dhoogest
commented
1 year ago Weirdly I can't seem to reproduce this on the test/fastq/ data (which contains an empty read set) via
dhoogest@gattaca:~/src/dada2-nf$ ./nextflow ./main.nf -params-file params.json
The error above is not seen, however there does appear to be an error in the join_counts step:
N E X T F L O W ~ version 22.04.3
Launching `./main.nf` [tiny_perlman] DSL1 - revision: 91de0426f7
executor > local (54)
[69/db55cc] process > copy_filelist [100%] 1 of 1 ✔
[0d/772e39] process > read_manifest (1) [100%] 1 of 1 ✔
[03/293f84] process > plot_quality (2) [100%] 10 of 10, cached: 2 ✔
[97/458525] process > barcodecop_dual (3) [100%] 10 of 10, cached: 2 ✔
[fa/361c7b] process > no_cutadapt (10) [100%] 10 of 10, cached: 2 ✔
[b2/bacac1] process > cm_split (6) [100%] 8 of 8, cached: 2 ✔
[46/c992e8] process > filter_and_trim (8) [100%] 8 of 8, cached: 2 ✔
[eb/b33534] process > learn_errors (2) [100%] 2 of 2 ✔
[6b/02b51b] process > dada_dereplicate (8) [100%] 8 of 8 ✔
[4a/6cb707] process > combined_overlaps [100%] 1 of 1 ✔
[bf/339a5c] process > write_seqs (3) [100%] 3 of 3 ✔
[35/f7b5fa] process > join_counts (1) [100%] 1 of 1, failed: 1 ✘
[ae/bd7b4f] process > save_params [100%] 1 of 1 ✔
Error executing process > 'join_counts (1)'
Caused by:
Process `join_counts (1)` terminated with an error exit status (1)
Command executed:
xsv cat rows --output cutadapt.csv cutadapt_*.csv
xsv cat rows --no-headers --output split.csv split_*.csv
xsv cat rows --no-headers --output bcop.csv bcop_*.csv
xsv cat rows --output dada.csv dada_*.csv
xsv cat rows --no-headers --output specimens.csv specimen_counts_*.csv
counts.py --out counts.csv raw.csv -1 cutadapt.csv split.csv bcop.csv dada.csv specimens.csv
Command exit status:
1
Command output:
(empty)
Command error:
Traceback (most recent call last):
File "/mnt/home/dhoogest/src/dada2-nf/bin/counts.py", line 142, in <module>
sys.exit(main(sys.argv[1:]))
File "/mnt/home/dhoogest/src/dada2-nf/bin/counts.py", line 42, in main
rows.extend(process_rows(raw, yld, 'raw', 'count'))
File "/mnt/home/dhoogest/src/dada2-nf/bin/counts.py", line 136, in process_rows
'yield': int(r[count]) / yld[si],
ZeroDivisionError: division by zero
Work dir:
/mnt/home/dhoogest/src/dada2-nf/work/35/f7b5fa22451bc2c34269094468195a
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line/cc @crosenth
Hit this today (and am surprised we haven't seen a problem previously):
Sample
23R157-U074has completely empty fastq.gz files and is presumably failing the acknowledged fragile logic here:@nhoffman any ideas at a glance to handle the error when attempting to gunzip an empty file?