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macs3-project / MACS

MACS -- Model-based Analysis of ChIP-Seq
https://macs3-project.github.io/MACS/
BSD 3-Clause "New" or "Revised" License
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Bug: Test scripts failing #609

Closed outpaddling closed 10 months ago

outpaddling commented 10 months ago

Are the test scripts and data currently up-to-date? I'm seeing failures with MACS 3.0.0 on multiple platforms (FreeBSD + python 3.9 + numpy 1.25.0, and Linux (Alma 8), macOS, and NetBSD all with python 3.11 and numpy 1.26.3.

Errors are different on different platforms, but here is a sample from macOS:

===> Testing for py311-macs3-3.0.0
(cd /Users/bacon/Pkgsrc/pkgsrc/wip/py-macs3/work/MACS-3.0.0/test && ./cmdlinetest tag)
1. callpeak
1.1 callpeak narrow
1.2 callpeak broad
1.3 callpeak on PE narrow/broad
2. pileup
3. filterdup
4. predictd
5. randsample
6. refinepeak
7. bdgcmp
8. bdgpeakcall
9. bdgbroadcall
10. bdgdiff
11. cmbreps
12. bdgopt
13. callvar
14. 50k contigs with buffersize
14.1 callpeak
14.2 filterdup
14.3 pileup
14.4 randsample
15. hmmratac save training regions bed file and model file
15.1 hmmratac load training regions from bedfile
15.2 hmmratac load hmm model file
16. search for errors or warnings in log files
 checking ../temp/tag_run_50kcontigs/run_callpeak_50kcontigs.log...
 ... clear!
 checking ../temp/tag_run_50kcontigs/run_filterdup_50kcontigs.log...
 ... clear!
 checking ../temp/tag_run_50kcontigs/run_pileup_ChIP.bed.log...
 ... clear!
 checking ../temp/tag_run_50kcontigs/run_randsample.log...
 ... clear!
 checking ../temp/tag_run_bdgbroadcall/run_bdgbroadcall_w_prefix.log...
 ... clear!
 checking ../temp/tag_run_bdgcmp/run_bdgcmp.log...
 ... clear!
 checking ../temp/tag_run_bdgdiff/run_bdgdiff_w_o_file.log...
 ... clear!
 checking ../temp/tag_run_bdgdiff/run_bdgdiff_w_prefix.log...
 ... clear!
 checking ../temp/tag_run_bdgopt/run_bdgopt_max.log...
 ... clear!
 checking ../temp/tag_run_bdgopt/run_bdgopt_min.log...
 ... clear!
 checking ../temp/tag_run_bdgpeakcall/run_bdgpeakcall_cutoff.log...
 ... clear!
 checking ../temp/tag_run_bdgpeakcall/run_bdgpeakcall_w_prefix.log...
 ... clear!
 checking ../temp/tag_run_callpeak_broad/run_callpeak_broad.log...
 ... clear!
 checking ../temp/tag_run_callpeak_narrow/run_callpeak_narrow0.log...
 ... clear!
 checking ../temp/tag_run_callpeak_narrow/run_callpeak_narrow1.log...
 ... clear!
 checking ../temp/tag_run_callpeak_narrow/run_callpeak_narrow2.log...
 ... clear!
 checking ../temp/tag_run_callpeak_narrow/run_callpeak_narrow3.log...
 ... clear!
 checking ../temp/tag_run_callpeak_narrow/run_callpeak_narrow4.log...
 ... clear!
 checking ../temp/tag_run_callpeak_narrow/run_callpeak_narrow5.log...
 ... clear!
 checking ../temp/tag_run_callpeak_narrow_revert/run_callpeak_narrow_revert.log...
 ... clear!
 checking ../temp/tag_run_callpeak_pe_broad/run_callpeak_bampe_broad.log...
 ... clear!
 checking ../temp/tag_run_callpeak_pe_broad/run_callpeak_bedpe_broad.log...
 ... clear!
 checking ../temp/tag_run_callpeak_pe_narrow/run_callpeak_bampe_narrow.log...
 ... clear!
 checking ../temp/tag_run_callpeak_pe_narrow/run_callpeak_bedpe_narrow.log...
 ... clear!
 checking ../temp/tag_run_callpeak_pe_narrow/run_callpeak_pe_narrow_onlychip.log...
 ... clear!
 checking ../temp/tag_run_callvar/run_callvar_PE.log...
 ... clear!
 checking ../temp/tag_run_cmbreps/run_cmbreps_fisher.log...
 ... clear!
 checking ../temp/tag_run_cmbreps/run_cmbreps_max.log...
 ... clear!
 checking ../temp/tag_run_cmbreps/run_cmbreps_mean.log...
 ... clear!
 checking ../temp/tag_run_filterdup/run_filterdup.log...
 ... clear!
 checking ../temp/tag_run_filterdup/run_filterdup_d.log...
 ... clear!
 checking ../temp/tag_run_filterdup/run_filterdup_pe.log...
 ... clear!
 checking ../temp/tag_run_filterdup/run_filterdup_pe_d.log...
 ... clear!
 checking ../temp/tag_run_hmmratac/run_hmmratac.log...
 ... clear!
 checking ../temp/tag_run_hmmratac/run_hmmratac_bedpe.log...
 ... clear!
 checking ../temp/tag_run_hmmratac/run_hmmratac_load_hmm_model.log...
 ... clear!
 checking ../temp/tag_run_hmmratac/run_hmmratac_load_training_regions.log...
 ... clear!
 checking ../temp/tag_run_pileup/run_pileup_CTRL.bed.log...
 ... clear!
 checking ../temp/tag_run_pileup/run_pileup_CTRLPE.bampe.log...
 ... clear!
 checking ../temp/tag_run_pileup/run_pileup_CTRLPE.bedpe.log...
 ... clear!
 checking ../temp/tag_run_pileup/run_pileup_ChIP.bed.log...
 ... clear!
 checking ../temp/tag_run_pileup/run_pileup_ChIPPE.bampe.log...
 ... clear!
 checking ../temp/tag_run_pileup/run_pileup_ChIPPE.bedpe.log...
 ... clear!
 checking ../temp/tag_run_predictd/run_predictd.log...
 ... clear!
 checking ../temp/tag_run_predictd/run_predictd_bampe.log...
 ... clear!
 checking ../temp/tag_run_predictd/run_predictd_bedpe.log...
 ... clear!
 checking ../temp/tag_run_randsample/run_randsample.log...
 ... clear!
 checking ../temp/tag_run_randsample/run_randsample_bampe.log...
 ... clear!
 checking ../temp/tag_run_randsample/run_randsample_bedpe.log...
 ... clear!
 checking ../temp/tag_run_refinepeak/run_refinepeak_w_ofile.log...
 ... clear!
 checking ../temp/tag_run_refinepeak/run_refinepeak_w_prefix.log...
 ... clear!
17. compare with standard outputs
16.1.1 checking 50kcontigs run_callpeak_50kcontigs_peaks.narrowPeak ...
sort: No such file or directory
 ... success!
16.1.2 checking 50kcontigs run_callpeak_50kcontigs_summits.bed ...
sort: No such file or directory
 ... success!
16.1.3 checking 50kcontigs run_filterdup_result.bed ...
sort: No such file or directory
 ... failed! Difference:
0a1,199981
> unitig0       15      115     .       .       +
> unitig0       15      115     .       .       +
> unitig0       43      143     .       .       +
> unitig0       87      187     .       .       +
> unitig1       1       101     .       .       +
> unitig1       56      156     .       .       +
> unitig1       79      179     .       .       +
> unitig1       82      182     .       .       +
> unitig10      12      112     .       .       +
16.1.4 checking 50kcontigs run_pileup_ChIP.bed.bdg ...
sort: No such file or directory
 ... failed! Difference:
outpaddling commented 10 months ago

Never mind, I got it working on some platforms by installing before running tests. The cmdlinetest output didn't indicate it, but digging into the logs, I found that it wasn't finding the macs3 command. There are still some issues, but the test scripts appear to be OK. I'll reopen if it seems to be a MACS issue.