Jobs caught in long term grey zone (!)

Question: Jobs caught in long term grey zone (!)

2.6 years ago by

United States

larry.moss • 10 wrote:

Cufflinks job was in grey history with (!) for > 24hrs. "This is a new dataset and not all of its data are available yet" Reran job with same outcome. Concerned that the Tophat output was at fault, reran Tophat. Now the Tophat job is is in the same grey zone. I had performed the same pipeline with identical .fa & .gtf files & groomed FASTQ from a common batch.last weekend with no problems. Other Galaxy functions like import/export to GenomeSpace are active. No idea what to do...

rna-seq tophat cufflinks galaxy • 1000 views

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modified 2.3 years ago by yutao • 10 • written 2.6 years ago by larry.moss • 10

This is the advice we have been giving today: C: TopHat, Cufflinks, and CuffDiff jobs still querying

That said, given this is still a problem some are facing with reruns, I have asked our admin if there is something else going on. More feedback soon.

Jen, Galaxy team

ADD REPLY • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

2.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The most current update is that the cluster deployment issue was resolved a few hours ago. Approximately 1 PM EST.

This means:

Any jobs "stuck" in grey status "preparing job" before then can be restarted and rerun.
Any jobs started fresh since then should be allowed to completely process.

The backlog queue of jobs is large and certain jobs may take up to a day (or longer) to process. You do not want to restart any of type 2, since the regular rules apply: any newly restarted job will end up back at the end of the queue - extending wait time.

https://wiki.galaxyproject.org/Support#Dataset_status_and_how_jobs_execute

Sorry for the complexity of this and thanks for asking the question. Hopefully, others will see it and learn the correct path for completing jobs.

Jen, Galaxy team

ADD COMMENT • link modified 2.6 years ago • written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

2.3 years ago by

yutao • 10

yutao • 10 wrote:

hi,i have a problem with the tophat alignment summary ,would you please answer for me,thanks！ outcome Left reads: Input : 31687844 Mapped : 30305735 (95.6% of input) of these: 5499207 (18.1%) have multiple alignments (1287284 have >20) Right reads: Input : 31687844 Mapped : 30305735 (95.6% of input) of these: 5499207 (18.1%) have multiple alignments (1287284 have >20) 95.6% overall read mapping rate.

Aligned pairs: 30305735 of these: 5499207 (18.1%) have multiple alignments 30305218 (100.0%) are discordant alignments 0.0% concordant pair alignment rate.

Left reads: Input : 31687844 Mapped : 30305735 (95.6% of input) of these: 5499207 (18.1%) have multiple alignments (1287284 have >20) Right reads: Input : 31687844 Mapped : 30305735 (95.6% of input) of these: 5499207 (18.1%) have multiple alignments (1287284 have >20) 95.6% overall read mapping rate.

Aligned pairs: 30305735 of these: 5499207 (18.1%) have multiple alignments 30305218 (100.0%) are discordant alignments
other than this sanmple's concordant pair alignment rate is 0%,others are all up to 85%,so,is it normal?if not,what should i do? thank you!

ADD COMMENT • link written 2.3 years ago by yutao • 10

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