interproscan 的使用和遇到的问题

错误一：

2014-10-08 13:09:32,238 [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:193] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution.  All database activity rolled back.

java.lang.IllegalStateException: IOException thrown when attempting to run binary

Caused by: java.io.IOException: Cannot run program "bin/coils/ncoils": error=2, No such file or directory

2014-10-08 13:09:42,510 [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:24] FATAL - Analysis step 3 : Run fingerprintscan Binary for selected proteins for proteins 1 to 5 has failed irretrievably.  Available StackTraces follow.

2014-10-08 13:09:42,510 [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL - The JVM will now exit with a non-zero exit status.

2014-10-08 13:09:42,511 [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:105] ERROR - Exception thrown by StandaloneBlackBoxMaster:

java.lang.IllegalStateException: InterProScan exiting with non-zero status, see logs for further information.

本来以为是java的问题， 以为要把openJDK 换成JRE， 但是问了老师，没那回事，最关键的问题是这句：

Caused by: java.io.IOException: Cannot run program "bin/coils/ncoils": error=2, No such file or directory

说明ncoils没法运行。是ncoils的问题， google后发现：

https://code.google.com/p/interproscan/wiki/CompilingBinaries#BLASTALL

所以要重新搞个ncoils把以前的给替换掉。

步骤：

mkdir tmp
cd tmp

wget ftp://ftp.ebi.ac.uk/pub/software/unix/coils-2.2/ncoils.tar.gz

tar zxvf ncoils.tar.gz

cd coils/

要把coils加到环境变量里：

export COILSDIR=/share/bioinfo/miaochenyong/interproscan-software/tars/interproscan-5.7-48.0/tmp/coils
echo $COILSDIR

这样是暂时的，永久性的需要编辑你的./bash_profile 然后source ~/.bash_profile生效

cd /share/bioinfo/miaochenyong/interproscan-software/tars/interproscan-5.7-48.0/bin/coils

将旧的移除新的加入

mv ncoils ncoils.bak

cp ../../tmp/coils/ncoils-osf ncoils

问题解决！

错误二：

Matches for any sequences that are not represented in the lookup service will be calculated locally.
2014-10-09 09:14:11,069 [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:193] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution.  All database activity rolled back.
java.lang.IllegalArgumentException: You have submitted a protein sequence which contains an asterix (*). This may be from an ORF prediction program. '*' is not a valid IUPAC amino acid character and amino acid sequences which go through our pipeline should not contain it. Please strip out all asterix characters from your sequence and resubmit your search.

原因是序列中有*号， 而interproscan是不允许有这种字符的，所以要删掉， 写了个脚本，执行：

python /share/Public/cmiao/MyScripts/interproscan/rm_star.py your_fasta_file

问题解决

错误三：

[Thu Oct 09 09:56:34] cmiao@apple /share/bioinfo/miaochenyong/interproscan-software/tars/interproscan-5.7-48.0 $ ./run_commands.sh 09/10/2014 09:56:39:511 Welcome to InterProScan-5.7-48.0 09/10/2014 09:56:52:065 Running InterProScan v5 in STANDALONE mode... Loading file /share/bioinfo/miaochenyong/interproscan-software/tars/interproscan-5.7-48.0/myprotein/6-5001--6000removed_star.fasta 09/10/2014 09:57:02:643 Running the following analyses: [jobTIGRFAM-13.0,jobProDom-2006.1,jobSMART-6.2,jobHAMAP-201311.27,jobPrositePatterns-20.97,jobSuperFamily-1.75,jobPRINTS-42.0,jobPanther-9.0,jobGene3d-3.5.0,jobPIRSF-2.84,jobPfamA-27.0,jobPrositeProfiles-20.97,jobCoils-2.2] Available matches will be retrieved from the pre-calculated match lookup service.

Matches for any sequences that are not represented in the lookup service will be calculated locally. 09/10/2014 09:57:29:950 25% completed 09/10/2014 09:57:51:467 51% completed 2014-10-09 09:58:26,440 [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:193] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution.  All database activity rolled back. java.lang.IllegalStateException: IOException thrown when attempting to run binary

Caused by: java.io.IOException: Cannot run program "bin/blast/2.2.6/blastall": error=2, No such file or directory

这次是blastall出问题，

发现在/share/bioinfo/miaochenyong/interproscan-software/tars/interproscan-5.7-48.0/bin/blast下有两个版本的blastall， 经过测试2.2.6版本不能用， 但是2.2.19能用， 直接编辑interproscan.properties 

 将2.2.6版本地址直接改为2.2.19， 然后OK 了。

错误四：

[root@melon interproscan-5.7-48.0]# ./interproscan.sh -t n -i /share/bioinfo/miaochenyong/interproscan-software/tars/interproscan-5.7-48.0/mygenes/253,12601--12650.fasta -b my_genes_results/253,12601--12650
23/10/2015 17:01:54:572 Welcome to InterProScan-5.7-48.0
23/10/2015 17:02:08:731 Running InterProScan v5 in STANDALONE mode...
2015-10-23 17:02:19,592 [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:146] ERROR - Command line failed with exit code: 127
Command: bin/nucleotide/getorf -sf pearson -sequence /share/bioinfo/miaochenyong/interproscan-software/tars/interproscan-5.7-48.0/mygenes/253,12601--12650.fasta -outseq /share/bioinfo/miaochenyong/interproscan-software/tars/interproscan-5.7-48.0/temp/melon_20151023_170219353_cwl4//jobLoadNucleicAcidSequence/orfs.fasta -minsize 50
Error output from binary:
bin/nucleotide/getorf: error while loading shared libraries: libgd.so.2: cannot open shared object file: No such file or directory

InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details

错误原因：“Error output from binary:

bin/nucleotide/getorf: error while loading shared libraries: libgd.so.2: cannot open shared object file: No such file or directory“

发现在/usr/lib64/ 下面没有libgd.so.2

需要安装GD库！！！！

解决办法：

[root@melon interproscan-5.7-48.0]# yum install gd

安装成功后就解决了！

错误五：

2015-10-23 17:20:14,305 [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:146] ERROR - Command line failed w ith exit code: 255
Command: bin/coils/ncoils -c -m data/coils/2.2/new_coil.mat
Error output from binary:
error: environment variable COILSDIR must be set

2015-10-23 17:20:14,308 [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:193] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 255
Command: bin/coils/ncoils -c -m data/coils/2.2/new_coil.mat
Error output from binary:
error: environment variable COILSDIR must be set

错误原因：

”error: environment variable COILSDIR must be set“在apple上装的，在melon上跑，在apple上设置的环境变量并没有在melon上设置。重新设置coil的环境变量

vi /etc/profile.d/soft.sh

添加：export COILSDIR=/share/bioinfo/miaochenyong/interproscan-software/tars/interproscan-5.7-48.0/tmp/coils

source /etc/profile.d/soft.sh

错误六：

cmiao@c01n10 /share/bioinfo/miaochenyong/interproscan-software/tars/interproscan-5.7-48.0
$ ./interproscan.sh -t n -i /share/bioinfo/miaochenyong/interproscan-software/tars/interproscan-5.7-48.0/mygenes/284,14151--14200.fasta -b my_genes_results/284,14151--14200
24/10/2015 10:31:09:448 Welcome to InterProScan-5.7-48.0
Exception in thread "main" org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'htmlWriter' defined in class path resource [spring/jobs/outputWriter/html/htmlWriter-context.xml]: Cannot resolve reference to bean 'freeMarkerConfigHtmlWriter' while setting bean property 'freeMarkerConfig'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'freeMarkerConfigHtmlWriter' defined in class path resource [spring/jobs/outputWriter/html/htmlWriter-context.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [freemarker.template.Configuration]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods

错误原因：

java 版本问题，服务器是1.8，要用1.7

alternatives --config java

选择1.7版本！

错误七：

cmiao@c01n10 /share/bioinfo/miaochenyong/interproscan-software/tars/interproscan-5.7-48.0
$ ./interproscan.sh -t n -i /share/bioinfo/miaochenyong/interproscan-software/tars/interproscan-5.7-48.0/mygenes/284,14151--14200.fasta -b my_genes_results/284,14151--14200
24/10/2015 10:35:30:263 Welcome to InterProScan-5.7-48.0
24/10/2015 10:35:39:334 Running InterProScan v5 in STANDALONE mode...
2015-10-24 10:35:50,111 [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:146] ERROR - Command line failed with exit code: 127
Command: bin/nucleotide/getorf -sf pearson -sequence /share/bioinfo/miaochenyong/interproscan-software/tars/interproscan-5.7-48.0/mygenes/284,14151--14200.fasta -outseq /share/bioinfo/miaochenyong/interproscan-software/tars/interproscan-5.7-48.0/temp/c01n10_20151024_103550061_7ug8//jobLoadNucleicAcidSequence/orfs.fasta -minsize 50
Error output from binary:
bin/nucleotide/getorf: error while loading shared libraries: libpq.so.5: cannot open shared object file: No such file or directory

2015-10-24 10:35:50,116 [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:193] 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/nucleotide/getorf -sf pearson -sequence /share/bioinfo/miaochenyong/interproscan-software/tars/interproscan-5.7-48.0/mygenes/284,14151--14200.fasta -outseq /share/bioinfo/miaochenyong/interproscan-software/tars/interproscan-5.7-48.0/temp/c01n10_20151024_103550061_7ug8//jobLoadNucleicAcidSequence/orfs.fasta -minsize 50
Error output from binary:
bin/nucleotide/getorf: error while loading shared libraries: libpq.so.5: cannot open shared object file: No such file or directory

错误原因：

缺少库文件

解决办法：

yum install postgresql-libs

by freemao

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