ctat-mutations-WorkflowFailedState #104
Comments
|
hi,
Try running with --boosting_method none
and it should finish with the standard results.
I'm not seeing an error message that indicates why the process failed with
the boosting set. Usually it'll indicate a stderr file from the workflow
that indicates where it failed with the intermediate results and logs,
which we'd use to troubleshoot further.
Boosting generally slightly improves the results, but you can do without it
if it continues to crash. You can also try using our singularity or docker
images that have everything preinstalled and tested.
best,
~brian
…On Sun, Jan 9, 2022 at 10:50 AM taot2007 ***@***.***> wrote:
Hi, I am running the CTAT-mutations (v3.2.0) pipeline, the library version
is StarFv1.10. I used the commamd:
$ nohup time ~/src/CTAT-Mutations-v3.2.0/ctat_mutations --cpu 15
--genome_lib_dir
~/Share/CTAT_resource_lib/GRCh38_GENECODE_v38/build/ctat_genome_lib_build_dir/
--left ~/data/6015_R1_val_1.fq.gz
--right ~/data/6015_R2_val_2.fq.gz
--sample_id 6015
--output ~/data/CTATmutations/6015/ >
~/data/CTATmutations/ctat_mutations.nohup.out 2>&1 &
It stopped at this point, looks pretty end. Can you help to address this?
Thanks so much!
##########################
Running CTAT Boosting
##########################
07:49:32 : INFO : Preprocess Data ...
07:49:32 : INFO : Removing RNAediting sites ...
07:49:32 : INFO : Note: detected 80 virtual cores but NumExpr set to
maximum of 64, check "NUMEXPR_MAX_THREADS" environment variable.
07:49:32 : INFO : Note: NumExpr detected 80 cores but
"NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.
07:49:32 : INFO : NumExpr defaulting to 8 threads.
07:49:32 : INFO : Number of variants after removing RNAediting sites:
679499
07:49:32 : INFO : -examining AC
07:49:32 : INFO : -AC has 2 uniq entries
07:49:32 : INFO : -examining ALT
07:49:32 : INFO : -ALT has 3 uniq entries
07:49:32 : INFO : -examining BaseQRankSum
07:49:32 : INFO : -BaseQRankSum has 11417 uniq entries
07:49:32 : INFO : -examining DJ
07:49:32 : INFO : -DJ has 140547 uniq entries
07:49:32 : INFO : -examining DP
07:49:32 : INFO : -DP has 1202 uniq entries
07:49:32 : INFO : -examining ED
07:49:32 : INFO : -ED has 910 uniq entries
07:49:32 : INFO : -examining Entropy
07:49:32 : INFO : -Entropy has 11 uniq entries
07:49:32 : INFO : -examining ExcessHet
07:49:32 : INFO : -ExcessHet has 1 uniq entries
07:49:32 : INFO : -pruning feature column ExcessHet as theres no complexity
07:49:32 : INFO : -examining FS
07:49:32 : INFO : -FS has 9440 uniq entries
07:49:32 : INFO : -examining Homopolymer
07:49:32 : INFO : -Homopolymer has 2 uniq entries
07:4
[2022-01-09 07:50:14,24] [info] WorkflowManagerActor
WorkflowActor-5da239af-2b16-4a5e-913a-f2324734f2a5 is in a terminal state:
WorkflowFailedState
[2022-01-09 07:50:23,59] [info] SingleWorkflowRunnerActor workflow
finished with status 'Failed'.
[2022-01-09 07:50:27,05] [info] SingleWorkflowRunnerActor writing metadata
to /tmp/tmptdvu1uzx.json
[2022-01-09 07:50:27,08] [info] Workflow polling stopped
[2022-01-09 07:50:27,10] [info] Shutting down WorkflowStoreActor - Timeout
= 5 seconds
[2022-01-09 07:50:27,10] [info] Shutting down WorkflowLogCopyRouter -
Timeout = 5 seconds
[2022-01-09 07:50:27,10] [info] Shutting down JobExecutionTokenDispenser -
Timeout = 5 seconds
[2022-01-09 07:50:27,10] [info] 0 workflows released by cromid-a657c44
[2022-01-09 07:50:27,10] [info] JobExecutionTokenDispenser stopped
[2022-01-09 07:50:27,11] [info] Aborting all running workflows.
[2022-01-09 07:50:27,11] [info] WorkflowStoreActor stopped
[2022-01-09 07:50:27,11] [info] Shutting down WorkflowManagerActor -
Timeout = 3600 seconds
[2022-01-09 07:50:27,11] [info] WorkflowLogCopyRouter stopped
[2022-01-09 07:50:27,11] [info] WorkflowManagerActor All workflows finished
[2022-01-09 07:50:27,11] [info] WorkflowManagerActor stopped
[2022-01-09 07:50:27,32] [info] Connection pools shut down
[2022-01-09 07:50:27,32] [info] Shutting down SubWorkflowStoreActor -
Timeout = 1800 seconds
[2022-01-09 07:50:27,32] [info] Shutting down JobStoreActor - Timeout =
1800 seconds
[2022-01-09 07:50:27,32] [info] Shutting down CallCacheWriteActor -
Timeout = 1800 seconds
[2022-01-09 07:50:27,32] [info] Shutting down ServiceRegistryActor -
Timeout = 1800 seconds
[2022-01-09 07:50:27,32] [info] Shutting down DockerHashActor - Timeout =
1800 seconds
[2022-01-09 07:50:27,32] [info] Shutting down IoProxy - Timeout = 1800
seconds
[2022-01-09 07:50:27,32] [info] SubWorkflowStoreActor stopped
[2022-01-09 07:50:27,33] [info] CallCacheWriteActor Shutting down: 0
queued messages to process
[2022-01-09 07:50:27,33] [info] JobStoreActor stopped
[2022-01-09 07:50:27,33] [info] KvWriteActor Shutting down: 0 queued
messages to process
[2022-01-09 07:50:27,33] [info] CallCacheWriteActor stopped
[2022-01-09 07:50:27,33] [info] WriteMetadataActor Shutting down: 0 queued
messages to process
[2022-01-09 07:50:27,33] [info] IoProxy stopped
[2022-01-09 07:50:27,33] [info] ServiceRegistryActor stopped
[2022-01-09 07:50:27,34] [info] DockerHashActor stopped
[2022-01-09 07:50:27,36] [info] Database closed
[2022-01-09 07:50:27,36] [info] Stream materializer shut down
[2022-01-09 07:50:27,37] [info] WDL HTTP import resolver closed
Workflow 5da239af-2b16-4a5e-913a-f2324734f2a5 transitioned to state Failed
1408.72user 545.12system 21:31:31elapsed 2%CPU (0avgtext+0avgdata
1979140maxresident)k
166870624inputs+305136outputs (1major+9823645minor)pagefaults 0swaps
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It worked! Thanks so much! |
|
Great, thanks for letting me know!
…On Mon, Jan 10, 2022 at 10:42 PM taot2007 ***@***.***> wrote:
It worked! Thanks so much!
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Hi Brian, Traceback (most recent call last): |
|
hi,
would you be able to share one of the data sets with me that's causing this
problem? It'll make it possible for me to debug it.
best,
~b
…On Mon, Jan 24, 2022 at 10:20 PM taot2007 ***@***.***> wrote:
Hi Brian,
I used the same command as above, most of the samples were processed
successfully, but a few had an issue as below. How to get this solved?
Thanks so much！
Traceback (most recent call last):
File "/home/TT/src/CTAT-Mutations-v3.2.0/src/annotate_ED.py", line 165, in
main()
File "/home/TT/src/CTAT-Mutations-v3.2.0/src/annotate_ED.py", line 118, in
main
val1 = abs(int(names[i][1]) - psl_df["T start"][i])
ValueError: invalid literal for int() with base 10: ''
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Hi, I am running the CTAT-mutations (v3.2.0) pipeline, the library version is StarFv1.10. I used the commamd:
$ nohup time ~/src/CTAT-Mutations-v3.2.0/ctat_mutations --cpu 15
--genome_lib_dir ~/Share/CTAT_resource_lib/GRCh38_GENECODE_v38/build/ctat_genome_lib_build_dir/
--left ~/data/6015_R1_val_1.fq.gz
--right ~/data/6015_R2_val_2.fq.gz
--sample_id 6015
--output ~/data/CTATmutations/6015/ > ~/data/CTATmutations/ctat_mutations.nohup.out 2>&1 &
It stopped at this point, looks pretty end. Can you help to address this? Thanks so much!
##########################
Running CTAT Boosting
##########################
07:49:32 : INFO : Preprocess Data ...
07:49:32 : INFO : Removing RNAediting sites ...
07:49:32 : INFO : Note: detected 80 virtual cores but NumExpr set to maximum of 64, check "NUMEXPR_MAX_THREADS" environment variable.
07:49:32 : INFO : Note: NumExpr detected 80 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.
07:49:32 : INFO : NumExpr defaulting to 8 threads.
07:49:32 : INFO : Number of variants after removing RNAediting sites: 679499
07:49:32 : INFO : -examining AC
07:49:32 : INFO : -AC has 2 uniq entries
07:49:32 : INFO : -examining ALT
07:49:32 : INFO : -ALT has 3 uniq entries
07:49:32 : INFO : -examining BaseQRankSum
07:49:32 : INFO : -BaseQRankSum has 11417 uniq entries
07:49:32 : INFO : -examining DJ
07:49:32 : INFO : -DJ has 140547 uniq entries
07:49:32 : INFO : -examining DP
07:49:32 : INFO : -DP has 1202 uniq entries
07:49:32 : INFO : -examining ED
07:49:32 : INFO : -ED has 910 uniq entries
07:49:32 : INFO : -examining Entropy
07:49:32 : INFO : -Entropy has 11 uniq entries
07:49:32 : INFO : -examining ExcessHet
07:49:32 : INFO : -ExcessHet has 1 uniq entries
07:49:32 : INFO : -pruning feature column ExcessHet as theres no complexity
07:49:32 : INFO : -examining FS
07:49:32 : INFO : -FS has 9440 uniq entries
07:49:32 : INFO : -examining Homopolymer
07:49:32 : INFO : -Homopolymer has 2 uniq entries
07:4
[2022-01-09 07:50:14,24] [info] WorkflowManagerActor WorkflowActor-5da239af-2b16-4a5e-913a-f2324734f2a5 is in a terminal state: WorkflowFailedState
[2022-01-09 07:50:23,59] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'.
[2022-01-09 07:50:27,05] [info] SingleWorkflowRunnerActor writing metadata to /tmp/tmptdvu1uzx.json
[2022-01-09 07:50:27,08] [info] Workflow polling stopped
[2022-01-09 07:50:27,10] [info] Shutting down WorkflowStoreActor - Timeout = 5 seconds
[2022-01-09 07:50:27,10] [info] Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds
[2022-01-09 07:50:27,10] [info] Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds
[2022-01-09 07:50:27,10] [info] 0 workflows released by cromid-a657c44
[2022-01-09 07:50:27,10] [info] JobExecutionTokenDispenser stopped
[2022-01-09 07:50:27,11] [info] Aborting all running workflows.
[2022-01-09 07:50:27,11] [info] WorkflowStoreActor stopped
[2022-01-09 07:50:27,11] [info] Shutting down WorkflowManagerActor - Timeout = 3600 seconds
[2022-01-09 07:50:27,11] [info] WorkflowLogCopyRouter stopped
[2022-01-09 07:50:27,11] [info] WorkflowManagerActor All workflows finished
[2022-01-09 07:50:27,11] [info] WorkflowManagerActor stopped
[2022-01-09 07:50:27,32] [info] Connection pools shut down
[2022-01-09 07:50:27,32] [info] Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds
[2022-01-09 07:50:27,32] [info] Shutting down JobStoreActor - Timeout = 1800 seconds
[2022-01-09 07:50:27,32] [info] Shutting down CallCacheWriteActor - Timeout = 1800 seconds
[2022-01-09 07:50:27,32] [info] Shutting down ServiceRegistryActor - Timeout = 1800 seconds
[2022-01-09 07:50:27,32] [info] Shutting down DockerHashActor - Timeout = 1800 seconds
[2022-01-09 07:50:27,32] [info] Shutting down IoProxy - Timeout = 1800 seconds
[2022-01-09 07:50:27,32] [info] SubWorkflowStoreActor stopped
[2022-01-09 07:50:27,33] [info] CallCacheWriteActor Shutting down: 0 queued messages to process
[2022-01-09 07:50:27,33] [info] JobStoreActor stopped
[2022-01-09 07:50:27,33] [info] KvWriteActor Shutting down: 0 queued messages to process
[2022-01-09 07:50:27,33] [info] CallCacheWriteActor stopped
[2022-01-09 07:50:27,33] [info] WriteMetadataActor Shutting down: 0 queued messages to process
[2022-01-09 07:50:27,33] [info] IoProxy stopped
[2022-01-09 07:50:27,33] [info] ServiceRegistryActor stopped
[2022-01-09 07:50:27,34] [info] DockerHashActor stopped
[2022-01-09 07:50:27,36] [info] Database closed
[2022-01-09 07:50:27,36] [info] Stream materializer shut down
[2022-01-09 07:50:27,37] [info] WDL HTTP import resolver closed
Workflow 5da239af-2b16-4a5e-913a-f2324734f2a5 transitioned to state Failed
1408.72user 545.12system 21:31:31elapsed 2%CPU (0avgtext+0avgdata 1979140maxresident)k
166870624inputs+305136outputs (1major+9823645minor)pagefaults 0swaps
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