cant locate FASTA.pm ERROR message

[JanVHenkel]

Hey!

I ran into a problem with interproscan. I found an issue from 2019 (https://github.com/ebi-pf-team/interproscan/issues/68) with similar problems and followed your suggestions.

with: perl /home/janvhenkel/my_interproscan/interproscan-5.48-83.0/bin/signalp/4.1/signalp -T

i got the output: Can't locate FASTA.pm in @inc (you may need to install the FASTA module) (@inc contains: /usr/opt/www/pub/CBS/services/SignalP-4.1/signalp-4.1/lib /home/janvhenkel/miniconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/janvhenkel/miniconda3/lib/site_perl/5.26.2 /home/janvhenkel/miniconda3/lib/5.26.2/x86_64-linux-thread-multi /home/janvhenkel/miniconda3/lib/5.26.2 .) at /home/janvhenkel/my_interproscan/interproscan-5.48-83.0/bin//signalp/4.1/signalp line 80. BEGIN failed--compilation aborted at /home/janvhenkel/my_interproscan/interproscan-5.48-83.0/bin//signalp/4.1/signalp line 80.

However, in the lib directory FASTA.pm is present.

As interproscan did work before i started working with programs using bioconda, this may have produced this issue. Unfortunately, i am not experienced enough to resolve this problem by myself.

best, Jan

[gsn7]

can you check if you have the following in bin/signalp/4.1/signalp file: BEGIN { $ENV{SIGNALP} = 'bin/signalp/4.1'; } if you don't have these lines add then just below the header: GENERAL SETTINGS: CUSTOMIZE TO YOUR SITE

then again try: perl /home/janvhenkel/my_interproscan/interproscan-5.48-83.0/bin/signalp/4.1/signalp -T

Do you have signalp running under bioconda?

[JanVHenkel]

I had signalP running with interproscan and started to work with bioconda afterwards but without signalp as far as i remember (as i just started with bioinformatics recently i jumped a lot between different programs without a master plan...)

The following is stated in the signalp file:

full path to the signalp-4.1 directory on your system (mandatory)

BEGIN { $ENV{SIGNALP} = '/usr/opt/www/pub/CBS/services/SignalP-4.1/signalp-4.1'; }

I changed it according to your comment.

With perl /home/janvhenkel/my_interproscan/interproscan-5.48-83.0/bin/signalp/4.1/signalp -T

I now get:

Description: Predict signal peptide and cleavage site.

Usage: /home/janvhenkel/my_interproscan/interproscan-5.48-83.0/bin/signalp/4.1/signalp -f -p -k -s -t -m -n -v -l -u -U -w -h -c -T -V <fasta-file(s)> Options: -f Setting the output format ('short', 'long', 'summary' or 'all'). Default: 'short' -g Graphics 'png' or 'png+eps'. Default: 'Off' -k Keep temporary directory. Default: 'Off' -s Signal peptide networks to use ('best' or 'notm'). Default: 'best' -t Organism type> (euk, gram+, gram-). Default: 'euk' -m Make fasta file with mature sequence. Default: 'Off' -n Make gff file of processed sequences. Default: 'Off' -T Specify temporary file directory. Default: /var/tmp -w web predictions. Default: 'Off' -u user defined D-cutoff for noTM networks -U user defined D-cutoff for TM networks -M Minimal predicted signal peptide length. Default: [10] -c truncate to sequence length - 0 means no truncation. Default '70' -l Logfile if -v is defined. Default: 'STDERR' -v Verbose. Default: 'Off' -V Print SignalP version and exit -h Print this help information

So this seems to work fine, thank you very much!

I then proceeded to run the test case commands again:

./interproscan.sh -i test_all_appl.fasta -f tsv -dp

But i get an error with phobius:

2021-02-16 16:10:37,694 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:215] ERROR - The exception is : java.lang.IllegalStateException: Command line failed with exit code: 127 Command: bin/phobius/1.01/phobius.pl /home/janvhenkel/my_interproscan/interproscan-5.48-83.0/temp/Notebook-Jan_20210216_160929288_hzhc//jobPhobius/000000000001_000000000005.fasta Error output from binary: Phobius ver 1.01 (c) 2004 Lukas Kall, Anders Krogh, Erik Sonnhammer

Could not read provided fasta sequence at bin/phobius/1.01/phobius.pl line 408.

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
    at jdk.internal.reflect.GeneratedMethodAccessor91.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:343)
    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:294)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:197)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076)
    at java.base/java.lang.Thread.run(Thread.java:834)

2021-02-16 16:10:37,697 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - 2. The exception is :java.lang.IllegalStateException: Command line failed with exit code: 127 Command: bin/phobius/1.01/phobius.pl /home/janvhenkel/my_interproscan/interproscan-5.48-83.0/temp/Notebook-Jan_20210216_160929288_hzhc//jobPhobius/000000000001_000000000005.fasta Error output from binary: Phobius ver 1.01 (c) 2004 Lukas Kall, Anders Krogh, Erik Sonnhammer

Could not read provided fasta sequence at bin/phobius/1.01/phobius.pl line 408.

2021-02-16 16:10:37,697 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:219] ERROR - StepExecution with errors - stepName: stepPhobiusRunBinary 2021-02-16 16:10:37,732 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:25] FATAL - Analysis step 79 : Run Phobius Binary for selected proteins for proteins 1 to 5 has failed irretrievably. Available StackTraces follow. 2021-02-16 16:10:37,732 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:42] FATAL - The JVM will now exit with a non-zero exit status. 2021-02-16 16:10:37,734 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:332] 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:157) [interproscan-5.jar:?] at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:475) [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:157) at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:475) InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details

[JanVHenkel]

Can you please tell me how to make the gray shading to code lines? I would like to write questions and answers in a structured way without you having to guess where something starts or ends. Im really sorry for that

[gsn7]

issue the following command: file bin/phobius/1.01/decodeanhmm |grep 32-bit you will most likely get output with 32-bit highlighted in red then issue the following command: uname -a|grep '_64' if you get output that has _64 highlighted, it might mean you need to replace the phobius binary with a 64 bit binary. go to http://phobius.sbc.su.se/data.html to get a new phobius tar file unzip the phobius tar file you get and copy the file decodeanhmm.64bit to bin/phobius/1.01/decodeanhmm

this should solve the problem. to highlight code you need to click on the symbols <> at the top of the message box and insert all the code in the quotes given ``

[JanVHenkel]

In bin/phobius/1.01/ decodeanhmm and decodeanhmm.64bit were present. I got a new tar file and extracted decodeanhmm.64bit with which i replaced the other one in bin/phobius/1.01/.

As decodeanhmm.64bit was already present i also deleted decodeanhmm in case there could be intereference and tried ./interproscan.sh -i test_all_appl.fasta -f tsv -dp with and without decodeanhmm.

The output was an error as follows:

`(base) janvhenkel@Notebook-Jan:~/my_interproscan/interproscan-5.48-83.0$ ./interproscan.sh -i test_all_appl.fasta -f tsv -dp 18/02/2021 18:22:09:259 Welcome to InterProScan-5.48-83.0 18/02/2021 18:22:09:261 Running InterProScan v5 in STANDALONE mode... on Linux 18/02/2021 18:22:30:380 Loading file /home/janvhenkel/my_interproscan/interproscan-5.48-83.0/test_all_appl.fasta 18/02/2021 18:22:30:385 Running the following analyses: [CDD-3.18,Coils-2.2.1,Gene3D-4.2.0,Hamap-2020_05,MobiDBLite-2.0,PANTHER-15.0,Pfam-33.1,Phobius-1.01,PIRSF-3.10,PRINTS-42.0,ProSitePatterns-2019_11,ProSiteProfiles-2019_11,SFLD-4,SignalP_EUK-4.1,SignalP_GRAM_NEGATIVE-4.1,SignalP_GRAM_POSITIVE-4.1,SMART-7.1,SUPERFAMILY-1.75,TIGRFAM-15.0] Pre-calculated match lookup service DISABLED. Please wait for match calculations to complete... 18/02/2021 18:22:45:837 25% completed 2021-02-18 18:22:45,998 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 127 Command: bin/phobius/1.01/phobius.pl /home/janvhenkel/my_interproscan/interproscan-5.48-83.0/temp/Notebook-Jan_20210218_182215232_cce9//jobPhobius/000000000001_000000000005.fasta Error output from binary: Phobius ver 1.01 (c) 2004 Lukas Kall, Anders Krogh, Erik Sonnhammer

Could not read provided fasta sequence at bin/phobius/1.01/phobius.pl line 408.

2021-02-18 18:22:46,009 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:213] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back. java.lang.IllegalStateException: Command line failed with exit code: 127 Command: bin/phobius/1.01/phobius.pl /home/janvhenkel/my_interproscan/interproscan-5.48-83.0/temp/Notebook-Jan_20210218_182215232_cce9//jobPhobius/000000000001_000000000005.fasta Error output from binary: Phobius ver 1.01 (c) 2004 Lukas Kall, Anders Krogh, Erik Sonnhammer

Could not read provided fasta sequence at bin/phobius/1.01/phobius.pl line 408.

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.48-83.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.GeneratedMethodAccessor92.invoke(Unknown Source) ~[?:?]
    at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
    at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:197) [interproscan-5.jar:?]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at java.lang.Thread.run(Thread.java:834) [?:?]

2021-02-18 18:22:46,027 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:215] ERROR - The exception is : java.lang.IllegalStateException: Command line failed with exit code: 127 Command: bin/phobius/1.01/phobius.pl /home/janvhenkel/my_interproscan/interproscan-5.48-83.0/temp/Notebook-Jan_20210218_182215232_cce9//jobPhobius/000000000001_000000000005.fasta Error output from binary: Phobius ver 1.01 (c) 2004 Lukas Kall, Anders Krogh, Erik Sonnhammer

Could not read provided fasta sequence at bin/phobius/1.01/phobius.pl line 408.

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
    at jdk.internal.reflect.GeneratedMethodAccessor92.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:343)
    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:294)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:197)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076)
    at java.base/java.lang.Thread.run(Thread.java:834)

2021-02-18 18:22:46,028 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - 2. The exception is :java.lang.IllegalStateException: Command line failed with exit code: 127 Command: bin/phobius/1.01/phobius.pl /home/janvhenkel/my_interproscan/interproscan-5.48-83.0/temp/Notebook-Jan_20210218_182215232_cce9//jobPhobius/000000000001_000000000005.fasta Error output from binary: Phobius ver 1.01 (c) 2004 Lukas Kall, Anders Krogh, Erik Sonnhammer

Could not read provided fasta sequence at bin/phobius/1.01/phobius.pl line 408.

2021-02-18 18:22:46,029 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:219] ERROR - StepExecution with errors - stepName: stepPhobiusRunBinary 2021-02-18 18:22:46,062 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:166] WARN - StepInstance 42 is being re-run following a failure. 2021-02-18 18:22:52,185 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 127 Command: bin/phobius/1.01/phobius.pl /home/janvhenkel/my_interproscan/interproscan-5.48-83.0/temp/Notebook-Jan_20210218_182215232_cce9//jobPhobius/000000000001_000000000005.fasta Error output from binary: Phobius ver 1.01 (c) 2004 Lukas Kall, Anders Krogh, Erik Sonnhammer

Could not read provided fasta sequence at bin/phobius/1.01/phobius.pl line 408.

2021-02-18 18:22:52,185 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:213] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back. java.lang.IllegalStateException: Command line failed with exit code: 127 Command: bin/phobius/1.01/phobius.pl /home/janvhenkel/my_interproscan/interproscan-5.48-83.0/temp/Notebook-Jan_20210218_182215232_cce9//jobPhobius/000000000001_000000000005.fasta Error output from binary: Phobius ver 1.01 (c) 2004 Lukas Kall, Anders Krogh, Erik Sonnhammer

Could not read provided fasta sequence at bin/phobius/1.01/phobius.pl line 408.

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.48-83.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.GeneratedMethodAccessor92.invoke(Unknown Source) ~[?:?]
    at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
    at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:197) [interproscan-5.jar:?]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at java.lang.Thread.run(Thread.java:834) [?:?]

2021-02-18 18:22:52,187 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:215] ERROR - The exception is : java.lang.IllegalStateException: Command line failed with exit code: 127 Command: bin/phobius/1.01/phobius.pl /home/janvhenkel/my_interproscan/interproscan-5.48-83.0/temp/Notebook-Jan_20210218_182215232_cce9//jobPhobius/000000000001_000000000005.fasta Error output from binary: Phobius ver 1.01 (c) 2004 Lukas Kall, Anders Krogh, Erik Sonnhammer

Could not read provided fasta sequence at bin/phobius/1.01/phobius.pl line 408.

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
    at jdk.internal.reflect.GeneratedMethodAccessor92.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:343)
    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:294)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:197)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076)
    at java.base/java.lang.Thread.run(Thread.java:834)

2021-02-18 18:22:52,189 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - 2. The exception is :java.lang.IllegalStateException: Command line failed with exit code: 127 Command: bin/phobius/1.01/phobius.pl /home/janvhenkel/my_interproscan/interproscan-5.48-83.0/temp/Notebook-Jan_20210218_182215232_cce9//jobPhobius/000000000001_000000000005.fasta Error output from binary: Phobius ver 1.01 (c) 2004 Lukas Kall, Anders Krogh, Erik Sonnhammer

Could not read provided fasta sequence at bin/phobius/1.01/phobius.pl line 408.

2021-02-18 18:22:52,189 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:219] ERROR - StepExecution with errors - stepName: stepPhobiusRunBinary 2021-02-18 18:22:52,286 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:166] WARN - StepInstance 42 is being re-run following a failure. 2021-02-18 18:23:04,736 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 127 Command: bin/phobius/1.01/phobius.pl /home/janvhenkel/my_interproscan/interproscan-5.48-83.0/temp/Notebook-Jan_20210218_182215232_cce9//jobPhobius/000000000001_000000000005.fasta Error output from binary: Phobius ver 1.01 (c) 2004 Lukas Kall, Anders Krogh, Erik Sonnhammer

Could not read provided fasta sequence at bin/phobius/1.01/phobius.pl line 408.

2021-02-18 18:23:04,736 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:213] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back. java.lang.IllegalStateException: Command line failed with exit code: 127 Command: bin/phobius/1.01/phobius.pl /home/janvhenkel/my_interproscan/interproscan-5.48-83.0/temp/Notebook-Jan_20210218_182215232_cce9//jobPhobius/000000000001_000000000005.fasta Error output from binary: Phobius ver 1.01 (c) 2004 Lukas Kall, Anders Krogh, Erik Sonnhammer

Could not read provided fasta sequence at bin/phobius/1.01/phobius.pl line 408.

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.48-83.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.GeneratedMethodAccessor92.invoke(Unknown Source) ~[?:?]
    at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
    at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:197) [interproscan-5.jar:?]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at java.lang.Thread.run(Thread.java:834) [?:?]

2021-02-18 18:23:04,738 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:215] ERROR - The exception is : java.lang.IllegalStateException: Command line failed with exit code: 127 Command: bin/phobius/1.01/phobius.pl /home/janvhenkel/my_interproscan/interproscan-5.48-83.0/temp/Notebook-Jan_20210218_182215232_cce9//jobPhobius/000000000001_000000000005.fasta Error output from binary: Phobius ver 1.01 (c) 2004 Lukas Kall, Anders Krogh, Erik Sonnhammer

Could not read provided fasta sequence at bin/phobius/1.01/phobius.pl line 408.

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
    at jdk.internal.reflect.GeneratedMethodAccessor92.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:343)
    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:294)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:197)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076)
    at java.base/java.lang.Thread.run(Thread.java:834)

2021-02-18 18:23:04,740 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - 2. The exception is :java.lang.IllegalStateException: Command line failed with exit code: 127 Command: bin/phobius/1.01/phobius.pl /home/janvhenkel/my_interproscan/interproscan-5.48-83.0/temp/Notebook-Jan_20210218_182215232_cce9//jobPhobius/000000000001_000000000005.fasta Error output from binary: Phobius ver 1.01 (c) 2004 Lukas Kall, Anders Krogh, Erik Sonnhammer

Could not read provided fasta sequence at bin/phobius/1.01/phobius.pl line 408.

2021-02-18 18:23:04,740 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:219] ERROR - StepExecution with errors - stepName: stepPhobiusRunBinary 2021-02-18 18:23:04,816 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:25] FATAL - Analysis step 42 : Run Phobius Binary for selected proteins for proteins 1 to 5 has failed irretrievably. Available StackTraces follow. 2021-02-18 18:23:04,817 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:42] FATAL - The JVM will now exit with a non-zero exit status. 2021-02-18 18:23:04,817 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:332] 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:157) [interproscan-5.jar:?] at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:475) [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:157) at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:475) InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details`

[gsn7]

what is the output you get when you issue the command: file bin/phobius/1.01/decodeanhmm |grep 32-bit

[JanVHenkel]

the following: bin/phobius/1.01/decodeanhmm: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), dynamically linked, interpreter /lib/ld-linux.so.2, for GNU/Linux 2.0.30, stripped

[gsn7]

if you have the file decodeanhmm.64bit in bin/phobius/1.01/ folder, then issue the following command: cp bin/phobius/1.01/decodeanhmm.64bit bin/phobius/1.01/decodeanhmm

let me know the output you get now when you issue the command: file bin/phobius/1.01/decodeanhmm |grep 32-bit

[JanVHenkel]

I get no output

[JanVHenkel]

./interproscan.sh -i test_all_appl.fasta -f tsv -dp

is now running without any error. Thank you very much for your help!