Comments (3)
leepc12
commented on July 21, 2024
I tested git clone https://github.com/kundajelab/phantompeakqualtools but it works now.
I think this should be a temporary problem of github server?
Please uninstall dependencies and install them again.
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jloupe
commented on July 21, 2024
Thank you for the quick response.
We tried it a couple of times across different days, including this morning. I am not sure how it could be the server.
Since the error states run_spp.R is not in any directory, I manually added it to the chipseq_pipeline-master directory. I did a quick run starting with tagAligns and stopping at xcor, and it appears to have run that pipeline correctly. I am repeating the experiment through IDR currently to see if this fixes it.
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leepc12
commented on July 21, 2024
Pipeline is not guaranteed to run correctly if the dependency installer fails. Please don't use any hacky way to install dependencies. All dependencies must be installed by install_dependencies.sh.
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Related Issues (20)
- aquas_chipseq pipline SPP error HOT 6
- Trimmed data-sets HOT 1
- Read length HOT 2
- shuf: end of file HOT 8
- "-q [SLURM_ACCOUNT_NAME]" interpreted as file HOT 1
- ERROR:root:--extsize must >= 1! HOT 2
- Fatal error: chipseq.bds, line 1354, pos 2. Task/s failed. HOT 4
- [fread] Unexpected end of file (bwa_sai2sam_pe_core) HOT 6
- dead loop HOT 18
- job submission command HOT 2
- [Error] two same tag align file in (z)cat and shuf in pipe HOT 1
- Missing `-c` for `macs2 peakcall` ? HOT 1
- pipeline deprecated? HOT 2
- Can't download hg19 genome data HOT 2
- Some reps get ERROR:root:--extsize must >= 1! HOT 2
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- Citing the AQUAS Pipeline HOT 1
- ERROR:root:--extsize must >= 1! and chipseq.bds can not get all replicates go through HOT 25
- mm10 HOT 1
- JSD error: "RuntimeError: module compiled against API version 0xc but this version of numpy is 0xa" HOT 1
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