Error while running kma

[rafalkolenda]

I was thinking that I was able to get through the hard process of installing this software, but after some success with few reads I got this error:

subprocess.CalledProcessError: Command 'kma -ipe /home/ubuntu/kingsley-group/Food_Isolates/ConFindr/MC1883-1887-29_S55_/trimmed_R1.fastq.gz /home/ubuntu/kingsley-group/Food_Isolates/ConFindr/MC1883-1887-29_S55_/trimmed_R2.fastq.gz -t_db /home/ubuntu/kingsley-group/Rafal_Kolenda/confindr_databases/rMLST/rMLST_combined_kma -o /home/ubuntu/kingsley-group/Food_Isolates/ConFindr/MC1883-1887-29_S55_/kma_rmlst -t 4' returned non-zero exit status 1

[pcrxn]

Hi @rafalkolenda, could you please provide the command that you used to run ConFindr, the names of your files, and the output of running ls on the directory containing your files?

[rafalkolenda]

Hello,
command:
from confindr_src import confindr

# Find read files.
paired_reads = confindr.find_paired_reads('/home/ubuntu/kingsley-group/Food_Isolates/raw_reads/', forward_id='R1', reverse_id='R2')
for pair in paired_reads:
    confindr.find_contamination(pair=pair,
                                forward_id='R1', # change if yours is different
                                threads=8,
                                xmx='30g',
                                output_folder='/home/ubuntu/kingsley-group/Food_Isolates/ConFindr',
                                databases_folder='/home/ubuntu/kingsley-group/Rafal_Kolenda/confindr_databases/rMLST',
                                use_rmlst=True,
                                cross_details=True)

Name of my files: MC1883-1887-29_S55_R1_001.fastq.gz, MC1883-1887-29_S55_R2_001.fastq.gz
ls of directory containing the results of my run:
A20__contamination.csv LA_GT63__rmlst.csv
A20__rmlst.csv LA_GT64__contamination.csv
B101__contamination.csv LA_GT64__rmlst.csv
B101__rmlst.csv LA_GT65__contamination.csv
B104__contamination.csv LA_GT65__rmlst.csv
B104__rmlst.csv LA_GT67__contamination.csv
B105__contamination.csv LA_GT67__rmlst.csv
B105__rmlst.csv LA_GT68__contamination.csv
B111__contamination.csv LA_GT68__rmlst.csv
B111__rmlst.csv LA_GT70__contamination.csv
B113__contamination.csv LA_GT70__rmlst.csv
B113__rmlst.csv LA_GT71__contamination.csv
B118__contamination.csv LA_GT71__rmlst.csv
B118__rmlst.csv LA_GT72__contamination.csv
B119__contamination.csv LA_GT72__rmlst.csv
B119__rmlst.csv LA_GT73__contamination.csv
B35__contamination.csv LA_GT73__rmlst.csv
B35__rmlst.csv LA_GT74__contamination.csv
B82__contamination.csv LA_GT74__rmlst.csv
B82__rmlst.csv LA_GT75__contamination.csv
B90__contamination.csv LA_GT75__rmlst.csv
B90__rmlst.csv LA_GT76__contamination.csv
B98__contamination.csv LA_GT76__rmlst.csv
B98__rmlst.csv LA_GT77__contamination.csv
confindr_log.txt LA_GT77__rmlst.csv
confindr_report.csv LA_GT78__contamination.csv
LA_GT50__contamination.csv LA_GT78__rmlst.csv
LA_GT50__rmlst.csv LA_GT79__contamination.csv
LA_GT51__contamination.csv LA_GT79__rmlst.csv
LA_GT51__rmlst.csv MC1018-1022-45_S45__contamination.csv
LA_GT52__contamination.csv MC1018-1022-45_S45__rmlst.csv
LA_GT52__rmlst.csv MC1023-1027-49_S46__contamination.csv
LA_GT53__contamination.csv MC1023-1027-49_S46__rmlst.csv
LA_GT53__rmlst.csv MC1023-1027-50_S47__contamination.csv
LA_GT54__contamination.csv MC1023-1027-50_S47__rmlst.csv
LA_GT54__rmlst.csv MC1033-1037-63_S48__contamination.csv
LA_GT55__contamination.csv MC1033-1037-63_S48__rmlst.csv
LA_GT55__rmlst.csv MC1043-1047-67_S49__contamination.csv
LA_GT56__contamination.csv MC1043-1047-67_S49__rmlst.csv
LA_GT56__rmlst.csv MC1053-1057-78_S50__contamination.csv
LA_GT57__contamination.csv MC1053-1057-78_S50__rmlst.csv
LA_GT57__rmlst.csv MC1368-1372-11_S63__contamination.csv
LA_GT58__contamination.csv MC1368-1372-11_S63__rmlst.csv
LA_GT58__rmlst.csv MC1863-1867-10_S52__contamination.csv
LA_GT59__contamination.csv MC1863-1867-10_S52__rmlst.csv
LA_GT59__rmlst.csv MC1863-1867-9_S51__contamination.csv
LA_GT60__contamination.csv MC1863-1867-9_S51__rmlst.csv
LA_GT60__rmlst.csv MC1883-1887-28_S54__contamination.csv
LA_GT61__contamination.csv MC1883-1887-28_S54__rmlst.csv
LA_GT61__rmlst.csv MC1883-1887-29_S55_
LA_GT63__contamination.csv

[pcrxn]

Hi @rafalkolenda,

Thanks for sharing that output. Can you please run the following within the same environment as before, and share the output?

kma -ipe /home/ubuntu/kingsley-group/Food_Isolates/ConFindr/MC1883-1887-29_S55_/trimmed_R1.fastq.gz /home/ubuntu/kingsley-group/Food_Isolates/ConFindr/MC1883-1887-29_S55_/trimmed_R2.fastq.gz -t_db /home/ubuntu/kingsley-group/Rafal_Kolenda/confindr_databases/rMLST/rMLST_combined_kma -o /home/ubuntu/kingsley-group/Food_Isolates/ConFindr/MC1883-1887-29_S55_/kma_rmlst -t 4

[pcrxn]

Will close this in a couple of weeks unless an update is provided from the author.

[pcrxn]

Closed due to inactivity.