFS/zhangli_lab_permanent/shaoyi/software/mambaforge/envs/snakePipes/lib/python3.11/site-packages/snakePipes/workflows/ATAC-seq/internals.snakefile", line 33, in <module>
File "<frozen _sitebuiltins>", line 26, in __call__
ERROR: Required file "/GPFS/zhangli_lab_permanent/shaoyi/snakePipe/testData/ATAC/bamCoverage/SRR7013050.filtered.seq_depth_norm.bw" for sample "SRR7013050" specified in configuration file is NOT available.
Error: snakemake returned an error code of 1, so processing is incomplete!
----
I suppose it is because bamCoverage/SRR7013050.filtered.seq_depth_norm.bw is missing.
I notice files in filtered_bam folder are links to Bowtie2. So I run with flag --fromBAM. This runs for a while and slurm goes well, yet end with error in the step of link_bam_bai_external and its' error message is
-----
(snakePipes) ***@***.*** ~/DATA/snakePipe/testData/ATAC $ATAC-seq -d . --sampleSheet sampleSheet.tsv --DAG --fromBAM filtered_bam dm6_ensembl_release94
...
[Thu Jul 27 11:25:09 2023]
Error in rule link_bam_bai_external:
jobid: 10
input: EXTERNAL_BAM/SRR7013046.bam, EXTERNAL_BAM/SRR7013046.bam.bai
output: filtered_bam/SRR7013046.filtered.bam, filtered_bam/SRR7013046.filtered.bam.bai
shell:
ln -s ../EXTERNAL_BAM/SRR7013046.bam filtered_bam/SRR7013046.filtered.bam;
ln -s ../EXTERNAL_BAM/SRR7013046.bam.bai filtered_bam/SRR7013046.filtered.bam.bai
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
cluster_jobid: Submitted batch job 5652530
Error executing rule link_bam_bai_external on cluster (jobid: 10, external: Submitted batch job 5652530, jobscript: /GPFS/zhangli_lab_permanent/shaoyi/snakePipe/testData/ATAC/.snakemake/tmp.onwy0y99/snakejob.link_bam_bai_external.10.sh). For error details see the cluster log and the log files of the involved rule(s).
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2023-07-27T110334.970475.snakemake.log
!!! ERROR in the ATAC-seq open chromatin workflow! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Error: snakemake returned an error code of 1, so processing is incomplete!
-----
I notice that EXTERNAL_BAM are links to files in filtered_bam, and this command is trying to link files in filtered_bam back to EXTERNAL_BAM.
I would appreciate if *.filtered.seq_depth_norm.bw files are provided. Or any other suggestions that would help me go through the test.
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#910
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Message ID: ***@***.***>
|
Hi, did your DNA-mapping run prior to running the ATAC-seq workflow in it produce any errors? Second: when you run ATAC-seq with Best wishes, Katarzyna |
Hi, thank you for replying. Also, I tried with -d for the ./(where I extract test data) and --fromBAM for the filtered_bam(where the extracted data with soft links of bam files) from the second run, I did specified the output folder with '-d' which is the upper level directory of the bam file folder.
Do you mean I should change the -d to another folder? OK, I'll test that. 84 of 84 steps (100%) done ---- This analysis has been done using snakePipes version 2.7.3 ---- It seems this works fine. thank you. |
Oh I see. I'll have a look if either the test data or the command.sh script on zenodo should be updated to reflect the latest workflow version. Thanks for clarifying that! |
ATAC-seq -d . --sampleSheet sampleSheet.tsv --local --DAG dm6 --fromBAM Bowtie2 --bamExt .bam |
I have installed snakepipes and downloaded ATACseq example for test run. However, the example does not run as I expected.
I first run following the suggestion from command.sh and get this:
(snakePipes) shaoyi@login02 ~/DATA/snakePipe/testData/ATAC $ATAC-seq -d . --sampleSheet sampleSheet.tsv --DAG dm6_ensembl_release94
Sample sheet found and header is ok!
---- This analysis has been done using snakePipes version 2.7.3 ----
Sample sheet found and header is ok!
SystemExit in line 33 of /GPFS/zhangli_lab_permanent/shaoyi/software/mambaforge/envs/snakePipes/lib/python3.11/site-packages/snakePipes/workflows/ATAC-seq/internals.snakefile:
1
File "/GPFS/zhangli_lab_permanent/shaoyi/software/mambaforge/envs/snakePipes/lib/python3.11/site-packages/snakePipes/workflows/ATAC-seq/Snakefile", line 26, in
File "/GPFS/zhangli_lab_permanent/shaoyi/software/mambaforge/envs/snakePipes/lib/python3.11/site-packages/snakePipes/workflows/ATAC-seq/internals.snakefile", line 33, in
File "", line 26, in call
ERROR: Required file "/GPFS/zhangli_lab_permanent/shaoyi/snakePipe/testData/ATAC/bamCoverage/SRR7013050.filtered.seq_depth_norm.bw" for sample "SRR7013050" specified in configuration file is NOT available.
Error: snakemake returned an error code of 1, so processing is incomplete!
I suppose it is because bamCoverage/SRR7013050.filtered.seq_depth_norm.bw is missing.
I notice files in filtered_bam folder are links to Bowtie2. So I run with flag --fromBAM. This runs for a while and slurm goes well, yet end with error in the step of link_bam_bai_external and its' error message is
(snakePipes) shaoyi@login01 ~/DATA/snakePipe/testData/ATAC $ATAC-seq -d . --sampleSheet sampleSheet.tsv --DAG --fromBAM filtered_bam dm6_ensembl_release94
...
[Thu Jul 27 11:25:09 2023]
Error in rule link_bam_bai_external:
jobid: 10
input: EXTERNAL_BAM/SRR7013046.bam, EXTERNAL_BAM/SRR7013046.bam.bai
output: filtered_bam/SRR7013046.filtered.bam, filtered_bam/SRR7013046.filtered.bam.bai
shell:
Error executing rule link_bam_bai_external on cluster (jobid: 10, external: Submitted batch job 5652530, jobscript: /GPFS/zhangli_lab_permanent/shaoyi/snakePipe/testData/ATAC/.snakemake/tmp.onwy0y99/snakejob.link_bam_bai_external.10.sh). For error details see the cluster log and the log files of the involved rule(s).
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2023-07-27T110334.970475.snakemake.log
!!! ERROR in the ATAC-seq open chromatin workflow! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Error: snakemake returned an error code of 1, so processing is incomplete!
I notice that EXTERNAL_BAM are links to files in filtered_bam, and this command is trying to link files in filtered_bam back to EXTERNAL_BAM.
I would appreciate if *.filtered.seq_depth_norm.bw files are provided. Or any other suggestions that would help me go through the test.
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