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smith-chem-wisc / Spritz

Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data
https://smith-chem-wisc.github.io/Spritz/
MIT License
7 stars 11 forks source link

Error running workflow #181

Closed finnbenned closed 3 years ago

finnbenned commented 3 years ago

Hi,

Our team is using MSMS to study heart diseases and are getting access to RNA-Seq data. Your software looks to potentially be very useful.I have installed Docker Desktop and been trying to run your suggested 'Test it out' but so far w/ success as the program terminates with errors, lately after completing 9 of 26 steps (35%)

I have mounted my drives and My Docker Desktop resource settings are as follows:

docker setting

The log file contains:

workflow_2020-08-11-12-19-19.txt

Would be great if you could help out-.

Best,

Finn

trishorts commented 3 years ago

thanks for reporting the error. There is a couple things you can try. You can rename to the log file and start the run again. It will go faster, having already completed the initial steps. Some times the workflow has to be restarted a couple times to complete.

One thing that was worked better for me is to update my docker to allow WSL 2 (windows subsystem for linux). It can be a little hard to do the update. But, I think that it will be worth it. Let us know how it goes. We can provide additional support.

https://docs.microsoft.com/en-us/windows/wsl/wsl2-index

image

finnbenned commented 3 years ago

Thnx for your answer. Sorry to be a bit slow here but what is meant/what steps are done to “You can rename to the log file”?

Best,

Finn

Finn Benned Hansen Ph.D Visiting Scientist

Dept. of Biomedical Sciences Faculty of Health and Medical Sciences The Lundby Lab (https://www.cardiacproteomics.com) University of Copenhagen Blegdamsvej 3B Deliveries to Nørre Allé 14 | Mærsk Tower | Room 07-09-11 2200 Copenhagen N Denmark Phone +45 42349464

From: trishorts notifications@github.com Sent: Tuesday, August 11, 2020 2:49 PM To: smith-chem-wisc/Spritz Spritz@noreply.github.com Cc: Finn Benned Hansen finn.hansen@sund.ku.dk; Author author@noreply.github.com Subject: Re: [smith-chem-wisc/Spritz] Error running workflow (#181)

thanks for reporting the error. There is a couple things you can try. You can rename to the log file and start the run again. It will go faster, having already completed the initial steps. Some times the workflow has to be restarted a couple times to complete.

One thing that was worked better for me is to update my docker to allow WSL 2 (windows subsystem for linux). It can be a little hard to do the update. But, I think that it will be worth it. Let us know how it goes. We can provide additional support.

https://docs.microsoft.com/en-us/windows/wsl/wsl2-indexhttps://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.microsoft.com%2Fen-us%2Fwindows%2Fwsl%2Fwsl2-index&data=02%7C01%7Cfinn.hansen%40sund.ku.dk%7C77a544f460534cb6240008d83df4e8d2%7Ca3927f91cda14696af898c9f1ceffa91%7C0%7C0%7C637327469370905721&sdata=tSsy37c8WYjWoi1TiA9tsgCRXhDf0MVvmKX%2FN099ymQ%3D&reserved=0

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trishorts commented 3 years ago

I apologize. I type too fast and leave many errors in my wake.

I meant that you can rename to existing log file to something else to preserve the contents. Then restart. A new log file will be generated.

If you just restart, the new log file will overwrite the original and you won't be able to see what was there in the previous attempt. This can help with debugging.

Does that help?

finnbenned commented 3 years ago

Yes, thnx, got it. Will try to upgrade to WSL2 – but we’re strictly managed by our university IT dept.

Currently trying to run two fastq files but also here get the following error several times (job keeps on running though) :

[Tue Aug 11 13:19:14 2020] rule download_snpeff: output: SnpEff/snpEff.config, SnpEff/snpEff.jar log: data/SnpEffInstall.log jobid: 5

[Tue Aug 11 13:20:56 2020] Error in rule download_snpeff: jobid: 5 output: SnpEff/snpEff.config, SnpEff/snpEff.jar log: data/SnpEffInstall.log

RuleException: CalledProcessError in line 11 of /app/rules/variants.smk: Command ' set -euo pipefail; (rm -rf SnpEff git clone --depth=1 https://github.com/smith-chem-wisc/SnpEff cd SnpEff mvn install:install-file -Dfile=lib/antlr-4.5.1-complete.jar -DgroupId=org.antlr -DartifactId=antlr -Dversion=4.5.1 -Dpackaging=jar mvn install:install-file -Dfile=lib/biojava3-core-3.0.7.jar -DgroupId=org.biojava -DartifactId=biojava3-core -Dversion=3.0.7 -Dpackaging=jar mvn install:install-file -Dfile=lib/biojava3-structure-3.0.7.jar -DgroupId=org.biojava -DartifactId=biojava3-structure -Dversion=3.0.7 -Dpackaging=jar export VERSION=4.3 export VERSIONUND=`echo $VERSION | tr '.' ''` mvn clean compile assembly:assembly mvn install:install-file -Dfile=target/SnpEff-$VERSION.jar -DgroupId=org.snpeff -DartifactId=SnpEff -Dversion=$VERSION -Dpackaging=jar -DgeneratePom=true --quiet cp target/SnpEff-$VERSION-jar-with-dependencies.jar snpEff.jar cd ..) &> data/SnpEffInstall.log ' returned non-zero exit status 1. File "/app/rules/variants.smk", line 11, in __rule_download_snpeff File "/usr/local/envs/spritz/lib/python3.6/concurrent/futures/thread.py", line 56, in run Removing output files of failed job download_snpeff since they might be corrupted: SnpEff/snpEff.config

Any ideas?

Best,

Finn From: trishorts notifications@github.com Sent: Tuesday, August 11, 2020 3:36 PM To: smith-chem-wisc/Spritz Spritz@noreply.github.com Cc: Finn Benned Hansen finn.hansen@sund.ku.dk; Author author@noreply.github.com Subject: Re: [smith-chem-wisc/Spritz] Error running workflow (#181)

I apologize. I type too fast and leave many errors in my wake.

I meant that you can rename to existing log file to something else to preserve the contents. Then restart. A new log file will be generated.

If you just restart, the new log file will overwrite the original and you won't be able to see what was there in the previous attempt. This can help with debugging.

Does that help?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsmith-chem-wisc%2FSpritz%2Fissues%2F181%23issuecomment-671950599&data=02%7C01%7Cfinn.hansen%40sund.ku.dk%7Cd8f8df069495445e95db08d83dfb6e9a%7Ca3927f91cda14696af898c9f1ceffa91%7C0%7C0%7C637327497388700479&sdata=cVgvPybiCgYUzBG%2BhNDRKZrf%2FZkFvw8dLkV7XkpfS%2Fc%3D&reserved=0, or unsubscribehttps://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAQSLJJZGNMNOLFXXZK4B7CDSAFCKRANCNFSM4P273OSQ&data=02%7C01%7Cfinn.hansen%40sund.ku.dk%7Cd8f8df069495445e95db08d83dfb6e9a%7Ca3927f91cda14696af898c9f1ceffa91%7C0%7C0%7C637327497388700479&sdata=Xy9eAZfLkexWCsnhtMRTlnEtoEedPuCvOc2geqDouCM%3D&reserved=0.

acesnik commented 3 years ago

Hi there,

I believe this error is fixed in the upcoming release. Please stay tuned, and I'll try to have that out today or tomorrow.

If you could provide the data/SnpEffInstall.log file and the output of docker info from the CMD or Powershell terminals, that might be helpful.

My best guess for why this is happening is that the maven libraries needed to build SnpEff aren't installing properly, so the upcoming release avoids that entirely.

Best regards,

Anthony

finnbenned commented 3 years ago

Hi Anthony,

Great, looking forward to the new release.

Attach the SnpEffInstall log file. Below is the output from docker info w/o any containers running – hope ok:

PS C:\Users\pgl367> docker info Client: Debug Mode: false

Server: Containers: 0 Running: 0 Paused: 0 Stopped: 0 Images: 2 Server Version: 19.03.12 Storage Driver: overlay2 Backing Filesystem: extfs Supports d_type: true Native Overlay Diff: true Logging Driver: json-file Cgroup Driver: cgroupfs Plugins: Volume: local Network: bridge host ipvlan macvlan null overlay Log: awslogs fluentd gcplogs gelf journald json-file local logentries splunk syslog Swarm: inactive Runtimes: runc Default Runtime: runc Init Binary: docker-init containerd version: 7ad184331fa3e55e52b890ea95e65ba581ae3429 runc version: dc9208a3303feef5b3839f4323d9beb36df0a9dd init version: fec3683 Security Options: seccomp Profile: default Kernel Version: 4.19.76-linuxkit Operating System: Docker Desktop OSType: linux Architecture: x86_64 CPUs: 7 Total Memory: 49.53GiB Name: docker-desktop ID: KDSO:HOIQ:OAC6:2V6E:U567:4PC7:CJWR:PQTZ:5RI5:OTT5:EVKM:ZR6M Docker Root Dir: /var/lib/docker Debug Mode: true File Descriptors: 39 Goroutines: 51 System Time: 2020-08-12T11:19:54.628520958Z EventsListeners: 4 Registry: https://index.docker.io/v1/ Labels: Experimental: false Insecure Registries: 127.0.0.0/8 Live Restore Enabled: false Product License: Community Engine

My Windows version (Ver 1909, Build 18363.959) is btw too old to install WSL 2 – and Windows upgrades are tightly managed by our IP dept, so regrettably ptobably not an avenue to pursue.

Thanks again for your support,

Finn

From: Anthony notifications@github.com Sent: Tuesday, August 11, 2020 5:50 PM To: smith-chem-wisc/Spritz Spritz@noreply.github.com Cc: Finn Benned Hansen finn.hansen@sund.ku.dk; Author author@noreply.github.com Subject: Re: [smith-chem-wisc/Spritz] Error running workflow (#181)

Hi there,

I believe this error is fixed in the upcoming release. Please stay tuned, and I'll try to have that out today or tomorrow.

If you could provide the data/SnpEffInstall.log file and the output of docker info from the CMD or Powershell terminals, that might be helpful.

My best guess for why this is happening is that the maven libraries needed to build SnpEff aren't installing properly, so the upcoming release avoids that entirely.

Best regards,

Anthony

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acesnik commented 3 years ago

Hi Finn,

The docker info output all looks okay, and it should work without WSL2 given those settings.

I've committed the simplified installation of our customized SnpEff fork here https://github.com/smith-chem-wisc/Spritz/pull/183. You should be able to use the current version (0.1.3) again, and it will automatically download the updated docker image with these changes.

Best regards,

Anthony

finnbenned commented 3 years ago

Hi Anthony,

Unfortunately I still get errors icw downloading SnpEff_4.3_SmithChemWisc_v2.zip (Docker log):

log: data/TransferUniProtModifications.build.log jobid: 6 [Thu Aug 13 10:47:53 2020] rule download_snpeff: output: SnpEff/snpEff.config, SnpEff/snpEff.jar, SnpEff_4.3_SmithChemWisc_v2.zip log: data/SnpEffInstall.log jobid: 8 [Thu Aug 13 10:47:53 2020] rule tmpdir: output: tmp, temporary jobid: 3 [Thu Aug 13 10:47:53 2020] Finished job 3. 1 of 17 steps (6%) done [Thu Aug 13 10:48:04 2020] Finished job 6. 2 of 17 steps (12%) done [Thu Aug 13 10:49:45 2020] Error in rule download_snpeff: jobid: 8 output: SnpEff/snpEff.config, SnpEff/snpEff.jar, SnpEff_4.3_SmithChemWisc_v2.zip log: data/SnpEffInstall.log RuleException: CalledProcessError in line 12 of /app/rules/variants.smk: Command ' set -euo pipefail; (wget https://github.com/smith-chem-wisc/SnpEff/releases/download/4.3_SCW1/SnpEff_4.3_SmithChemWisc_v2.zip && unzip SnpEff_4.3_SmithChemWisc_v2.zip -d SnpEff) &> data/SnpEffInstall.log ' returned non-zero exit status 127. File "/app/rules/variants.smk", line 12, in rule_download_snpeff File "/usr/local/envs/spritz/lib/python3.6/concurrent/futures/thread.py", line 56, in run Removing output files of failed job download_snpeff since they might be corrupted: SnpEff_4.3_SmithChemWisc_v2.zip Trying to restart job 8. [Thu Aug 13 10:49:45 2020] rule download_snpeff: output: SnpEff/snpEff.config, SnpEff/snpEff.jar, SnpEff_4.3_SmithChemWisc_v2.zip log: data/SnpEffInstall.log jobid: 8 Analysis complete for test.trim_1.fastq.gz Analysis complete for test.trim_2.fastq.gz Analysis complete for test_2.fastq Analysis complete for test_1.fastq [Thu Aug 13 10:51:32 2020] Finished job 24. 3 of 17 steps (18%) done [Thu Aug 13 10:51:32 2020] rule hisat2_align_bam: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.1.ht2, analysis/trimmed/test.trim_1_fastqc.html, analysis/trimmed/test.trim_1.fastq.gz, analysis/trimmed/test.trim_2.fastq.gz, data/ensembl/Homo_sapiens.GRCh38.82.splicesites.txt output: analysis/test.sorted.bam log: analysis/test.hisat2.log jobid: 21 wildcards: dir=analysis, fq=test threads: 12 [Thu Aug 13 10:51:41 2020] Error in rule download_snpeff: jobid: 8 output: SnpEff/snpEff.config, SnpEff/snpEff.jar, SnpEff_4.3_SmithChemWisc_v2.zip log: data/SnpEffInstall.log RuleException: CalledProcessError in line 12 of /app/rules/variants.smk: Command ' set -euo pipefail; (wget https://github.com/smith-chem-wisc/SnpEff/releases/download/4.3_SCW1/SnpEff_4.3_SmithChemWisc_v2.zip && unzip SnpEff_4.3_SmithChemWisc_v2.zip -d SnpEff) &> data/SnpEffInstall.log ' returned non-zero exit status 127. File "/app/rules/variants.smk", line 12, in rule_download_snpeff File "/usr/local/envs/spritz/lib/python3.6/concurrent/futures/thread.py", line 56, in run Removing output files of failed job download_snpeff since they might be corrupted: SnpEff_4.3_SmithChemWisc_v2.zip Trying to restart job 8. [Thu Aug 13 10:51:41 2020] rule download_snpeff: output: SnpEff/snpEff.config, SnpEff/snpEff.jar, SnpEff_4.3_SmithChemWisc_v2.zip log: data/SnpEffInstall.log jobid: 8 [Thu Aug 13 10:53:21 2020] Error in rule download_snpeff: jobid: 8 output: SnpEff/snpEff.config, SnpEff/snpEff.jar, SnpEff_4.3_SmithChemWisc_v2.zip log: data/SnpEffInstall.log RuleException: CalledProcessError in line 12 of /app/rules/variants.smk: Command ' set -euo pipefail; (wget https://github.com/smith-chem-wisc/SnpEff/releases/download/4.3_SCW1/SnpEff_4.3_SmithChemWisc_v2.zip && unzip SnpEff_4.3_SmithChemWisc_v2.zip -d SnpEff) &> data/SnpEffInstall.log ' returned non-zero exit status 127. File "/app/rules/variants.smk", line 12, in __rule_download_snpeff File "/usr/local/envs/spritz/lib/python3.6/concurrent/futures/thread.py", line 56, in run Removing output files of failed job download_snpeff since they might be corrupted: SnpEff_4.3_SmithChemWisc_v2.zip [Thu Aug 13 11:08:44 2020] Finished job 21. 4 of 17 steps (24%) done Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /app/.snakemake/log/2020-08-13T104752.609569.snakemake.log

Best,

Finn From: Anthony notifications@github.com Sent: Wednesday, August 12, 2020 11:09 PM To: smith-chem-wisc/Spritz Spritz@noreply.github.com Cc: Finn Benned Hansen finn.hansen@sund.ku.dk; Author author@noreply.github.com Subject: Re: [smith-chem-wisc/Spritz] Error running workflow (#181)

Hi Finn,

The docker info output all looks okay, and it should work without WSL2 given those settings.

I've committed the simplified installation of our customized SnpEff fork here #183https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsmith-chem-wisc%2FSpritz%2Fpull%2F183&data=02%7C01%7Cfinn.hansen%40sund.ku.dk%7Cc1bd3eda69e64ce2df0808d83f03faab%7Ca3927f91cda14696af898c9f1ceffa91%7C0%7C0%7C637328633606469734&sdata=glbDIvVtAHDm2vrGnoABGL5msKPgQzktqDY59xZmUmI%3D&reserved=0. You should be able to use the current version (0.1.3) again, and it will automatically download the updated docker image with these changes.

Best regards,

Anthony

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acesnik commented 3 years ago

Hi Finn,

I forgot to add unzip into the environment, and my testing didn't catch that. I updated the environment here: https://github.com/smith-chem-wisc/Spritz/pull/184, and the docker image is built again, so feel free to try it again.

I was able to replicate the error:

2020-08-13 18:16:18 (1.18 MB/s) - 'SnpEff_4.3_SmithChemWisc_v2.zip' saved [179641071/179641071]
/bin/bash: unzip: command not found

And now, it completes that step:

2020-08-13 18:37:28 (1.11 MB/s) - 'SnpEff_4.3_SmithChemWisc_v2.zip' saved [179641071/179641071]

Archive:  SnpEff_4.3_SmithChemWisc_v2.zip
  inflating: SnpEff/.classpath       
 extracting: SnpEff/.gitattributes   
  inflating: SnpEff/.gitignore       
 . . .
finnbenned commented 3 years ago

Dear Anthony,

Now the software finishes like a charm – thanks much for your help.

Best,

Finn

From: Anthony notifications@github.com Sent: Thursday, August 13, 2020 8:40 PM To: smith-chem-wisc/Spritz Spritz@noreply.github.com Cc: Finn Benned Hansen finn.hansen@sund.ku.dk; Author author@noreply.github.com Subject: Re: [smith-chem-wisc/Spritz] Error running workflow (#181)

Hi Finn,

I forgot to add unzip into the environment, and my testing didn't catch that. I updated the environment here: #184https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsmith-chem-wisc%2FSpritz%2Fpull%2F184&data=02%7C01%7Cfinn.hansen%40sund.ku.dk%7C266880ef73244c76957d08d83fb858d5%7Ca3927f91cda14696af898c9f1ceffa91%7C0%7C0%7C637329408289871698&sdata=BphvMTeLhMjZylPP%2Byj8TcymC22%2BhBcnC1Flkaf4%2Bys%3D&reserved=0, and the docker image is built again, so feel free to try it again.

I was able to replicate the error:

2020-08-13 18:16:18 (1.18 MB/s) - 'SnpEff_4.3_SmithChemWisc_v2.zip' saved [179641071/179641071]

/bin/bash: unzip: command not found

And now, it completes that step:

2020-08-13 18:37:28 (1.11 MB/s) - 'SnpEff_4.3_SmithChemWisc_v2.zip' saved [179641071/179641071]

Archive: SnpEff_4.3_SmithChemWisc_v2.zip

inflating: SnpEff/.classpath

extracting: SnpEff/.gitattributes

inflating: SnpEff/.gitignore

. . .

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acesnik commented 3 years ago

That's great to hear! Glad to help.