Comments (18)
leepc12
commented on July 28, 2024
This will be fixed in the next release (v1.1.3). Until then, please try with singularity or docker instead.
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sjquon
commented on July 28, 2024
I see. Thank you.
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dcdxy
commented on July 28, 2024
I updated to v1.1.3 and obtain the same error (again on the test data). I'm also running the pipeline with Conda but through SGE.
debug_61_2.tar.gz
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leepc12
commented on July 28, 2024
It's a different error.
Error occurred during initialization of VM
Could not reserve enough space for 4194304KB object heap
How much memory do you have on your virtual machine?
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dcdxy
commented on July 28, 2024
Ok. Should I create a new issue?
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leepc12
commented on July 28, 2024
@dcdxy : Please look at the error message above. Give enough memory (>8GB for test samples, >16GB for real samples) to your VM.
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dcdxy
commented on July 28, 2024
Sorry, I thought you were referring to sjquon (VM) as I'm using a compute cluster. Do you mean that I should set resources per task in the input JSON (i.e. "atac.filter_mem_mb")? Or is there a global parameter that I should set in sge.json?
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leepc12
commented on July 28, 2024
Resource settings are not in sge.json. Yes, it's "atac.filter_mem_mb" in your input JSON file. But it's 16GB by default. I think your cluster has some limit on max. memory of Java VM?
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dcdxy
commented on July 28, 2024
I increased "atac.filter_mem_mb" from 4000 to 20000 which eliminated the VM initialization error. I received another memory error for a different step, so I increased all memory settings in the test sample's input JSON file as a precaution:
"atac.bowtie2_mem_mb" : 20000,
"atac.filter_mem_mb" : 20000,
"atac.macs2_mem_mb" : 20000,
"atac.ataqc.mem_mb" : 20000,
I now receive a new error in the final step:
Picked up _JAVA_OPTIONS: -Xms256M -Xmx16000M -XX:ParallelGCThreads=1
Picked up _JAVA_OPTIONS: -Xms256M -Xmx16000M -XX:ParallelGCThreads=1
IOError: [Errno 2] No such file or directory:
'ENCFF641SFZ.subsampled.400.trim.merged.picardcomplexity.qc'
ln: failed to access ‘*_qc.html’: No such file or directory
ln: failed to access ‘*_qc.txt’: No such file or directory
which seems to arise from earlier errors in the reproducibility steps:
ln: failed to access ‘conservative_peak.*.hammock_gz*’: No such file or directory
Please find log files here:
debug_61_3.tar.gz
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leepc12
commented on July 28, 2024
That hammock_gz error has already been fixed in v1.1.4 (on current master branch). Which version are you using? Can you update the pipeline and try again?
BTW is there any reason for you to use VM instead of simply running pipelines on a OSX terminal?
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dcdxy
commented on July 28, 2024
I updated the pipeline to v1.1.4 which eliminates the hammock_gz error, but I still get the first error:
IOError: [Errno 2] No such file or directory: 'ENCFF341MYG.subsampled.400.trim.merged.picardcomplexity.qc'
From stdout in the same directory (call-ataqc), it appears that it's another VM initialization error:
Error occurred during initialization of VM
Could not reserve enough space for 16384000KB object heap
but I have "atac.ataqc.mem_mb" : 16000 which is the default in the example input JSON. I just noticed that there is a different parameter "atac.ataqc_mem_java_mb" that I haven't set... the default in the example JSON is also 16000 but it looks like the VM would require more space? Should I increase both of these parameters?
Please find log files here:
debug_61_4.tar.gz
Also I'm running the pipelines on our SGE cluster because this is where the data is stored and where I do the rest of my analyses, but I could potentially switch to using my local machine if necessary.
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leepc12
commented on July 28, 2024
Please reduce both atac.ataqc_mem_mb and atac.ataqc_mem_java_mb to 6000 and 5000 and then try again.
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dcdxy
commented on July 28, 2024
I made those changes and now receive the following:
#
# A fatal error has been detected by the Java Runtime Environment:
#
# Internal Error (g1PageBasedVirtualSpace.cpp:43), pid=15064, tid=15065
# guarantee(rs.is_reserved()) failed: Given reserved space must have been reserved already.
#
# JRE version: (11.0.1+13) (build )
# Java VM: OpenJDK 64-Bit Server VM (11.0.1+13-LTS, mixed mode, aot, sharing, tiered, compressed oops, g1 gc, linux-amd64)
# Core dump will be written. Default location: Core dumps may be processed with "/usr/libexec/abrt-hook-ccpp %s %c %p %u %g %t e"
Please see attached: debug_61_5.tar.gz
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leepc12
commented on July 28, 2024
Can you play with those parameters a bit more, like changing them to 7000 or 9000 keeping ataqc_mem_java_mb lower than ataqc_mem_mb?
Also please try with other kind of Java (e.g. Oracle JRE instead of OpenJDK).
If none of these works, disable ATAQC with "atac.disable_ataqc" : true in your input JSON.
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dcdxy
commented on July 28, 2024
I tried various values ranging from 4000-19000 but each time received the same VM initialization error. It doesn't seem like I can install Oracle JRE because that would require system administrator privileges. When I disabled the ataqc step as you suggested, I obtained a different error:
[2019-01-09 11:33:47,65] [error] WorkflowManagerActor Workflow 06b307a1-8549-43bd-87a2-c7eb08c5f48b failed (during ExecutingWorkflowState): Job atac.qc_report:NA:1 exited with return code 2 which has not been de
clared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
Check the content of stderr for potential additional information: /mnt/work1/users/home2/ddenisko/atac-seq-pipeline/cromwell-executions/atac/06b307a1-8549-43bd-87a2-c7eb08c5f48b/call-qc_report/execution/stderr.
usage: ENCODE DCC generate HTML report and QC JSON. [-h] [--name NAME]
[--desc DESC]
[--multimapping MULTIMAPPING]
[--paired-end]
--pipeline-type
{atac,dnase,tf,histone}
--peak-caller PEAK_CALLER
[--macs2-cap-num-peak MACS2_CAP_NUM_PEAK]
[--spp-cap-num-peak SPP_CAP_NUM_PEAK]
--idr-thresh IDR_THRESH
[--flagstat-qcs [FLAGSTAT_QCS [FLAGSTAT_QCS ...]]]
[--nodup-flagstat-qcs [NODUP_FLAGSTAT_QCS [NODUP_FLAGSTAT_QCS ...]]]
[--dup-qcs [DUP_QCS [DUP_QCS ...]]]
[--pbc-qcs [PBC_QCS [PBC_QCS ...]]]
[--ctl-flagstat-qcs [CTL_FLAGSTAT_QCS [CTL_FLAGSTAT_QCS ...]]]
[--ctl-nodup-flagstat-qcs [CTL_NODUP_FLAGSTAT_QCS [CTL_NODUP_FLAGSTAT_QCS ...]]]
[--ctl-dup-qcs [CTL_DUP_QCS [CTL_DUP_QCS ...]]]
[--ctl-pbc-qcs [CTL_PBC_QCS [CTL_PBC_QCS ...]]]
[--xcor-plots [XCOR_PLOTS [XCOR_PLOTS ...]]]
[--xcor-scores [XCOR_SCORES [XCOR_SCORES ...]]]
[--jsd-plot [JSD_PLOT [JSD_PLOT ...]]]
[--jsd-qcs [JSD_QCS [JSD_QCS ...]]]
[--idr-plots [IDR_PLOTS [IDR_PLOTS ...]]]
[--idr-plots-pr [IDR_PLOTS_PR [IDR_PLOTS_PR ...]]]
[--idr-plot-ppr [IDR_PLOT_PPR [IDR_PLOT_PPR ...]]]
[--frip-macs2-qcs [FRIP_MACS2_QCS [FRIP_MACS2_QCS ...]]]
[--frip-macs2-qcs-pr1 [FRIP_MACS2_QCS_PR1 [FRIP_MACS2_QCS_PR1 ...]]]
[--frip-macs2-qcs-pr2 [FRIP_MACS2_QCS_PR2 [FRIP_MACS2_QCS_PR2 ...]]]
[--frip-macs2-qc-pooled [FRIP_MACS2_QC_POOLED [FRIP_MACS2_QC_POOLED ...]]]
[--frip-macs2-qc-ppr1 [FRIP_MACS2_QC_PPR1 [FRIP_MACS2_QC_PPR1 ...]]]
[--frip-macs2-qc-ppr2 [FRIP_MACS2_QC_PPR2 [FRIP_MACS2_QC_PPR2 ...]]]
[--frip-spp-qcs [FRIP_SPP_QCS [FRIP_SPP_QCS ...]]]
[--frip-spp-qcs-pr1 [FRIP_SPP_QCS_PR1 [FRIP_SPP_QCS_PR1 ...]]]
[--frip-spp-qcs-pr2 [FRIP_SPP_QCS_PR2 [FRIP_SPP_QCS_PR2 ...]]]
[--frip-spp-qc-pooled [FRIP_SPP_QC_POOLED [FRIP_SPP_QC_POOLED ...]]]
[--frip-spp-qc-ppr1 [FRIP_SPP_QC_PPR1 [FRIP_SPP_QC_PPR1 ...]]]
[--frip-spp-qc-ppr2 [FRIP_SPP_QC_PPR2 [FRIP_SPP_QC_PPR2 ...]]]
[--frip-idr-qcs [FRIP_IDR_QCS [FRIP_IDR_QCS ...]]]
[--frip-idr-qcs-pr [FRIP_IDR_QCS_PR [FRIP_IDR_QCS_PR ...]]]
[--frip-idr-qc-ppr [FRIP_IDR_QC_PPR [FRIP_IDR_QC_PPR ...]]]
[--frip-overlap-qcs [FRIP_OVERLAP_QCS [FRIP_OVERLAP_QCS ...]]]
[--frip-overlap-qcs-pr [FRIP_OVERLAP_QCS_PR [FRIP_OVERLAP_QCS_PR ...]]]
[--frip-overlap-qc-ppr [FRIP_OVERLAP_QC_PPR [FRIP_OVERLAP_QC_PPR ...]]]
[--idr-reproducibility-qc [IDR_REPRODUCIBILITY_QC [IDR_REPRODUCIBILITY_QC ...]]]
[--overlap-reproducibility-qc [OVERLAP_REPRODUCIBILITY_QC [OVERLAP_REPRODUCIBILITY_QC ...]]]
[--ataqc-txts [ATAQC_TXTS [ATAQC_TXTS ...]]]
[--ataqc-htmls [ATAQC_HTMLS [ATAQC_HTMLS ...]]]
[--out-qc-html OUT_QC_HTML]
[--out-qc-json OUT_QC_JSON]
[--log-level {NOTSET,DEBUG,INFO,WARNING,CRITICAL,ERROR,CRITICAL}]
ENCODE DCC generate HTML report and QC JSON.: error: unrecognized arguments: --pipeline-ver v1.1.5 --title ENCSR356KRQ (subsampled 1/400 reads) --genome hg38_local.tsv
ln: failed to access ‘*qc.html’: No such file or directory
ln: failed to access ‘*qc.json’: No such file or directory
I also tried installing the pipeline locally (CentOS 7 machine, Conda) and running it with the test data; however, it hangs at the atac.bowtie2 stage for a few hours before throwing a "dead letters encountered" message:
[2019-01-09 14:20:37,99] [info] Message [cromwell.docker.DockerHashActor$DockerHashSuccessResponse] from Actor[akka://cromwell-system/user/HealthMonitorDockerHashActor#-2092529480] to Actor[akka://cromwell-system/deadLetters] was not delivered. [1] dead letters encountered, no more dead letters will be logged. If this is not an expected behavior, then [Actor[akka://cromwell-system/deadLetters]] may have terminated unexpectedly, This logging can be turned off or adjusted with configuration settings 'akka.log-dead-letters' and 'akka.log-dead-letters-during-shutdown'
which I then eventually interrupt. I downloaded the latest version of Cromwell (36).
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leepc12
commented on July 28, 2024
- I think it's almost done. Pipeline failed at the final HTML reporting step because you didn't update the conda environment after updating the pipeline. Please run this on your pipeline git directory.
$ bash conda/update_conda_env.sh
-
The latest cromwell (36) has some known bugs/issues. Please use cromwell-34 until it's fixed in 37.
-
You can simply ignore that "dead letters encountered" warning.
-
BTW installing OracleJRE does not require super-user privileges.
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dcdxy
commented on July 28, 2024
Thank you--I ran the above command and successfully ran the test samples through the pipeline (keeping "atac.disable_ataqc" : true).
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leepc12
commented on July 28, 2024
That sounds good. I still wonder why you have such a strange software configuration (MacOS + VirtualBox + SGE) on your laptop.
Can you try running pipelines directly on MacOS terminal without VBox and SGE? I think VBox is somewhat related to your Java VM memory issue.
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