bwa failed: -1 issue

[Chris-Jun]

Hi, I got an issue when using proovread after Seqchunker.

[Tue Sep  3 04:58:18 2019] Running mode: mr
[Tue Sep  3 04:58:18 2019] Preparing long reads
ls #------------------------------------------------------------------------------#
perl -I/data/download/correction/proovread/proovread/bin/../lib/ /data/download/correction/proovread/proovread/bin/SeqFilter --fasta --in 20190226/r\
ead-long/20190226.fq --line-width 80 --lower-case --out 20190226/read-long/2019\
0226.masked.fa --phred-offset 33
#------------------------------------------------------------------------------#
[Tue Sep  3 05:45:42 2019] Read IDs don't look like proper PacBio subread IDs.
Falling back to running mode: mr-noccs

[Tue Sep  3 05:47:46 2019] Running task bwa-mr-1
[Tue Sep  3 05:50:41 2019] Indexing Long reads
#------------------------------------------------------------------------------#
/data2/jji/download/correction/proovread/proovread/bin/../util/bwa/bwa-proovrea\
d index 20190226/read-long/20190226.masked.fa 20190226/read-long/20190226.maske\
d.fa 2>20190226/bwa-mr-1/20190226_bwa.log
#------------------------------------------------------------------------------#
Can't open 20190226/bwa-mr-1/20190226_bwa.log: No such file or directory at /data/download/correction/proovread/proovread/bin/proovread line 1277.
#------------------------------------------------------------------------------#
  bwa failed: -1

        Exited at 'main'
        '/data/download/correction/proovread/proovread/bin/proovread', line 1277
        Last call 'main::run_bwa'
        '/data/download/correction/proovread/proovread/bin/proovread', line 853

The command I used is /data/download/correction/proovread/proovread/bin/proovread -l /data/compare/chunk_LR.fq -s /data/Nanopore_WGS/0_RawData/20190116/PM-AU-0011-T-A1/PM-AU-0011-T-A1_merged_piped_hg38.sortfix_mrkdup.BQSR.chr21-22.merged.fastq --pre /data/compare/PM-AU

I have produced several outputs perfectly fine before using these inputs, but it doesn't work all of a sudden with showing this error.

I checked the inputs again, but I don't see any problems.

Thanks

[thackl]

Odd. This also doesn't look like an issue with the data or even proovread. Things fail at the very basic step of trying to open a file using a shell command. Basically this doesn't seem to work

echo "blabla" 2>20190226/bwa-mr-1/20190226_bwa.log
# Can't open 20190226/bwa-mr-1/20190226_bwa.log...

This seems to indicate some issues with you system. Are you on cluster? Did you run into a file quota maybe?