crashfrog
commented
1 year ago Hi Curtis,
Yeah, looks like a bug. I’m currently traveling back from ASM-NGS so I’ll look into this more closely in a couple of days.
Justin On Oct 21, 2022 at 2:45 PM -0400, Curtis Kapsak @.***>, wrote:
When I use the -n sample_name option with shigatyper 2.0.1, it does not seem to honor the string that I feed into the option. Instead it seems to use the FASTQ file name prefix as the prefix for the shigatyper output files: $ docker run --rm -v $PWD:/data -u $(id -u):$(id -g) staphb/shigatyper:2.0.1 shigatyper --R1 sample001_L001_R1_001.fastq.gz --R2 sample001_L001_R2_001.fastq.gz -n TEST_SAMPLE_ID [CRITICAL::ShigaTyper] ShigaTyper v2.0.0 [M::mm_idx_gen::0.0161.13] collected minimizers [M::mm_idx_gen::0.0251.47] sorted minimizers [M::main::0.0321.38] loaded/built the index for 95 target sequence(s) [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 95 [M::mm_idx_stat::0.0331.36] distinct minimizers: 21938 (99.78% are singletons); average occurrences: 1.002; average spacing: 5.442; total length: 119664 [M::main] Version: 2.24-r1122 [M::main] CMD: minimap2 -d /tmp/tmpcvmo38fk/ShigellaRef5.mmi /usr/local/lib/python3.8/dist-packages/ShigaTyper-2.0.1-py3.8.egg/shigatyper/resources/ShigellaRef5.fasta [M::main] Real time: 0.036 sec; CPU: 0.047 sec; Peak RSS: 0.006 GB [WARNING] Indexing parameters (-k, -w or -H) overridden by parameters used in the prebuilt index. [M::main::0.0071.14] loaded/built the index for 95 target sequence(s) [M::mm_mapopt_update::0.0071.14] mid_occ = 1000 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 95 [M::mm_idx_stat::0.0081.12] distinct minimizers: 21938 (99.78% are singletons); average occurrences: 1.002; average spacing: 5.442; total length: 119664 [M::worker_pipeline::2.8991.93] mapped 175312 sequences [M::worker_pipeline::4.3392.24] mapped 175144 sequences [M::worker_pipeline::5.6632.55] mapped 174848 sequences [M::worker_pipeline::6.413*2.45] mapped 155712 sequences [M::main] Version: 2.24-r1122 [M::main] CMD: minimap2 -ax sr /tmp/tmpcvmo38fk/ShigellaRef5.mmi /data/sample001_L001_R1_001.fastq.gz /data/sample001_L001_R2_001.fastq.gz [M::main] Real time: 6.416 sec; CPU: 15.712 sec; Peak RSS: 0.352 GB [mpileup] 1 samples in 1 input files Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid [warning] samtools mpileup option
gis functional, but deprecated. Please switch to using bcftools mpileup in future. [mpileup] 1 samples in 1 input files [CRITICAL::ShigaTyper.run.report] sample001 is predicted to be Shigella boydii serotype 14. [CRITICAL::ShigaTyper.run.report] this strain is ipaB+, suggesting that it retains the virulent invasion plasmid. [CRITICAL::ShigaTyper.run.report] Writing hits to sample001-hits.tsv [CRITICAL::ShigaTyper.run.report] Writing final serotype prediction to sample001.tsv [CRITICAL::ShigaTyper.run.report] Complete in 9.017 milliseconds. Hit Number of reads Length Covered reference length % covered Number of variants % accuracy 0 ipaH_c 597 775 780 99.4 6.0 99.2 1 ipaB 140 1384 1743 79.4 13.0 99.1 2 Sb14_wzx 219 1441 1458 98.8 0.0 100.0 3 Sb14_wzy 179 1146 1212 94.6 0.0 100.0 sample prediction ipaB notes sample001 Shigella boydii serotype 14 + this strain is ipaB+, suggesting that it retains the virulent invasion plasmid.$ ls sample001-hits.tsv sample001.tsv sample001_L001_R1_001.fastq.gz sample001_L001_R2_001.fastq.gz In this example I would expect the 2 output files to be named: TEST_SAMPLE_ID-hits.tsv and TEST_SAMPLE_ID.tsv, but it seems to be using the FASTQ filename prefix to write the output files due to this line (I think?): https://github.com/CFSAN-Biostatistics/shigatyper/blob/7865ef17cbac4f5fef91d5bb0dc0785b014d7f28/shigatyper/shigatyper.py#L476 — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.***>
kapsakcj
When I use the
-n sample_nameoption with shigatyper 2.0.1, it does not seem to honor the string that I feed into the option.Instead it seems to use the FASTQ file name prefix as the prefix for the shigatyper output files:
In this example I would expect the 2 output files to be named:
TEST_SAMPLE_ID-hits.tsvandTEST_SAMPLE_ID.tsv, but it seems to be using the FASTQ filename prefix to write the output files due to this line (I think?):https://github.com/CFSAN-Biostatistics/shigatyper/blob/7865ef17cbac4f5fef91d5bb0dc0785b014d7f28/shigatyper/shigatyper.py#L476