Comments (4)
Please post stdout/stderr logs here
/home/simon/git/atacomate/pipeline/cromwell-executions/atac/9f195d75-602d-4df8-822d-d4737d7c99c8/call-xcor/shard-0/execution/stderr
/home/simon/git/atacomate/pipeline/cromwell-executions/atac/9f195d75-602d-4df8-822d-d4737d7c99c8/call-xcor/shard-0/execution/stdout
from atac-seq-pipeline.
Thanks for looking at this, here are the files:
from atac-seq-pipeline.
The error log says that subsampled TAG-ALIGN file is empty. Please run the following command on your working directory for more debugging info.
$ find -name SRR6667571_pass_1*.tagAlign.gz` | xargs ls -l
from atac-seq-pipeline.
Closing this due to long inactivity
from atac-seq-pipeline.
Related Issues (20)
- Finished parsing without consuming all tokens HOT 1
- How are mitochondrial reads aligned? HOT 1
- How are DNAse-seq data processed with this pipeline?
- Reuse the same files in case of error.
- Help with running the pipeline HOT 1
- Unable to run the pipeline. invalid jar file error HOT 3
- 6 days stuck on task=atac.read_genome_tsv:-1, retry=0, status=Running
- More than 10 replicates HOT 3
- Encode-atac-seq-pipeline environment can't be found?
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- --read-len selection
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- The pipeline stalled at "chip.read_genome_tsv" for local backend HOT 2
- Differences in qc when validating installation HOT 3
- Failed on fastqs having identical filename but different path HOT 3
- Confirming that separate conditions/treatments should be analyzed by separate pipelines HOT 2
- Don't need to trim adapters
- Add --ntasks-per-node or --exclusive option for your multi-process jobs.
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