STEP10 -> 10.mapsamples.pl failled due to cp command not finding second read pair

[bbalog87]

Hi,

STEP10 -> 10.mapsamples.pl failled due to cp command not findiong second pair for bowtie mapping. syslog.zip

[bam_sort_core] merging from 0 files and 8 in-memory blocks...
  Calculating contig coverage
  Reading contig length from /home/nguinkal/human_metagenome/intermediate/01.human_metagenome.lon
  Counting with sqm_counter: Opening 8 threads
  49428 reads counted
  247136 reads counted
  98855 reads counted
  197709 reads counted
  395417 reads counted
  296563 reads counted
  345990 reads counted
  148282 reads counted
  Working with sample 3: SRR1646959
  Getting raw reads
cp: missing destination file operand after '/home/nguinkal/human_metagenome/temp/human_metagenome.SRR1646959.current_1'
Try 'cp --help' for more information.
  Aligning to reference with bowtie
stat: No such file or directory
Warning: Could not open read file "/home/nguinkal/human_metagenome/temp/human_metagenome.SRR1646959.current_1" for reading; skipping...
Error: No input read files were valid
(ERR): bowtie2-align exited with value 1
An error occurred during mapping with command       /home/nguinkal/amrFlow/Miniconda3/envs/SqueezeMeta/SqueezeMeta/bin/bowtie2/bowtie2 -x /home/nguinkal/human_metagenome/data/human_metagenome.bowtie  -1 /home/nguinkal/human_metagenome/temp/human_metagenome.SRR1646959.current_1 -2 /home/nguinkal/human_metagenome/temp/human_metagenome.SRR1646959.current_2.gz --quiet -p 8 -S /home/nguinkal/human_metagenome/data/bam/human_metagenome.SRR1646959.sam --very-sensitive-local! at /home/nguinkal/amrFlow/Miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/10.mapsamples.pl line 184.
Stopping in STEP10 -> 10.mapsamples.pl. Program finished abnormally

Based on this standard error, the forward reads file human_metagenome.SRR1646959.current_1 was not readable. The reason is that this file does n't exist under this path, as the copying (cp) failed as we can see above.

[jtamames]

Hello!

I think that, by mistake, you specified sample SRR1646959_1.fastq.gz as "pair2" in your samples file TestSqueeMeta/samples.txt (probably you intended SRR1646959_2.fastq.gz). Could you check that, please?

Best,

J

[bbalog87]

@jtamames thank you very. It was a tiny typos in the samples.txt, which I did notice. the sample SRR1646959_1.fastq.gz was duplicated, instead of having SRR1646959_2.fastq.gz for reverse reads.

Best, julien

[bbalog87]

I will close the issue. Thanks.