fastq files - join_paired_ends.py problem with pairend reads and multiple folders

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Dominik Strapagiel

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Mar 25, 2016, 8:42:25 AM3/25/16
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Hello All,
I am new,
have got problem with fastq-join, but now I have it from eu-utils
This is mine command:
multiple_join_paired_ends.py --input_dir /media/blul/NSEQ/FASTQ/Genomy/Bakterie/16sRNA/PILOT_PUPILS/ --read1_indicator _R1 --read2_indicator _R2 --output_dir /media/blul/NSEQ/FASTQ/Genomy/Bakterie/16sRNA/PILOT_PUPILS_MJP/
started form folder with fastq-join

Another error occured:

Logging started at 13:24:56 on 25 Mar 2016
QIIME version: 1.9.1

qiime_config values:
pick_otus_reference_seqs_fp    /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
sc_queue    all.q
pynast_template_alignment_fp    /usr/local/lib/python2.7/dist-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    /usr/local/lib/python2.7/dist-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    /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
temp_dir    /tmp/
blastall_fp    blastall
seconds_to_sleep    1

parameter file values:

Executing commands.

# join_paired_ends.py: /media/blul/NSEQ/FASTQ/Genomy/Bakterie/16sRNA/PILOT_PUPILS/ANT516/ANT516_R1.fastq command
join_paired_ends.py  -f /media/blul/NSEQ/FASTQ/Genomy/Bakterie/16sRNA/PILOT_PUPILS/ANT516/ANT516_R1.fastq -r /media/blul/NSEQ/FASTQ/Genomy/Bakterie/16sRNA/PILOT_PUPILS/ANT516/ANT516_R2.fastq -o /media/blul/NSEQ/FASTQ/Genomy/Bakterie/16sRNA/PILOT_PUPILS_MJP/ANT516_R1



*** ERROR RAISED DURING STEP: join_paired_ends.py: /media/blul/NSEQ/FASTQ/Genomy/Bakterie/16sRNA/PILOT_PUPILS/ANT516/ANT516_R1.fastq
Command run was:
 join_paired_ends.py  -f /media/blul/NSEQ/FASTQ/Genomy/Bakterie/16sRNA/PILOT_PUPILS/ANT516/ANT516_R1.fastq -r /media/blul/NSEQ/FASTQ/Genomy/Bakterie/16sRNA/PILOT_PUPILS/ANT516/ANT516_R2.fastq -o /media/blul/NSEQ/FASTQ/Genomy/Bakterie/16sRNA/PILOT_PUPILS_MJP/ANT516_R1
Command returned exit status: 1
Stdout:

Stderr
Traceback (most recent call last):
  File "/usr/local/bin/join_paired_ends.py", line 178, in <module>
    main()
  File "/usr/local/bin/join_paired_ends.py", line 155, in main
    working_dir=output_dir)
  File "/usr/local/lib/python2.7/dist-packages/bfillings/fastq_join.py", line 207, in join_paired_end_reads_fastqjoin
    result = fastq_join_app(infile_paths)
  File "/usr/local/lib/python2.7/dist-packages/burrito/util.py", line 303, in __call__
    result_paths)
  File "/usr/local/lib/python2.7/dist-packages/burrito/util.py", line 325, in _handle_app_result_build_failure
    raise ApplicationError("Error constructing CommandLineAppResult.")
burrito.util.ApplicationError: Error constructing CommandLineAppResult.


Logging stopped at 13:24:56 on 25 Mar 2016


Can you help me with that? Where is the problem right now?
Best,
Dominik
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