multiple_join_paired_ends.py not running at all and outputs no errors

[Taruna]

Hello,

I have a directory full of R1 and R2 fastq files for several samples and am trying to run the multiple_join_paired_ends.py script but the script runs for a sec and the only thing in the output directory is the log file. My command, parameters file and the log file are below. Any help would be great! Thank you!

Command:

multiple_join_paired_ends.py -i data-raw/ -o data-clean -p qiime-files/parameters/join_PE_parameters.txt

Parameter file:

#join_paired_ends.py parameters

join_paired_ends:min_overlap 10

join_paired_ends:perc_max_diff 15

Log file:

Logging started at 20:15:30 on 18 Jan 2017

QIIME version: 1.9.1

qiime_config values:

pick_otus_reference_seqs_fp /opt/anaconda/anaconda3/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta

sc_queue all.q

pynast_template_alignment_fp /opt/anaconda/anaconda3/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta

cluster_jobs_fp start_parallel_jobs.py

assign_taxonomy_reference_seqs_fp /opt/anaconda/anaconda3/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta

torque_queue friendlyq

jobs_to_start 1

denoiser_min_per_core 50

assign_taxonomy_id_to_taxonomy_fp /opt/anaconda/anaconda3/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt

temp_dir /data/tmp/

blastall_fp blastall

seconds_to_sleep 1

parameter file values:

join_paired_ends:perc_max_diff 15

join_paired_ends:min_overlap 10

Executing commands.

Logging stopped at 20:15:30 on 18 Jan 2017

[Stefan Janssen]

Hi Taruna,
can you also post the file names. I am asking because it might be the case that they don't follow the necessary naming schema.

[Taruna]

Hi Stefan,

You are correct. Its the way the files are named. I had a '_' before the fastq instead of a '.' Thanks for your help!

[Stefan Janssen]

you are welcome. Glad that the problem was so easy to solve.