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bpeacock44 / targeted_microbiome_via_blast

For developing wrapper scripts for our lab's targeted amplicon microbiome pipeline that utilizes blast for taxonomic assignments
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mbio_part3.sh issue with usearch otutab command #17

Closed mcuaya1 closed 2 days ago

mcuaya1 commented 3 days ago

https://github.com/bpeacock44/targeted_microbiome_via_blast/blob/88060b10cb5bd677506f403c622767a1fef6bf3a/pipeline_scripts/mbio_part3.sh#L204

The following line referenced here seems to cause the following issue.

Log file for Part 3 of the Microbiome Pipeline. Processed the following arguments:
Working Directory: /sf/bigdata/mcuay001/pipeline_sample_data
Data IDs: JB118 JB116
Trim Length: 150
Output Directory: SAMPLE_DATA_OUTPUT
 - -- --- ---- ---- --- -- -

 - -- --- ---- ---- --- -- -
Trimming and Filtering Reads
 - -- --- ---- ---- --- -- -
mkdir: created directory '/sf/bigdata/mcuay001/pipeline_sample_data/SAMPLE_DATA_OUTPUT'
usearch v11.0.667_i86linux64, 528Gb RAM, 128 cores
(C) Copyright 2013-18 Robert C. Edgar, all rights reserved.
https://drive5.com/usearch

License: cbernasc@ucr.edu, max 1 process(es)

00:00 278Mb   100.0% Word stats
00:00 278Mb   100.0% Alloc rows
00:00 278Mb   100.0% Build index
00:00 245Mb  CPU has 128 cores, defaulting to 10 threads
00:00 872Mb   100.0% Searching combined.fq, 2.0% matched
usearch v11.0.667_i86linux64, 528Gb RAM, 128 cores
(C) Copyright 2013-18 Robert C. Edgar, all rights reserved.
https://drive5.com/usearch

License: cbernasc@ucr.edu, max 1 process(es)

00:00 278Mb   100.0% Word stats
00:00 278Mb   100.0% Alloc rows
00:00 278Mb   100.0% Build index
00:00 245Mb  CPU has 128 cores, defaulting to 10 threads
00:00 872Mb   100.0% Searching combined.fq, 2.0% matched

 - -- --- ---- ---- --- -- -
Pooling Samples and Creating ASVs
 - -- --- ---- ---- --- -- -
mkdir: created directory '/sf/bigdata/mcuay001/pipeline_sample_data/SAMPLE_DATA_OUTPUT/asvs'
renamed '/sf/bigdata/mcuay001/pipeline_sample_data/SAMPLE_DATA_OUTPUT/asvs/z.fa' -> '/sf/bigdata/mcuay001/pipeline_sample_data/SAMPLE_DATA_OUTPUT/asvs/asvs.fa'

 - -- --- ---- ---- --- -- -
Creating Initial ASV Table
 - -- --- ---- ---- --- -- -

Invalid command line
Invalid option or missing value -mapout

Error on line usearch --otutab "${output_dir}/phix_clean.combined.fq" -quiet -zotus "${output_dir}/asvs/asvs.fa" -otutabout "${output_dir}/asvs/asv_table_00.txt" -mapout

According the to the documentation for the otutab command there seems to be a need to specify the output location. 

usearch -otutab reads.fq -otus otus.udb -otutabout otutab.txt -biomout otutab.json \
  -mapout map.txt -notmatched unmapped.fa

Running the following command again but specifying a output location gets rid of the issue

export output_dir=$PWD/pipeline_sample_data/SAMPLE_DATA_OUTPUT
usearch --otutab "${output_dir}/phix_clean.combined.fq" -quiet -zotus "${output_dir}/asvs/asvs.fa" -otutabout "${output_dir}/asvs/asv_table_00.txt" -mapout test.txt

I'm not entirely sure what the mapout flag is supposed to do but the way it is now will throw an issue.

bpeacock44 commented 2 days ago

Apologies, that must be left over from a test I was running - I will remove the mapout flag.