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ENCODE-DCC / chip-seq-pipeline2

ENCODE ChIP-seq pipeline
MIT License
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Issue with build_genome_data.sh #163

Closed mhayes8520 closed 3 years ago

mhayes8520 commented 4 years ago

Describe the bug I'm stuck trying to build the genome data for sacCer3 since it's not supported already. The build_genome_data.sh script seems to be stuck here:

Entering Ebwt loop

and I think it is specifically stuck trying to build the .bt2 files of the bowtie2 index since they are not yet completed and haven't increased in file size in a long while. I'd say it's been stuck here for about and hour or so. Any ideas?

I also made sure to update the build_genome_data.sh script with the appropriate inputs (genome, chrM, and url to fa.gz file for saccer3)

Finally this was being run in an sdev node in sherlock with 8GB of memory and 2 hours of time

OS/Platform

Caper configuration file Paste contents of ~/.caper/default.conf.

Input JSON file Paste contents of your input JSON file.

Error log Using parameters --bmax 1139729 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1139729 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:01 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:00 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 Sanity-checking and returning Building samples Reserving space for 22 sample suffixes Generating random suffixes QSorting 22 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 22 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Split 3, merged 9; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 3; iterating... Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 810473 (target: 1139728) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop

leepc12 commented 3 years ago

Please upload your shell script here. I will test it on my cluster.

leepc12 commented 3 years ago

Closing this.