#312 FASTQ quality name line too long in read

[Mahul Chakraborty]

I am running rc2 to correct PB reads from a fly. The PBcR pipeline stopped right after corrected reads are generated. Apparently the fastq file containing the corrected reads (corrected.fastq) has at least one line where a qual line and a seq line got joined. I have noticed that this happens when some of the consensus jobs fail (with -sensitive) and I restart the pipeline (after removing runPartition.sh). This did not happen before rc1 (rc1 was also doing this but I thought it was an issue with our system, so never reported it). Do you know what might be responsible for this?

A summary of the error:

$ less runPBcR.runCA.sge.out.00
/dfs1/bio/mchakrab/pacbio/wgs-8.3rc2/Linux-amd64/bin/gatekeeper -o /share//pacbio/dtes/pacbio_assembly/dtes_hq/asm.gkpStore.BUILDING -T -F /share/dtes/pacbio_assembly/dtes_hq.longest25.frg > /share/pacbio/dtes/pacbio_assembly/dtes_hq/asm.gkpStore.err 2>&1
----------------------------------------END Tue Jun 23 12:04:26 2015 (81 seconds)
ERROR: Failed with signal HUP (1)
================================================================================

runCA failed.

---

Stack trace:

at /dfs1/pacbio/wgs-8.3rc2/Linux-amd64/bin/runCA line 1629
main::caFailure('gatekeeper failed', '/share/pacbio/dtes/pacbio_assembly/dtes_hq/asm.g...') called at /dfs1/pacbio/wgs-8.3rc2/Linux-amd64/bin/runCA line 1958
main::preoverlap('/share/pacbio/dtes/pacbio_assembly/dtes_hq.longe...') called at /dfs1/pacbio/wgs-8.3rc2/Linux-amd64/bin/runCA line 6251

---

Last few lines of the relevant log file (/share/pacbio/dtes/pacbio_assembly/dtes_hq/asm.gkpStore.err):

Starting file '/share//pacbio/dtes/pacbio_assembly/dtes_hq.longest25.frg'.

Processing SINGLE-ENDED SANGER QV encoding reads from:
'/share//pacbio/dtes/pacbio_assembly//dtes_hq.fastq'
FASTQ quality name line too long in read 'T.......GC'

---

Failure message:

gatekeeper failed

[Sergey Koren]

I've seen some instability in PBDAGCON on various systems because of it's static compilation. If you are using the PBDAGCON that came with rc2 (if there is a pbdagcon executable in Linux-amd64/bin/) you can try replacing it with one built on your system or copied from your installation of SMRTportal. If that doesn't fix it, you can also try editing the runPartition.sh script to use one thread to see if that removes the instability.

[Mahul Chakraborty]

OK. I will try that. Thanks, Sergey.

On Mon, Jul 6, 2015 at 2:44 PM Sergey Koren skoren@users.sf.net wrote:

I've seen some instability in PBDAGCON on various systems because of it's
static compilation. If you are using the PBDAGCON that came with rc2 (if
there is a pbdagcon executable in Linux-amd64/bin/) you can try replacing
it with one built on your system or copied from your installation of
SMRTportal. If that doesn't fix it, you can also try editing the
runPartition.sh script to use one thread to see if that removes the
instability.

---

• [bugs:#312] http://sourceforge.net/p/wgs-assembler/bugs/312 FASTQ
  quality name line too long in read*

Status: open
Group: correction
Created: Tue Jun 23, 2015 08:32 PM UTC by Mahul Chakraborty
Last Updated: Tue Jun 23, 2015 08:32 PM UTC
Owner: nobody

I am running rc2 to correct PB reads from a fly. The PBcR pipeline stopped
right after corrected reads are generated. Apparently the fastq file
containing the corrected reads (corrected.fastq) has at least one line
where a qual line and a seq line got joined. I have noticed that this
happens when some of the consensus jobs fail (with -sensitive) and I
restart the pipeline (after removing runPartition.sh). This did not happen
before rc1 (rc1 was also doing this but I thought it was an issue with our
system, so never reported it). Do you know what might be responsible for
this?

A summary of the error:

$ less runPBcR.runCA.sge.out.00
/dfs1/bio/mchakrab/pacbio/wgs-8.3rc2/Linux-amd64/bin/gatekeeper -o
/share//pacbio/dtes/pacbio_assembly/dtes_hq/asm.gkpStore.BUILDING -T -F
/share/dtes/pacbio_assembly/dtes_hq.longest25.frg >
/share/pacbio/dtes/pacbio_assembly/dtes_hq/asm.gkpStore.err 2>&1
----------------------------------------END Tue Jun 23 12:04:26 2015 (81
seconds)
ERROR: Failed with signal HUP (1)

================================================================================

runCA failed.

Stack trace:

at /dfs1/pacbio/wgs-8.3rc2/Linux-amd64/bin/runCA line 1629
main::caFailure('gatekeeper failed',
'/share/pacbio/dtes/pacbio_assembly/dtes_hq/asm.g...') called at
/dfs1/pacbio/wgs-8.3rc2/Linux-amd64/bin/runCA line 1958
main::preoverlap('/share/pacbio/dtes/pacbio_assembly/dtes_hq.longe...')
called at /dfs1/pacbio/wgs-8.3rc2/Linux-amd64/bin/runCA line 6251

---

Last few lines of the relevant log file
(/share/pacbio/dtes/pacbio_assembly/dtes_hq/asm.gkpStore.err):

Starting file '/share//pacbio/dtes/pacbio_assembly/dtes_hq.longest25.frg'.

Processing SINGLE-ENDED SANGER QV encoding reads from:
'/share//pacbio/dtes/pacbio_assembly//dtes_hq.fastq'
FASTQ quality name line too long in read 'T.......GC'

---

Failure message:

gatekeeper failed

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