search

NBISweden / pipelines-nextflow

A set of workflows written in Nextflow for Genome Annotation.
GNU General Public License v3.0
43 stars 18 forks source link

issue with interproscan in functional pipeline #109

Closed EmilieSmeets22 closed 7 months ago

EmilieSmeets22 commented 7 months ago

Hi,

I ran the functional pipeline but it never completed.

Query:

[doutree@plop] GFF $ conda activate nextflow-env
(nextflow-env) [doutree@plop] GFF $ nextflow run NBISweden/pipelines-nextflow -profile conda -params-file functional_annotation_param.yml

Error:

ERROR ~ Error executing process > 'FUNCTIONAL_ANNOTATION:INTERPROSCAN (my_crop.gene_chr)'

Caused by:
  Process `FUNCTIONAL_ANNOTATION:INTERPROSCAN (my_crop.gene_chr)` terminated with an error exit status (231)

Command executed:

  if [ "false" == "true" ]; then
      gzip -c -d my_crop.gene_chr_proteins.12.fasta > my_crop.gene_chr_proteins.12.fasta
  fi

  interproscan.sh \
      -cpu 8 \
      -i my_crop.gene_chr_proteins.12.fasta \
      -f tsv \
      -dp \
      --iprlookup --goterms -pa -t p -dra \
      -appl TIGRFAM,FunFam,SFLD,PANTHER,Gene3D,Hamap,ProSiteProfiles,Coils,SMART,CDD,PRINTS,PIRSR,ProSitePatterns,AntiFam,Pfam,MobiDBLite \
      -o my_crop.gene_chr.tsv

  cat <<-END_VERSIONS > versions.yml
  "FUNCTIONAL_ANNOTATION:INTERPROSCAN":
  interproscan: $(echo $(interproscan.sh --version 2>&1) | head -n 1 | sed 's/^.*InterProScan version//' | sed 's/\s*InterProScan.*//')
  END_VERSIONS

Command exit status:
  231

Command output:

  2024-02-19 16:24:59,380 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 76 is being re-run following a failure.
  2024-02-19 16:25:04,470 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:216] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution.  All database activity rolled back.
  java.lang.IllegalStateException: IOException thrown when attempting to run binary
  InterPat uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:183) ~[interproscan-management-5.59-91.0.jar:?]
  rk dirat uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
        at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) ~[?:?]
  p: wheat jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
        at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
  - Checat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
        at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
        at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
        at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
        at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
        at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
        at java.lang.Thread.run(Thread.java:829) [?:?]
  Caused by: java.io.IOException: Cannot run program "ps_scan.pl": error=2, No such file or directory
        at java.lang.ProcessBuilder.start(ProcessBuilder.java:1128) ~[?:?]
        at java.lang.ProcessBuilder.start(ProcessBuilder.java:1071) ~[?:?]
        at uk.ac.ebi.interpro.scan.io.cli.CommandLineConversationImpl.runCommand(CommandLineConversationImpl.java:147) ~[interproscan-io-5.59-91.0.jar:?]
        at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:181) ~[interproscan-management-5.59-91.0.jar:?]
        ... 22 more
  Caused by: java.io.IOException: error=2, No such file or directory
        at java.lang.ProcessImpl.forkAndExec(Native Method) ~[?:?]
        at java.lang.ProcessImpl.<init>(ProcessImpl.java:340) ~[?:?]
        at java.lang.ProcessImpl.start(ProcessImpl.java:271) ~[?:?]
        at java.lang.ProcessBuilder.start(ProcessBuilder.java:1107) ~[?:?]
        at java.lang.ProcessBuilder.start(ProcessBuilder.java:1071) ~[?:?]
        at uk.ac.ebi.interpro.scan.io.cli.CommandLineConversationImpl.runCommand(CommandLineConversationImpl.java:147) ~[interproscan-io-5.59-91.0.jar:?]
        at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:181) ~[interproscan-management-5.59-91.0.jar:?]
        ... 22 more
  2024-02-19 16:25:04,472 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
  2024-02-19 16:25:04,472 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrositePatternRunBinary
  2024-02-19 16:25:04,550 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:25] FATAL - Analysis step 76 : Run ps_scan.pl and pfscan Binary for selected proteins for proteins 1 to 996 has failed irretrievably.  Available StackTraces follow.
  2024-02-19 16:25:04,551 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:42] FATAL - The JVM will now exit with a non-zero exit status.
  2024-02-19 16:25:04,551 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:363] ERROR - Exception thrown by StandaloneBlackBoxMaster: 
  java.lang.IllegalStateException: InterProScan exiting with non-zero status, see logs for further information.
        at uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError.failed(NonZeroExitOnUnrecoverableError.java:43) ~[interproscan-5.jar:?]
        at uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster.run(StandaloneBlackBoxMaster.java:169) [interproscan-5.jar:?]
        at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:413) [interproscan-5.jar:?]

Command error:
        at java.base/java.lang.ProcessImpl.<init>(ProcessImpl.java:340)
        at java.base/java.lang.ProcessImpl.start(ProcessImpl.java:271)
        at java.base/java.lang.ProcessBuilder.start(ProcessBuilder.java:1107)
        ... 25 more
  2024-02-19 16:25:04,472 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrositePatternRunBinary
  java.io.IOException: Cannot run program "ps_scan.pl": error=2, No such file or directory
        at java.base/java.lang.ProcessBuilder.start(ProcessBuilder.java:1128)
        at java.base/java.lang.ProcessBuilder.start(ProcessBuilder.java:1071)
        at uk.ac.ebi.interpro.scan.io.cli.CommandLineConversationImpl.runCommand(CommandLineConversationImpl.java:147)
        at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:181)
        at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
        at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
        at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367)
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
        at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
        at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073)
        at java.base/java.lang.Thread.run(Thread.java:829)
  Caused by: java.io.IOException: error=2, No such file or directory
        at java.base/java.lang.ProcessImpl.forkAndExec(Native Method)
        at java.base/java.lang.ProcessImpl.<init>(ProcessImpl.java:340)
        at java.base/java.lang.ProcessImpl.start(ProcessImpl.java:271)
        at java.base/java.lang.ProcessBuilder.start(ProcessBuilder.java:1107)
        ... 25 more
  2024-02-19 16:25:04,550 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:25] FATAL - Analysis step 76 : Run ps_scan.pl and pfscan Binary for selected proteins for proteins 1 to 996 has failed irretrievably.  Available StackTraces follow.
  2024-02-19 16:25:04,551 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:42] FATAL - The JVM will now exit with a non-zero exit status.
  2024-02-19 16:25:04,551 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:363] ERROR - Exception thrown by StandaloneBlackBoxMaster: 
  java.lang.IllegalStateException: InterProScan exiting with non-zero status, see logs for further information.
        at uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError.failed(NonZeroExitOnUnrecoverableError.java:43) ~[interproscan-5.jar:?]
        at uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster.run(StandaloneBlackBoxMaster.java:169) [interproscan-5.jar:?]
        at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:413) [interproscan-5.jar:?]
  java.lang.IllegalStateException: InterProScan exiting with non-zero status, see logs for further information.
        at uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError.failed(NonZeroExitOnUnrecoverableError.java:43)
        at uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster.run(StandaloneBlackBoxMaster.java:169)
        at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:413)
  InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details

Work dir:
  /home/workspace/doutree/GFF/work/26/2cf8c6cfcbfe305b3c487b65c86250

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '.nextflow.log' file for details

.nextflow.log contains the sme command output sa pasted above.

Thank you already

mahesh-panchal commented 7 months ago

The exit code is unusual, and indicates there's potentially something wrong with the conda build for the environment. Can you check your conda environment to see if the file ps_scan.pl is present?

EmilieSmeets22 commented 7 months ago

Thank you for your reply. I checked and indeed I cannot find the ps_scan.pl script:

[doutree@plop] ~ $ conda activate nextflow-env
(nextflow-env) [doutree@plop] ~ $ which nextflow
/data/workspace/doutree/.conda/envs/nextflow-env/bin/nextflow
(nextflow-env) [doutree@plop] ~ $ cd /data/workspace/doutree/.conda/envs/nextflow-env/
(nextflow-env) [doutree@plop] nextflow-env $ find . | grep scan
./man/man3/pcre2_substring_nametable_scan.3
./man/man1/jdeprscan.1
./bin/fc-scan
./bin/jdeprscan
./lib/jvm/man/man1/jdeprscan.1
./lib/jvm/bin/jdeprscan
./share/man/man3/recursive_session_key_scan.3
./share/man/man3/recursive_key_scan.3
./share/terminfo/c/colorscan
./share/terminfo/s/scanset
./share/doc/pcre2/html/pcre2_substring_nametable_scan.html

Then I tried to recreate the conda env based on the instructions:


(nextflow-env) [doutree@plop] nextflow-env $ conda deactivate
[doutree@plop] nextflow-env $ conda create -c conda-forge -c bioconda -n nextflow-env2 nextflow
Channels:
 - conda-forge
 - bioconda
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /data/workspace/doutree/.conda/envs/nextflow-env2

  added / updated specs:
    - nextflow

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
  alsa-lib           conda-forge/linux-64::alsa-lib-1.2.10-hd590300_0
  bzip2              conda-forge/linux-64::bzip2-1.0.8-hd590300_5
  c-ares             conda-forge/linux-64::c-ares-1.26.0-hd590300_0
  ca-certificates    conda-forge/linux-64::ca-certificates-2024.2.2-hbcca054_0
  cairo              conda-forge/linux-64::cairo-1.18.0-h3faef2a_0
  coreutils          conda-forge/linux-64::coreutils-9.4-hd590300_0
  curl               conda-forge/linux-64::curl-8.5.0-hca28451_0
  expat              conda-forge/linux-64::expat-2.5.0-hcb278e6_1
  font-ttf-dejavu-s~ conda-forge/noarch::font-ttf-dejavu-sans-mono-2.37-hab24e00_0
  font-ttf-inconsol~ conda-forge/noarch::font-ttf-inconsolata-3.000-h77eed37_0
  font-ttf-source-c~ conda-forge/noarch::font-ttf-source-code-pro-2.038-h77eed37_0
  font-ttf-ubuntu    conda-forge/noarch::font-ttf-ubuntu-0.83-h77eed37_1
  fontconfig         conda-forge/linux-64::fontconfig-2.14.2-h14ed4e7_0
  fonts-conda-ecosy~ conda-forge/noarch::fonts-conda-ecosystem-1-0
  fonts-conda-forge  conda-forge/noarch::fonts-conda-forge-1-0
  freetype           conda-forge/linux-64::freetype-2.12.1-h267a509_2
  gettext            conda-forge/linux-64::gettext-0.21.1-h27087fc_0
  giflib             conda-forge/linux-64::giflib-5.2.1-h0b41bf4_3
  graphite2          conda-forge/linux-64::graphite2-1.3.13-h58526e2_1001
  harfbuzz           conda-forge/linux-64::harfbuzz-8.3.0-h3d44ed6_0
  icu                conda-forge/linux-64::icu-73.2-h59595ed_0
  keyutils           conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0
  krb5               conda-forge/linux-64::krb5-1.21.2-h659d440_0
  lcms2              conda-forge/linux-64::lcms2-2.16-hb7c19ff_0
  lerc               conda-forge/linux-64::lerc-4.0.0-h27087fc_0
  libcups            conda-forge/linux-64::libcups-2.3.3-h4637d8d_4
  libcurl            conda-forge/linux-64::libcurl-8.5.0-hca28451_0
  libdeflate         conda-forge/linux-64::libdeflate-1.19-hd590300_0
  libedit            conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
  libev              conda-forge/linux-64::libev-4.33-hd590300_2
  libexpat           conda-forge/linux-64::libexpat-2.5.0-hcb278e6_1
  libffi             conda-forge/linux-64::libffi-3.4.2-h7f98852_5
  libgcc-ng          conda-forge/linux-64::libgcc-ng-13.2.0-h807b86a_5
  libglib            conda-forge/linux-64::libglib-2.78.4-h783c2da_0
  libgomp            conda-forge/linux-64::libgomp-13.2.0-h807b86a_5
  libiconv           conda-forge/linux-64::libiconv-1.17-hd590300_2
  libjpeg-turbo      conda-forge/linux-64::libjpeg-turbo-3.0.0-hd590300_1
  libnghttp2         conda-forge/linux-64::libnghttp2-1.58.0-h47da74e_1
  libpng             conda-forge/linux-64::libpng-1.6.42-h2797004_0
  libssh2            conda-forge/linux-64::libssh2-1.11.0-h0841786_0
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-13.2.0-h7e041cc_5
  libtiff            conda-forge/linux-64::libtiff-4.6.0-ha9c0a0a_2
  libuuid            conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
  libwebp-base       conda-forge/linux-64::libwebp-base-1.3.2-hd590300_0
  libxcb             conda-forge/linux-64::libxcb-1.15-h0b41bf4_0
  libzlib            conda-forge/linux-64::libzlib-1.2.13-hd590300_5
  ncurses            conda-forge/linux-64::ncurses-6.4-h59595ed_2
  nextflow           bioconda/noarch::nextflow-23.10.1-hdfd78af_0
  openjdk            conda-forge/linux-64::openjdk-21.0.0-haa376d0_0
  openssl            conda-forge/linux-64::openssl-3.2.1-hd590300_0
  pcre2              conda-forge/linux-64::pcre2-10.42-hcad00b1_0
  pixman             conda-forge/linux-64::pixman-0.43.2-h59595ed_0
  pthread-stubs      conda-forge/linux-64::pthread-stubs-0.4-h36c2ea0_1001
  xorg-fixesproto    conda-forge/linux-64::xorg-fixesproto-5.0-h7f98852_1002
  xorg-inputproto    conda-forge/linux-64::xorg-inputproto-2.3.2-h7f98852_1002
  xorg-kbproto       conda-forge/linux-64::xorg-kbproto-1.0.7-h7f98852_1002
  xorg-libice        conda-forge/linux-64::xorg-libice-1.1.1-hd590300_0
  xorg-libsm         conda-forge/linux-64::xorg-libsm-1.2.4-h7391055_0
  xorg-libx11        conda-forge/linux-64::xorg-libx11-1.8.7-h8ee46fc_0
  xorg-libxau        conda-forge/linux-64::xorg-libxau-1.0.11-hd590300_0
  xorg-libxdmcp      conda-forge/linux-64::xorg-libxdmcp-1.1.3-h7f98852_0
  xorg-libxext       conda-forge/linux-64::xorg-libxext-1.3.4-h0b41bf4_2
  xorg-libxfixes     conda-forge/linux-64::xorg-libxfixes-5.0.3-h7f98852_1004
  xorg-libxi         conda-forge/linux-64::xorg-libxi-1.7.10-h7f98852_0
  xorg-libxrender    conda-forge/linux-64::xorg-libxrender-0.9.11-hd590300_0
  xorg-libxt         conda-forge/linux-64::xorg-libxt-1.3.0-hd590300_1
  xorg-libxtst       conda-forge/linux-64::xorg-libxtst-1.2.3-h7f98852_1002
  xorg-recordproto   conda-forge/linux-64::xorg-recordproto-1.14.2-h7f98852_1002
  xorg-renderproto   conda-forge/linux-64::xorg-renderproto-0.11.1-h7f98852_1002
  xorg-xextproto     conda-forge/linux-64::xorg-xextproto-7.3.0-h0b41bf4_1003
  xorg-xproto        conda-forge/linux-64::xorg-xproto-7.0.31-h7f98852_1007
  xz                 conda-forge/linux-64::xz-5.2.6-h166bdaf_0
  zlib               conda-forge/linux-64::zlib-1.2.13-hd590300_5
  zstd               conda-forge/linux-64::zstd-1.5.5-hfc55251_0

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate nextflow-env2
#
# To deactivate an active environment, use
#
#     $ conda deactivate

[doutree@plop] nextflow-env $  conda activate nextflow-env2

But I still cannot file the ps_scan.pl script:

(nextflow-env2) [doutree@plop] nextflow-env $ which nextflow
/data/workspace/doutree/.conda/envs/nextflow-env2/bin/nextflow
(nextflow-env2) [doutree@plop] nextflow-env $ cd /data/workspace/doutree/.conda/envs/nextflow-env2/
(nextflow-env2) [doutree@plop] nextflow-env2 $ find . | grep scan
./man/man3/pcre2_substring_nametable_scan.3
./man/man1/jdeprscan.1
./bin/fc-scan
./bin/jdeprscan
./lib/jvm/man/man1/jdeprscan.1
./lib/jvm/bin/jdeprscan
./share/man/man3/recursive_session_key_scan.3
./share/man/man3/recursive_key_scan.3
./share/terminfo/c/colorscan
./share/terminfo/s/scanset
./share/doc/pcre2/html/pcre2_substring_nametable_scan.html
(nextflow-env2) [doutree@plop] nextflow-env2 $

I copied the instructions to create the conda env so I am not sure what is going wrong.

mahesh-panchal commented 7 months ago

I think you've checked the wrong conda environment. Since you're using the conda profile, each process is creating an environment from the environment file included with the module ( specifically this one: https://github.com/NBISweden/pipelines-nextflow/blob/master/modules/nf-core/interproscan/environment.yml ). The created conda environments should be somewhere in your work directory I think.

EmilieSmeets22 commented 7 months ago

Thank you, you are right. I was able to find that script:

(nextflow-env2) [doutree@plop] GFF $ find | grep ps_scan.pl
./work/conda/interproscan-e9a89038da084d2a42fbea60b024d16b/share/InterProScan/bin/prosite/ps_scan.pl

So at least the environment was correctly set up, but somehow the script was not found during the pipeline.

mahesh-panchal commented 7 months ago

If you activate that environment, is ps_scan.pl in the PATH? Actually, is it executable?

conda activate ./work/conda/interproscan-e9a89038da084d2a42fbea60b024d16b
EmilieSmeets22 commented 7 months ago

Yes I can execute the script even if I activate that environment

(nextflow-env2) [doutree@plop] GFF $ conda activate ./work/conda/interproscan-e9a89038da084d2a42fbea60b024d16b
(workspace/doutree/GFF/work/conda/interproscan-e9a89038da084d2a42fbea60b024d16b) [doutree@plop] GFF $ ./work/conda/interproscan-e9a89038da084d2a42fbea60b024d16b/share/InterProScan/bin/prosite/ps_scan.pl -help
ps_scan.pl [options] sequence-file(s)
ps_scan version 1.90 options:
-h : this help screen

Input/Output:
  -e <string> : specify the ID or AC of an entry in sequence-file
  -o <string> : specify an output format : scan | fasta | psa | msa |
                gff | pff | epff | sequence | matchlist
  -d <file>   : specify a prosite motif file
  -p <string> : specify a pattern or the AC of a prosite motif
  -f <string> : specify a motif AC to scan against together with all its
                related post-processing motifs (but show only specified
                motif hits)

Selection:
  -r          : do not scan profiles
  -m          : only scan profiles
  -s          : skip frequently matching (unspecific) patterns and
                profiles
  -l <number> : cut-off level for profiles (default : 0)

Pattern option:
  -x <number> : specify maximum number of accepted matches of X's in
                sequence (default=0)
  -g          : Turn greediness off
  -v          : Turn overlaps off
  -i          : Allow included matches
  -b <file>   : use profiles from <f> to evaluate pattern matches
                (a LevelTag is assigned to each pattern match). If no
                file is specified, evaluator.dat will be used (searched
                in the paths $PROSITE/ and $PROSITE/prosite/)

profile options:
  -w pfsearch : Compares a query profile against a protein sequence
                library

Other expert options:
  --nopp             : do not post-process matches
  --reverse          : randomize the sequence database by taking the
                       reverse sequence of each individual entry
  --shuffle          : randomize the sequence database by local shuffling
                       of the residues in windows of 20 residues
  --gff <file>       : use an existing ps_scan gff result <file> as input to
                       e.g. post-process it and/or to reformat it into another
                       format (defined by -o <string>), instead of doing a
                       real scan.
  -w pfsearch -R     : use raw scores rather than normalized scores for
                       match selection
  -w pfsearch -C <x> : report only match scores higher than the specified
                       parameter <x>; an integer argument is interpreted
                       as a raw score value, a decimal argument as a
                       normalized score value. -R and -C options can be
                       combined.
  --pfscan <path>    : pathname to pfscan executable (if not defined will be
                       'pfscan', so executable has to be found within PATH env).
                       This option could be used e.g. to use pftool v3 pfscanV3.

Note:
  The sequence-file may be in Swiss-Prot or FASTA format.

  If no prosite motif file is specified, prosite.dat will be used
  (searched in the paths $PROSITE/ and $SPROT/prosite/).

  There may be several -d, -p and -e arguments.
mahesh-panchal commented 7 months ago

Can you also run it without prefixing the full path in the activated environment?

EmilieSmeets22 commented 7 months ago

No that does not work:

(workspace/doutree/GFF/work/conda/interproscan-e9a89038da084d2a42fbea60b024d16b) [doutree@plop] GFF $ ps_scan.pl
-bash: ps_scan.pl: command not found
mahesh-panchal commented 7 months ago

what's the output of the command env | grep -i "conda" in that environment?

EmilieSmeets22 commented 7 months ago 
[doutree@plop] GFF $ conda activate ./work/conda/interproscan-e9a89038da084d2a42fbea60b024d16b
(/workspace/doutree/GFF/work/conda/interproscan-e9a89038da084d2a42fbea60b024d16b) [doutree@plop] GFF $ env | grep -i "conda"
EBDEVELMINICONDA3=/tools/eb/software/Miniconda3/23.5.2-0/easybuild/General-Miniconda3-23.5.2-0-easybuild-devel
MANPATH=/tools/eb/software/Miniconda3/23.5.2-0/share/man:/tools/eb/software/Miniconda3/23.5.2-0/man:/gridware/biogrid2/uge/man:/usr/share/lmod/lmod/share/man::/opt/puppetlabs/puppet/share/man
JAVA_LD_LIBRARY_PATH=/workspace/doutree/GFF/work/conda/interproscan-e9a89038da084d2a42fbea60b024d16b/lib/jvm/lib/server
CONDA_SHLVL=1
CONDA_PROMPT_MODIFIER=(/workspace/doutree/GFF/work/conda/interproscan-e9a89038da084d2a42fbea60b024d16b)
GSETTINGS_SCHEMA_DIR_CONDA_BACKUP=
CONDA_EXE=/tools/eb/software/Miniconda3/23.5.2-0/bin/conda
EBVERSIONMINICONDA3=23.5.2-0
_CE_CONDA=
EBROOTMINICONDA3=/tools/eb/software/Miniconda3/23.5.2-0
PATH=/workspace/doutree/GFF/work/conda/interproscan-e9a89038da084d2a42fbea60b024d16b/bin:/tools/eb/software/Miniconda3/23.5.2-0/condabin:/tools/eb/software/Miniconda3/23.5.2-0:/tools/eb/software/Miniconda3/23.5.2-0/sbin:/tools/eb/software/Miniconda3/23.5.2-0/bin:/usr/lib64/qt-3.3/bin:/gridware/biogrid2/uge/bin/lx-amd64:/tools/eb/software/puppet/Queue-In-Grid/bin:/tools/general/bin:/usr/java/default/bin:/tools/bioinfo/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/doutree/bin
GSETTINGS_SCHEMA_DIR=/workspace/doutree/GFF/work/conda/interproscan-e9a89038da084d2a42fbea60b024d16b/share/glib-2.0/schemas
CONDA_PREFIX=/workspace/doutree/GFF/work/conda/interproscan-e9a89038da084d2a42fbea60b024d16b
JAVA_HOME=/workspace/doutree/GFF/work/conda/interproscan-e9a89038da084d2a42fbea60b024d16b/lib/jvm
_LMFILES_=/tools/eb/modules/puppet/modules/2022b.lua:/tools/eb/modules/puppet/tier/prod.lua:/tools/eb/modules/puppet/qig.lua:/tools/eb/gmns/modules/all/General/Miniconda3/23.5.2-0.lua
LOADEDMODULES=modules/2022b:tier/prod:qig:Miniconda3/23.5.2-0
__LMOD_REF_COUNT_PATH=/tools/eb/software/Miniconda3/23.5.2-0:1;/tools/eb/software/Miniconda3/23.5.2-0/sbin:1;/tools/eb/software/Miniconda3/23.5.2-0/bin:1;/usr/lib64/qt-3.3/bin:1;/gridware/biogrid2/uge/bin/lx-amd64:1;/tools/eb/software/puppet/Queue-In-Grid/bin:1;/tools/general/bin:2;/usr/java/default/bin:1;/tools/bioinfo/bin:1;/usr/local/bin:2;/usr/bin:1;/usr/local/sbin:1;/usr/sbin:1;/opt/puppetlabs/bin:1
CONDA_PYTHON_EXE=/tools/eb/software/Miniconda3/23.5.2-0/bin/python
JAVA_HOME_CONDA_BACKUP=/usr/java/default
CONDA_DEFAULT_ENV=/workspace/doutree/GFF/work/conda/interproscan-e9a89038da084d2a42fbea60b024d16b
PKG_CONFIG_PATH=/tools/eb/software/Miniconda3/23.5.2-0/share/pkgconfig:/tools/eb/software/Miniconda3/23.5.2-0/lib/pkgconfig
__LMOD_REF_COUNT_PKG_CONFIG_PATH=/tools/eb/software/Miniconda3/23.5.2-0/share/pkgconfig:1;/tools/eb/software/Miniconda3/23.5.2-0/lib/pkgconfig:1
__LMOD_REF_COUNT_MANPATH=/tools/eb/software/Miniconda3/23.5.2-0/share/man:1;/tools/eb/software/Miniconda3/23.5.2-0/man:1;/gridware/biogrid2/uge/man:1;/usr/share/lmod/lmod/share/man:1;/opt/puppetlabs/puppet/share/man:1
mahesh-panchal commented 7 months ago

Add the following to a custom config and see if this solves the issue.

env.PATH ='${CONDA_PREFIX}/share/InterProScan/bin/prosite:${PATH}'
EmilieSmeets22 commented 7 months ago

Thank you for the feedback.

I have create the custom config file:

(nextflow-env) [doutree@plop] GFF $ more custom_config.txt
env.PATH='${CONDA_PREFIX}/share/InterProScan/bin/prosite:${PATH}'

But the error was the same:

(nextflow-env) [doutree@plop] GFF $ nextflow run NBISweden/pipelines-nextflow -profile conda -params-file functional_annotation_param.yml -c custom_config.txt
N E X T F L O W  ~  version 23.10.1
Launching `https://github.com/NBISweden/pipelines-nextflow` [mad_williams] DSL2 - revision: 5f66ae3cf2 [master]

         _  _ ___ ___ ___
        | \| | _ )_ _/ __|
        | .` | _ \| |\__ \
        |_|\_|___/___|___/ Annotation Service

        Functional annotation workflow
        ===================================================

executor >  local (11)
[-        ] process > FUNCTIONAL_ANNOTATION:BLAST_MAKEBLASTDB                                -
[1f/dc10eb] process > FUNCTIONAL_ANNOTATION:GFF2PROTEIN (my_crop.gene_chr)             [100%] 1 of 1 ✔
[5b/2a0bc2] process > FUNCTIONAL_ANNOTATION:BLAST_BLASTP (my_crop.gene_chr_proteins.4) [  0%] 0 of 37
[5b/209e4f] process > FUNCTIONAL_ANNOTATION:INTERPROSCAN (my_crop.gene_chr)            [  0%] 0 of 37
[-        ] process > FUNCTIONAL_ANNOTATION:MERGE_FUNCTIONAL_ANNOTATION                      -
ERROR ~ Error executing process > 'FUNCTIONAL_ANNOTATION:INTERPROSCAN (my_crop.gene_chr)'

Caused by:
  Process `FUNCTIONAL_ANNOTATION:INTERPROSCAN (my_crop.gene_chr)` terminated with an error exit status (231)

Command executed:

  if [ "false" == "true" ]; then
      gzip -c -d my_crop.gene_chr_proteins.5.fasta > my_crop.gene_chr_proteins.5.fasta
  fi

  interproscan.sh \
      -cpu 8 \
      -i my_crop.gene_chr_proteins.5.fasta \
      -f tsv \
      -dp \
      --iprlookup --goterms -pa -t p -dra \
      -appl TIGRFAM,FunFam,SFLD,PANTHER,Gene3D,Hamap,ProSiteProfiles,Coils,SMART,CDD,PRINTS,PIRSR,ProSitePatterns,AntiFam,Pfam,MobiDBLite \
      -o my_crop.gene_chr.tsv

  cat <<-END_VERSIONS > versions.yml
  "FUNCTIONAL_ANNOTATION:INTERPROSCAN":
  interproscan: $(echo $(interproscan.sh --version 2>&1) | head -n 1 | sed 's/^.*InterProScan version//' | sed 's/\s*InterProScan.*//')
  END_VERSIONS

Command exit status:
  231
mahesh-panchal commented 7 months ago

So I just checked the module itself and found that the script should be in the path.

$ find | grep ps_scan.pl
./work/conda/env-980ead1ad9ca9871a0b8225a7098fd9c/bin/ps_scan.pl
./work/conda/env-980ead1ad9ca9871a0b8225a7098fd9c/share/InterProScan/bin/prosite/ps_scan.pl

The command you ran earlier should have returned both scripts as shown here. The one missing from your command is the one that the tool should be picking up.

workflow {
    TASK(1) | view
}

process TASK {
    input:
    val it

    conda "bioconda::interproscan=5.59_91.0"
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/interproscan:5.59_91.0--hec16e2b_1' :
        'quay.io/biocontainers/interproscan:5.59_91.0--hec16e2b_1' }"

    script:
    """
    which ps_scan.pl
    """

    output:
    stdout
}
profiles {
    conda {
        conda.enabled = true
    }

    docker {
        docker.enabled = true
    }
}
$ nextflow run main.nf -profile docker 
N E X T F L O W  ~  version 23.10.1
Launching `main.nf` [infallible_miescher] DSL2 - revision: 8e6cf3af2e
executor >  local (1)
[77/e930a8] process > TASK [100%] 1 of 1 ✔
/usr/local/bin/ps_scan.pl
$ nextflow run main.nf -profile conda
N E X T F L O W  ~  version 23.10.1
Launching `main.nf` [nasty_ramanujan] DSL2 - revision: 8e6cf3af2e
executor >  local (1)
[a7/e3716d] process > TASK [100%] 1 of 1 ✔
/workspace/Nextflow_sandbox/work/conda/env-980ead1ad9ca9871a0b8225a7098fd9c/bin/ps_scan.pl

Could you delete your interproscan environment and rerun so that Nextflow recreates it please? Before do so, could you also clear your conda cache by doing

conda clean all -a -y
EmilieSmeets22 commented 7 months ago

Hi,

I cleaned the workdir and that removed the interproscan environment, then I conda clean all and finally I re-ran the query. But the error was the same:


[doutree@plop] GFF $ conda activate nextflow-env
(nextflow-env) [doutree@plop] GFF $ conda clean -a -y
Will remove 1029 (4.53 GB) tarball(s).
Will remove 2 index cache(s).
There are no tempfile(s) to remove.
There are no logfile(s) to remove.
(nextflow-env) [doutree@plop] GFF $ nextflow run NBISweden/pipelines-nextflow -profile conda -params-file functional_annotation_param.yml
N E X T F L O W  ~  version 23.10.1
Launching `https://github.com/NBISweden/pipelines-nextflow` [berserk_church] DSL2 - revision: 5f66ae3cf2 [master]

         _  _ ___ ___ ___
        | \| | _ )_ _/ __|
        | .` | _ \| |\__ \
        |_|\_|___/___|___/ Annotation Service

        Functional annotation workflow
        ===================================================

executor >  local (1)
executor >  local (11)
[-        ] process > FUNCTIONAL_ANNOTATION:BLAST_MAKEBLASTDB                                 -
[f1/c8dc8c] process > FUNCTIONAL_ANNOTATION:GFF2PROTEIN (my_crop.gene_chr)              [100%] 1 of 1 ✔
[40/e45623] process > FUNCTIONAL_ANNOTATION:BLAST_BLASTP (my_crop.gene_chr_proteins.19) [  0%] 0 of 37
[19/765a92] process > FUNCTIONAL_ANNOTATION:INTERPROSCAN (my_crop.gene_chr)             [  0%] 0 of 37
[-        ] process > FUNCTIONAL_ANNOTATION:MERGE_FUNCTIONAL_ANNOTATION                       -
ERROR ~ Error executing process > 'FUNCTIONAL_ANNOTATION:INTERPROSCAN (my_crop.gene_chr)'

Caused by:
  Process `FUNCTIONAL_ANNOTATION:INTERPROSCAN (my_crop.gene_chr)` terminated with an error exit status (231)

Command executed:

  if [ "false" == "true" ]; then
      gzip -c -d my_crop.gene_chr_proteins.9.fasta > my_crop.gene_chr_proteins.9.fasta
  fi

  interproscan.sh \
      -cpu 8 \
      -i my_crop.gene_chr_proteins.9.fasta \
      -f tsv \
      -dp \
      --iprlookup --goterms -pa -t p -dra \
      -appl TIGRFAM,FunFam,SFLD,PANTHER,Gene3D,Hamap,ProSiteProfiles,Coils,SMART,CDD,PRINTS,PIRSR,ProSitePatterns,AntiFam,Pfam,MobiDBLite \
      -o my_crop.gene_chr.tsv

  cat <<-END_VERSIONS > versions.yml
  "FUNCTIONAL_ANNOTATION:INTERPROSCAN":
  interproscan: $(echo $(interproscan.sh --version 2>&1) | head -n 1 | sed 's/^.*InterProScan version//' | sed 's/\s*InterProScan.*//')
  END_VERSIONS

Command exit status:
  231

Command output:
        at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1538) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.query.internal.AbstractProducedQuery.doList(AbstractProducedQuery.java:1561) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.query.internal.AbstractProducedQuery.list(AbstractProducedQuery.java:1529) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        ... 37 more
  Caused by: org.h2.jdbc.JdbcSQLSyntaxErrorException: Table "PROSITE_PROF_RAW_MATCH" not found; SQL statement:
  select prositepro0_.id as id1_86_, prositepro0_.loc_fragment_dcs_tatus as loc_frag2_86_, prositepro0_.location_end as location3_86_, prositepro0_.location_start as location4_86_, prositepro0_.model_id as model_id5_86_, prositepro0_.numeric_sequence_id as numeric_6_86_, prositepro0_.sequence_id as sequence7_86_, prositepro0_.signature_library as signatur8_86_, prositepro0_.sig_lib_release as sig_lib_9_86_, prositepro0_.cigar_alignment as cigar_al1_67_, prositepro0_.pf_scan_level as pf_scan_1_80_, prositepro0_.score as score2_80_ from public.prosite_prof_raw_match prositepro0_ where prositepro0_.numeric_sequence_id>=? and prositepro0_.numeric_sequence_id<=? and prositepro0_.sig_lib_release=? [42102-199]
        at org.h2.message.DbException.getJdbcSQLException(DbException.java:451) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.message.DbException.getJdbcSQLException(DbException.java:427) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.message.DbException.get(DbException.java:205) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.message.DbException.get(DbException.java:181) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.readTableOrView(Parser.java:7146) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.readTableFilter(Parser.java:1895) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.parseSelectSimpleFromPart(Parser.java:2641) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.parseSelectSimple(Parser.java:2788) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.parseSelectSub(Parser.java:2636) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.parseSelectUnion(Parser.java:2469) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.parseSelect(Parser.java:2440) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.parsePrepared(Parser.java:814) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.parse(Parser.java:788) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.parse(Parser.java:760) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.prepareCommand(Parser.java:683) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.engine.Session.prepareLocal(Session.java:627) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.engine.Session.prepareCommand(Session.java:565) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.jdbc.JdbcConnection.prepareCommand(JdbcConnection.java:1292) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.jdbc.JdbcPreparedStatement.<init>(JdbcPreparedStatement.java:77) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.jdbc.JdbcConnection.prepareStatement(JdbcConnection.java:349) ~[h2-1.4.199.jar:1.4.199]
        at jdk.internal.reflect.GeneratedMethodAccessor63.invoke(Unknown Source) ~[?:?]
        at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
        at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
        at org.springframework.jdbc.datasource.LazyConnectionDataSourceProxy$LazyConnectionInvocationHandler.invoke(LazyConnectionDataSourceProxy.java:385) ~[spring-jdbc-5.2.22.RELEASE.jar:5.2.22.RELEASE]
        at com.sun.proxy.$Proxy30.prepareStatement(Unknown Source) ~[?:?]
        at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$5.doPrepare(StatementPreparerImpl.java:146) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPreparationTemplate.prepareStatement(StatementPreparerImpl.java:172) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.engine.jdbc.internal.StatementPreparerImpl.prepareQueryStatement(StatementPreparerImpl.java:148) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.prepareQueryStatement(Loader.java:1990) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1920) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1898) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.doQuery(Loader.java:937) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:340) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.doList(Loader.java:2695) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.doList(Loader.java:2678) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2512) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.list(Loader.java:2507) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:504) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.hql.internal.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:396) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.engine.query.spi.HQLQueryPlan.performList(HQLQueryPlan.java:224) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1538) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.query.internal.AbstractProducedQuery.doList(AbstractProducedQuery.java:1561) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.query.internal.AbstractProducedQuery.list(AbstractProducedQuery.java:1529) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        ... 37 more

Command error:
        at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1538) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.query.internal.AbstractProducedQuery.doList(AbstractProducedQuery.java:1561) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.query.internal.AbstractProducedQuery.list(AbstractProducedQuery.java:1529) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        ... 37 more
  Caused by: org.h2.jdbc.JdbcSQLSyntaxErrorException: Table "PROSITE_PROF_RAW_MATCH" not found; SQL statement:
  select prositepro0_.id as id1_86_, prositepro0_.loc_fragment_dcs_tatus as loc_frag2_86_, prositepro0_.location_end as location3_86_, prositepro0_.location_start as location4_86_, prositepro0_.model_id as model_id5_86_, prositepro0_.numeric_sequence_id as numeric_6_86_, prositepro0_.sequence_id as sequence7_86_, prositepro0_.signature_library as signatur8_86_, prositepro0_.sig_lib_release as sig_lib_9_86_, prositepro0_.cigar_alignment as cigar_al1_67_, prositepro0_.pf_scan_level as pf_scan_1_80_, prositepro0_.score as score2_80_ from public.prosite_prof_raw_match prositepro0_ where prositepro0_.numeric_sequence_id>=? and prositepro0_.numeric_sequence_id<=? and prositepro0_.sig_lib_release=? [42102-199]
        at org.h2.message.DbException.getJdbcSQLException(DbException.java:451) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.message.DbException.getJdbcSQLException(DbException.java:427) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.message.DbException.get(DbException.java:205) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.message.DbException.get(DbException.java:181) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.readTableOrView(Parser.java:7146) ~[h2-1.4.199.jar:1.4.199]
executor >  local (11)
[-        ] process > FUNCTIONAL_ANNOTATION:BLAST_MAKEBLASTDB                                 -
[f1/c8dc8c] process > FUNCTIONAL_ANNOTATION:GFF2PROTEIN (my_crop.gene_chr)              [100%] 1 of 1 ✔
[40/e45623] process > FUNCTIONAL_ANNOTATION:BLAST_BLASTP (my_crop.gene_chr_proteins.19) [  0%] 0 of 31
[19/765a92] process > FUNCTIONAL_ANNOTATION:INTERPROSCAN (my_crop.gene_chr)             [  2%] 1 of 34, failed: 1
[-        ] process > FUNCTIONAL_ANNOTATION:MERGE_FUNCTIONAL_ANNOTATION                       -
ERROR ~ Error executing process > 'FUNCTIONAL_ANNOTATION:INTERPROSCAN (my_crop.gene_chr)'

Caused by:
  Process `FUNCTIONAL_ANNOTATION:INTERPROSCAN (my_crop.gene_chr)` terminated with an error exit status (231)

Command executed:

  if [ "false" == "true" ]; then
      gzip -c -d my_crop.gene_chr_proteins.9.fasta > my_crop.gene_chr_proteins.9.fasta
  fi

  interproscan.sh \
      -cpu 8 \
      -i my_crop.gene_chr_proteins.9.fasta \
      -f tsv \
      -dp \
      --iprlookup --goterms -pa -t p -dra \
      -appl TIGRFAM,FunFam,SFLD,PANTHER,Gene3D,Hamap,ProSiteProfiles,Coils,SMART,CDD,PRINTS,PIRSR,ProSitePatterns,AntiFam,Pfam,MobiDBLite \
      -o my_crop.gene_chr.tsv

  cat <<-END_VERSIONS > versions.yml
  "FUNCTIONAL_ANNOTATION:INTERPROSCAN":
  interproscan: $(echo $(interproscan.sh --version 2>&1) | head -n 1 | sed 's/^.*InterProScan version//' | sed 's/\s*InterProScan.*//')
  END_VERSIONS

Command exit status:
  231

Command output:
        at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1538) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.query.internal.AbstractProducedQuery.doList(AbstractProducedQuery.java:1561) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.query.internal.AbstractProducedQuery.list(AbstractProducedQuery.java:1529) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        ... 37 more
  Caused by: org.h2.jdbc.JdbcSQLSyntaxErrorException: Table "PROSITE_PROF_RAW_MATCH" not found; SQL statement:
  select prositepro0_.id as id1_86_, prositepro0_.loc_fragment_dcs_tatus as loc_frag2_86_, prositepro0_.location_end as location3_86_, prositepro0_.location_start as location4_86_, prositepro0_.model_id as model_id5_86_, prositepro0_.numeric_sequence_id as numeric_6_86_, prositepro0_.sequence_id as sequence7_86_, prositepro0_.signature_library as signatur8_86_, prositepro0_.sig_lib_release as sig_lib_9_86_, prositepro0_.cigar_alignment as cigar_al1_67_, prositepro0_.pf_scan_level as pf_scan_1_80_, prositepro0_.score as score2_80_ from public.prosite_prof_raw_match prositepro0_ where prositepro0_.numeric_sequence_id>=? and prositepro0_.numeric_sequence_id<=? and prositepro0_.sig_lib_release=? [42102-199]
        at org.h2.message.DbException.getJdbcSQLException(DbException.java:451) ~[h2-1.4.199.jar:1.4.199]
  - Checat org.h2.message.DbException.getJdbcSQLException(DbException.java:427) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.message.DbException.get(DbException.java:205) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.message.DbException.get(DbException.java:181) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.readTableOrView(Parser.java:7146) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.readTableFilter(Parser.java:1895) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.parseSelectSimpleFromPart(Parser.java:2641) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.parseSelectSimple(Parser.java:2788) ~[h2-1.4.199.jar:1.4.199]
  RN: Kiat org.h2.command.Parser.parseSelectSub(Parser.java:2636) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.parseSelectUnion(Parser.java:2469) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.parseSelect(Parser.java:2440) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.parsePrepared(Parser.java:814) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.parse(Parser.java:788) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.parse(Parser.java:760) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.prepareCommand(Parser.java:683) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.engine.Session.prepareLocal(Session.java:627) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.engine.Session.prepareCommand(Session.java:565) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.jdbc.JdbcConnection.prepareCommand(JdbcConnection.java:1292) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.jdbc.JdbcPreparedStatement.<init>(JdbcPreparedStatement.java:77) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.jdbc.JdbcConnection.prepareStatement(JdbcConnection.java:349) ~[h2-1.4.199.jar:1.4.199]
        at jdk.internal.reflect.GeneratedMethodAccessor63.invoke(Unknown Source) ~[?:?]
        at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
        at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
        at org.springframework.jdbc.datasource.LazyConnectionDataSourceProxy$LazyConnectionInvocationHandler.invoke(LazyConnectionDataSourceProxy.java:385) ~[spring-jdbc-5.2.22.RELEASE.jar:5.2.22.RELEASE]
        at com.sun.proxy.$Proxy30.prepareStatement(Unknown Source) ~[?:?]
        at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$5.doPrepare(StatementPreparerImpl.java:146) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPreparationTemplate.prepareStatement(StatementPreparerImpl.java:172) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.engine.jdbc.internal.StatementPreparerImpl.prepareQueryStatement(StatementPreparerImpl.java:148) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.prepareQueryStatement(Loader.java:1990) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1920) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1898) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.doQuery(Loader.java:937) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:340) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.doList(Loader.java:2695) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.doList(Loader.java:2678) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2512) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.list(Loader.java:2507) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:504) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.hql.internal.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:396) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.engine.query.spi.HQLQueryPlan.performList(HQLQueryPlan.java:224) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1538) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.query.internal.AbstractProducedQuery.doList(AbstractProducedQuery.java:1561) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.query.internal.AbstractProducedQuery.list(AbstractProducedQuery.java:1529) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        ... 37 more

Command error:
        at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1538) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.query.internal.AbstractProducedQuery.doList(AbstractProducedQuery.java:1561) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.query.internal.AbstractProducedQuery.list(AbstractProducedQuery.java:1529) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        ... 37 more
  Caused by: org.h2.jdbc.JdbcSQLSyntaxErrorException: Table "PROSITE_PROF_RAW_MATCH" not found; SQL statement:
  select prositepro0_.id as id1_86_, prositepro0_.loc_fragment_dcs_tatus as loc_frag2_86_, prositepro0_.location_end as location3_86_, prositepro0_.location_start as location4_86_, prositepro0_.model_id as model_id5_86_, prositepro0_.numeric_sequence_id as numeric_6_86_, prositepro0_.sequence_id as sequence7_86_, prositepro0_.signature_library as signatur8_86_, prositepro0_.sig_lib_release as sig_lib_9_86_, prositepro0_.cigar_alignment as cigar_al1_67_, prositepro0_.pf_scan_level as pf_scan_1_80_, prositepro0_.score as score2_80_ from public.prosite_prof_raw_match prositepro0_ where prositepro0_.numeric_sequence_id>=? and prositepro0_.numeric_sequence_id<=? and prositepro0_.sig_lib_release=? [42102-199]
        at org.h2.message.DbException.getJdbcSQLException(DbException.java:451) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.message.DbException.getJdbcSQLException(DbException.java:427) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.message.DbException.get(DbException.java:205) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.message.DbException.get(DbException.java:181) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.readTableOrView(Parser.java:7146) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.readTableFilter(Parser.java:1895) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.parseSelectSimpleFromPart(Parser.java:2641) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.parseSelectSimple(Parser.java:2788) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.parseSelectSub(Parser.java:2636) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.parseSelectUnion(Parser.java:2469) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.parseSelect(Parser.java:2440) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.parsePrepared(Parser.java:814) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.parse(Parser.java:788) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.parse(Parser.java:760) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.command.Parser.prepareCommand(Parser.java:683) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.engine.Session.prepareLocal(Session.java:627) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.engine.Session.prepareCommand(Session.java:565) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.jdbc.JdbcConnection.prepareCommand(JdbcConnection.java:1292) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.jdbc.JdbcPreparedStatement.<init>(JdbcPreparedStatement.java:77) ~[h2-1.4.199.jar:1.4.199]
        at org.h2.jdbc.JdbcConnection.prepareStatement(JdbcConnection.java:349) ~[h2-1.4.199.jar:1.4.199]
        at jdk.internal.reflect.GeneratedMethodAccessor63.invoke(Unknown Source) ~[?:?]
        at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
        at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
        at org.springframework.jdbc.datasource.LazyConnectionDataSourceProxy$LazyConnectionInvocationHandler.invoke(LazyConnectionDataSourceProxy.java:385) ~[spring-jdbc-5.2.22.RELEASE.jar:5.2.22.RELEASE]
        at com.sun.proxy.$Proxy30.prepareStatement(Unknown Source) ~[?:?]
        at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$5.doPrepare(StatementPreparerImpl.java:146) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPreparationTemplate.prepareStatement(StatementPreparerImpl.java:172) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.engine.jdbc.internal.StatementPreparerImpl.prepareQueryStatement(StatementPreparerImpl.java:148) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.prepareQueryStatement(Loader.java:1990) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1920) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1898) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.doQuery(Loader.java:937) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:340) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.doList(Loader.java:2695) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.doList(Loader.java:2678) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2512) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.Loader.list(Loader.java:2507) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:504) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.hql.internal.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:396) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.engine.query.spi.HQLQueryPlan.performList(HQLQueryPlan.java:224) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1538) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.query.internal.AbstractProducedQuery.doList(AbstractProducedQuery.java:1561) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        at org.hibernate.query.internal.AbstractProducedQuery.list(AbstractProducedQuery.java:1529) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
        ... 37 more

Work dir:
  /workspace/doutree/GFF/work/e5/43440413e30314ad17465f92e96096

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '.nextflow.log' file for details
mahesh-panchal commented 7 months ago

Hi, this is a different error. It looks like some SQL table that interproscan was supposed to create doesn't exist.

Perhaps try again, and/or allocate a few more resources (i.e. more cpus and memory, although I don't think this is a resource problem ). The only other thing I can suggest here is to locate the -appl that's causing this and remove it from the string.

You can do this by providing a custom config:

process {
    withName: 'INTERPROSCAN' {
        cpus     = 20     // Example
        memory   = 256.GB // Example
        ext.args = [
            '--iprlookup',
            '--goterms',
            '-pa',
            '-t p',
            '-dra',
            '-appl TIGRFAM,FunFam,SFLD,PANTHER,Gene3D,Hamap,Coils,SMART,CDD,PRINTS,PIRSR,AntiFam,Pfam,MobiDBLite'
        ].join(" ").trim()
    }
}
EmilieSmeets22 commented 7 months ago

Thank you, it is running now!

mahesh-panchal commented 7 months ago

How did you solve it?

EmilieSmeets22 commented 7 months ago

and it completed :) thanks

EmilieSmeets22 commented 7 months ago

by adding the custom config you mentioned in your last comment:

[doutree@plop] GFF $ cat custom_config.txt
process {
    withName: 'INTERPROSCAN' {
        cpus     = 20     // Example
        memory   = 500.GB // Example
        ext.args = [
            '--iprlookup',
            '--goterms',
            '-pa',
            '-t p',
            '-dra',
            '-appl TIGRFAM,FunFam,SFLD,PANTHER,Gene3D,Hamap,Coils,SMART,CDD,PRINTS,PIRSR,AntiFam,Pfam,MobiDBLite'
        ].join(" ").trim()
    }
}
[doutree@plop] GFF $ nextflow run NBISweden/pipelines-nextflow -profile conda -params-file functional_annotation_param.yml -c custom_config.txt
N E X T F L O W  ~  version 22.10.1
Launching `https://github.com/NBISweden/pipelines-nextflow` [awesome_joliot] DSL2 - revision: 5f66ae3cf2 [master]

         _  _ ___ ___ ___
        | \| | _ )_ _/ __|
        | .` | _ \| |\__ \
        |_|\_|___/___|___/ Annotation Service

        Functional annotation workflow
        ===================================================

executor >  local (76)
[-        ] process > FUNCTIONAL_ANNOTATION:BLAST_MAKEBLASTDB                                    -
[15/050852] process > FUNCTIONAL_ANNOTATION:GFF2PROTEIN (my_crop.gene_chr)                 [100%] 1 of 1 ✔
[ff/338561] process > FUNCTIONAL_ANNOTATION:BLAST_BLASTP (my_crop.gene_chr_proteins.35)    [100%] 37 of 37 ✔
[dd/dc989e] process > FUNCTIONAL_ANNOTATION:INTERPROSCAN (my_crop.gene_chr)                [100%] 37 of 37 ✔
[d4/ca12e8] process > FUNCTIONAL_ANNOTATION:MERGE_FUNCTIONAL_ANNOTATION (my_crop.gene_chr) [100%] 1 of 1 ✔

        Workflow completed successfully.

        Thank you for using our workflow.
        Results are located in the folder: /home/doutree/workspace/GFF/test/functional_annotation

Completed at: 04-Mar-2024 16:28:24
Duration    : 3h 33m 1s
CPU hours   : 209.7
Succeeded   : 76
mahesh-panchal commented 7 months ago

Thanks for reporting back. Good to know it finished. I hope you didn't need anything from the prosite modules.

EmilieSmeets22 commented 6 months ago

no it seems all worked fine, thank you :)