Error in Alignment process : Call input and runtime attributes evaluation failed for align: Failed to evaluate input 'tmp_fastqs' (reason 1 of 1): transpose requires all collections have the same size
cafri1105 opened this issue · 2 comments
Describe the bug
Hi,
Thanks to you, I've been using the chip-seq-pipeline2 workflow since last year until earlier this year which was very helpful.
However, a few days ago, when I ran the new data on the same command as earlier this year, the following error appeared repeatedly.
Failed to evaluate input 'tmp_fastqs' (reason 1 of 1): transpose requires all collections have the same size
cromwell.engine.workflow.lifecycle.execution.job.preparation.JobPreparationActor$$anonfun$1$$anon$1: Call input and runtime attributes evaluation failed for align:
Failed to evaluate input 'tmp_fastqs' (reason 1 of 1): transpose requires all collections have the same size
cromwell.engine.workflow.lifecycle.execution.job.preparation.JobPreparationActor$$anonfun$1$$anon$1: Call input and runtime attributes evaluation failed for align_ctl:
Failed to evaluate input 'tmp_fastqs' (reason 1 of 1): transpose requires all collections have the same size
cromwell.engine.workflow.lifecycle.execution.job.preparation.JobPreparationActor$$anonfun$1$$anon$1: Call input and runtime attributes evaluation failed for align:
Failed to evaluate input 'tmp_fastqs' (reason 1 of 1): transpose requires all collections have the same size
The same alignment process error continues to occur despite updating the caper and chip-seq-pipeline2 to the latest version by referring to the previous issue.
#226 (comment)
I checked my fastq file , but there was no problem.
I wonder what caused this error.
can you please help?
Thanks!
OS/Platform
- OS/Platform: Ubuntu 21.04
- Pipeline version: v2.2.1
- Caper version: v2.2.3
Caper configuration file
caper run chip.wdl -i lmna_test.json --singularity --leader-job-name ChIP_TEST
Paste contents of ~/.caper/default.conf
.
backend=local
# Local directory for localized files and Cromwell's intermediate files.
# If not defined then Caper will make .caper_tmp/ on CWD or `local-out-dir`.
# /tmp is not recommended since Caper store localized data files here.
local-loc-dir=
cromwell=/home/hj/.caper/cromwell_jar/cromwell-82.jar
womtool=/home/hj/.caper/womtool_jar/womtool-82.jar
Input JSON file
{
"chip.title" : "LMNA ab TEST",
"chip.description" : "LMNA AB TEST chip data",
"chip.pipeline_type" : "histone",
"chip.aligner" : "bowtie2",
"chip.align_only" : false,
"chip.true_rep_only" : false,
"chip.genome_tsv" : "/mnt/NAS2/home/hj/chip-seq-pipeline2/hg19.tsv",
"chip.paired_end" : true,
"chip.ctl_paired_end" : true,
"chip.always_use_pooled_ctl" : true,
"chip.peak_caller" : "macs2",
"chip.pval_thresh" : 0.01,
"chip.fdr_thresh" : 0.01,
"chip.idr_thresh" : 0.05,
"chip.enable_jsd" : true,
"chip.enable_gc_bias" : true,
"chip.enable_count_signal_track" : true,
"chip.fastqs_rep1_R1" : ["/mnt/NAS2/home/hj/LMNA_ChIP_TEST/CM_LAab_1.fastq.gz"],
"chip.fastqs_rep1_R2" : ["/mnt/NAS2/home/hj/LMNA_ChIP_TEST/CM_LAab_2.fastq.gz"],
"chip.ctl_fastqs_rep1_R1" : ["/mnt/NAS2/home/hj/LMNA_ChIP_TEST/CM_input_1.fastq.gz"],
"chip.ctl_fastqs_rep1_R2" : ["/mnt/NAS2/home/hj/LMNA_ChIP_TEST/CM_input_2.fastq.gz"]
}
Troubleshooting result
2022-12-26 18:37:28,554 IoFO o- Running with database db.url = jdbc:hsqldb:mem:2332d49b-cffe-4946-9356-ad5653ee3016;shutdown=false;hsqldb.tx=mvcc
ut" 640L, 65209B 640,64 Bot
2022-12-26 20:32:23,077 cromwell-system-akka.dispatchers.backend-dispatcher-1526 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(faf8a76e)chip.align_R1:1:1]: Status change from WaitingForReturnCode to Done
2022-12-26 20:32:51,042 cromwell-system-akka.dispatchers.backend-dispatcher-1526 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(faf8a76e)chip.align_R1:0:1]: Status change from WaitingForReturnCode to Done
2022-12-26 20:32:55,845 cromwell-system-akka.dispatchers.engine-dispatcher-31 INFO - WorkflowManagerActor: Workflow faf8a76e-54b4-45ec-87a5-972b2408e03c failed (during ExecutingWorkflowState): cromwell.engine.workflow.lifecycle.execution.job.preparation.JobPreparationActor$$anonfun$1$$anon$1: Call input and runtime attributes evaluation failed for align_ctl:
Failed to evaluate input 'tmp_fastqs' (reason 1 of 1): transpose requires all collections have the same size
cromwell.engine.workflow.lifecycle.execution.job.preparation.JobPreparationActor$$anonfun$1$$anon$1: Call input and runtime attributes evaluation failed for align:
Failed to evaluate input 'tmp_fastqs' (reason 1 of 1): transpose requires all collections have the same size
cromwell.engine.workflow.lifecycle.execution.job.preparation.JobPreparationActor$$anonfun$1$$anon$1: Call input and runtime attributes evaluation failed for align_ctl:
Failed to evaluate input 'tmp_fastqs' (reason 1 of 1): transpose requires all collections have the same size
cromwell.engine.workflow.lifecycle.execution.job.preparation.JobPreparationActor$$anonfun$1$$anon$1: Call input and runtime attributes evaluation failed for align:
Failed to evaluate input 'tmp_fastqs' (reason 1 of 1): transpose requires all collections have the same size
2022-12-26 20:34:13,871 cromwell-system-akka.dispatchers.engine-dispatcher-20 INFO - WorkflowManagerActor: Workflow actor for faf8a76e-54b4-45ec-87a5-972b2408e03c completed with status 'Failed'. The workflow will be removed from the workflow store.
2022-12-26 20:34:14,538 cromwell-system-akka.dispatchers.engine-dispatcher-9 INFO - SingleWorkflowRunnerActor workflow finished with status 'Failed'.
2022-12-26 20:34:19,195 cromwell-system-akka.dispatchers.engine-dispatcher-9 INFO - SingleWorkflowRunnerActor writing metadata to /mnt/NAS2/home/hj/chip-seq-pipeline2/.caper_tmp/chip/20221226_183721_969493/metadata.json
2022-12-26 20:34:19,417 INFO - Workflow polling stopped
2022-12-26 20:34:19,422 INFO - 0 workflows released by cromid-497e9e3
2022-12-26 20:34:19,424 INFO - Shutting down WorkflowStoreActor - Timeout = 5 seconds
2022-12-26 20:34:19,427 INFO - Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds
2022-12-26 20:34:19,429 INFO - Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds
2022-12-26 20:34:19,431 INFO - WorkflowLogCopyRouter stopped
2022-12-26 20:34:19,431 INFO - JobExecutionTokenDispenser stopped
2022-12-26 20:34:19,432 cromwell-system-akka.dispatchers.engine-dispatcher-9 INFO - Aborting all running workflows.
2022-12-26 20:34:19,434 INFO - WorkflowStoreActor stopped
2022-12-26 20:34:19,434 INFO - Shutting down WorkflowManagerActor - Timeout = 3600 seconds
2022-12-26 20:34:19,434 cromwell-system-akka.dispatchers.engine-dispatcher-21 INFO - WorkflowManagerActor: All workflows finished
2022-12-26 20:34:19,434 INFO - WorkflowManagerActor stopped
2022-12-26 20:34:19,561 INFO - Connection pools shut down
2022-12-26 20:34:19,562 INFO - Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds
2022-12-26 20:34:19,562 INFO - Shutting down JobStoreActor - Timeout = 1800 seconds
2022-12-26 20:34:19,562 INFO - Shutting down CallCacheWriteActor - Timeout = 1800 seconds
2022-12-26 20:34:19,562 INFO - Shutting down ServiceRegistryActor - Timeout = 1800 seconds
2022-12-26 20:34:19,562 INFO - Shutting down DockerHashActor - Timeout = 1800 seconds
2022-12-26 20:34:19,562 INFO - Shutting down IoProxy - Timeout = 1800 seconds
2022-12-26 20:34:19,564 INFO - CallCacheWriteActor Shutting down: 0 queued messages to process
2022-12-26 20:34:19,568 INFO - SubWorkflowStoreActor stopped
2022-12-26 20:34:19,568 INFO - JobStoreActor stopped
2022-12-26 20:34:19,568 INFO - CallCacheWriteActor stopped
2022-12-26 20:34:19,568 INFO - IoProxy stopped
2022-12-26 20:34:19,574 INFO - DockerHashActor stopped
2022-12-26 20:34:19,575 INFO - Shutting down connection pool: curAllocated=1 idleQueues.size=1 waitQueue.size=0 maxWaitQueueLimit=256 closed=false
2022-12-26 20:34:19,576 INFO - Shutting down connection pool: curAllocated=0 idleQueues.size=0 waitQueue.size=0 maxWaitQueueLimit=256 closed=false
2022-12-26 20:34:19,576 INFO - Shutting down connection pool: curAllocated=0 idleQueues.size=0 waitQueue.size=0 maxWaitQueueLimit=256 closed=false
2022-12-26 20:34:19,577 INFO - WriteMetadataActor Shutting down: 0 queued messages to process
2022-12-26 20:34:19,577 INFO - KvWriteActor Shutting down: 0 queued messages to process
2022-12-26 20:34:19,582 INFO - ServiceRegistryActor stopped
2022-12-26 20:34:19,585 INFO - Database closed
2022-12-26 20:34:19,585 INFO - Stream materializer shut down
2022-12-26 20:34:19,587 INFO - WDL HTTP import resolver closed
I found a problem with my JSON file. I solved it. Sorry
Can you please share what problem you had with your JSON file? I had the same error and I can't find the problem with my JSON file.