Comments (4)
leepc12
commented on July 28, 2024
Did you follow the instruction (step 3 and 4) on https://github.com/ENCODE-DCC/atac-seq-pipeline/blob/master/docs/tutorial_sge.md? Pipeline failed to find genome database for a test sample.
Also reduce -Xmx16384M to 1GB or 2GB. It's too big.
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kirstyjamieson
commented on July 28, 2024
Yes, I had downloaded the genome database and test sample data. I checked the directories and discovered missing files and folders after the run failed. Somehow running the pipeline caused this. I downloaded everything again and reran and it worked. Not sure if this is a problem on my cluster or a bug with the pipeline. I'll let you know if it happens again.
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leepc12
commented on July 28, 2024
@kirstyjamieson: I see. BTW you can simply ignore the warning Localization via hard link has failed. If that fails then it automatically switches to soft link or physical copy.
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kirstyjamieson
commented on July 28, 2024
Thanks, good to know!
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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?
- [Question]: Do reads need to be deduped before FRiP calculation HOT 6
- Invalid MEMLIMIT unit value with LSF jobs on Linux
- two replicates and the combined have different signal
- --read-len selection
- Memory Saving: too many large files?
- 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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