Fix issue with RunRedup hanging on large duplicate cluster sizes #318
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rzlim08
approved these changes
Jan 26, 2024
| @@ -224,12 +228,13 @@ task RunRedup { | |||
| export SUBSAMPLED_READS_FILES=(~{sep=' ' subsampled_reads}) | |||
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| for index in ${!HOST_FILTERED_READS_FILES[@]}; do | |||
| seqkit grep -f duplicated-pairs.txt ${HOST_FILTERED_READS_FILES[$index]} | seqkit fq2fa -o duplicate_reads_$index.fasta | |||
| cat ${SUBSAMPLED_READS_FILES[$index]} duplicate_reads_$index.fasta > redups_$index.fasta | |||
| part=$(($index + 1)) | |||
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Is the change here just to ensure that the files are 1-indexed?
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| python3 <<CODE | ||
| pair_values = [] | ||
| passed_filters = set() | ||
| duplicates = set() | ||
| with open("passed_filters.txt", "r") as pf: | ||
| passed_filters.update(pf.read().splitlines()) | ||
| with open("duplicated-reads.txt", "r") as dr: | ||
| with open("duplicated_reads.txt", "r") as dr: | ||
| duplicates.update(dr.read().splitlines()) | ||
| with open("~{clusters}", "r") as clusters: | ||
| for line in clusters: | ||
| key, value = line.strip().split(",") | ||
| if key in duplicates and key in passed_filters and key != value: |
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I know I wrote this line, but I'm a bit dubious that all of it is necessary. If a key != value I think that by definition means that it'll be a duplicate. We should merge this in to get the fix out, but possibly consider removing this check entirely.
| @@ -185,8 +185,12 @@ task RunRedup { | |||
| } | |||
| command <<< | |||
| set -euxo pipefail | |||
| # exit if no duplicate reads | |||
| if [[ ! $(grep -v "^1\t" "~{cluster_sizes}") ]]; then | |||
| # extract duplicate read ids from the cluster sizes tsv; awk looks at the first column and prints | |||
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CZID-8963
grephas been replaced withawkwhen processing the duplicate cluster sizes tsv and clusters csv files._) instead of dashes (-).