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cougarlj / COMPSRA

COMPSRA: a COMprehensive Platform for Small RNA-Seq data Analysis
https://regepi.bwh.harvard.edu/circurna/
GNU General Public License v3.0
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Error opening file and FileNotFound #16

Open DAE-113 opened 3 years ago

DAE-113 commented 3 years ago

Hello,

I am trying to use the annotation module on its own and getting back 2 errors that I am unable to troubleshoot on my own.

My command is as follows with STARsamples leading to a text file and samples out being the output directory: java -jar $EBROOTCOMPSRA/COMPSRA.jar -ref hg38 -ann -ac 1,2,3,4,5,6 -inf "$STARsamples" -out "$samplesout"

There are 6 samples in the text file and all of them come back with the same two errors. The output folder has the following txt files made but nothing else: COMPSRA_DEG_0_circRNA.txt COMPSRA_DEG_0_miRNA.txt COMPSRA_DEG_0_piRNA.txt COMPSRA_DEG_0_snoRNA.txt COMPSRA_DEG_0_snRNA.txt COMPSRA_DEG_0_tRNA.txt

I get back the following errors:

+++++++++++++++++++++++++++++++++++++++

Thu Apr 15 16:13:28 EDT 2021 16:13:28.990 [pool-2-thread-1] ERROR edu.harvard.channing.compass.core.ann.SAMAnnotator - Error opening file: /gpfs/ysm/project/neugebauer/da498/20210303coilRNAseq/2_pipeline/8_COMPSRA/C2_Aligned/C2_Aligned_UnMapped.bam htsjdk.samtools.util.RuntimeIOException: Error opening file: /gpfs/ysm/project/neugebauer/da498/20210303coilRNAseq/2_pipeline/8_COMPSRA/C2_Aligned/C2_Aligned_UnMapped.bam at htsjdk.samtools.SAMFileWriterFactory.makeBAMWriter(SAMFileWriterFactory.java:246) at htsjdk.samtools.SAMFileWriterFactory.makeBAMWriter(SAMFileWriterFactory.java:215) at edu.harvard.channing.compass.core.ann.SAMAnnotator.Annotate(SAMAnnotator.java:60) at edu.harvard.channing.compass.core.ann.SAMAnnotator.call(SAMAnnotator.java:160) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:834) 16:13:29.061 [pool-2-thread-1] ERROR edu.harvard.channing.compass.core.ann.SAMAnnotator - Error opening file: /gpfs/ysm/project/neugebauer/da498/20210303coilRNAseq/2_pipeline/8_COMPSRA/C3_Aligned/C3_Aligned_UnMapped.bam htsjdk.samtools.util.RuntimeIOException: Error opening file: /gpfs/ysm/project/neugebauer/da498/20210303coilRNAseq/2_pipeline/8_COMPSRA/C3_Aligned/C3_Aligned_UnMapped.bam at htsjdk.samtools.SAMFileWriterFactory.makeBAMWriter(SAMFileWriterFactory.java:246) at htsjdk.samtools.SAMFileWriterFactory.makeBAMWriter(SAMFileWriterFactory.java:215) at edu.harvard.channing.compass.core.ann.SAMAnnotator.Annotate(SAMAnnotator.java:60) at edu.harvard.channing.compass.core.ann.SAMAnnotator.call(SAMAnnotator.java:160) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:834) 16:13:29.116 [pool-2-thread-1] ERROR edu.harvard.channing.compass.core.ann.SAMAnnotator - Error opening file: /gpfs/ysm/project/neugebauer/da498/20210303coilRNAseq/2_pipeline/8_COMPSRA/NT1_Aligned/NT1_Aligned_UnMapped.bam htsjdk.samtools.util.RuntimeIOException: Error opening file: /gpfs/ysm/project/neugebauer/da498/20210303coilRNAseq/2_pipeline/8_COMPSRA/NT1_Aligned/NT1_Aligned_UnMapped.bam at htsjdk.samtools.SAMFileWriterFactory.makeBAMWriter(SAMFileWriterFactory.java:246) at htsjdk.samtools.SAMFileWriterFactory.makeBAMWriter(SAMFileWriterFactory.java:215) at edu.harvard.channing.compass.core.ann.SAMAnnotator.Annotate(SAMAnnotator.java:60) at edu.harvard.channing.compass.core.ann.SAMAnnotator.call(SAMAnnotator.java:160) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:834) 16:13:29.158 [pool-2-thread-1] ERROR edu.harvard.channing.compass.core.ann.SAMAnnotator - Error opening file: /gpfs/ysm/project/neugebauer/da498/20210303coilRNAseq/2_pipeline/8_COMPSRA/NT2_Aligned/NT2_Aligned_UnMapped.bam htsjdk.samtools.util.RuntimeIOException: Error opening file: /gpfs/ysm/project/neugebauer/da498/20210303coilRNAseq/2_pipeline/8_COMPSRA/NT2_Aligned/NT2_Aligned_UnMapped.bam at htsjdk.samtools.SAMFileWriterFactory.makeBAMWriter(SAMFileWriterFactory.java:246) at htsjdk.samtools.SAMFileWriterFactory.makeBAMWriter(SAMFileWriterFactory.java:215) at edu.harvard.channing.compass.core.ann.SAMAnnotator.Annotate(SAMAnnotator.java:60) at edu.harvard.channing.compass.core.ann.SAMAnnotator.call(SAMAnnotator.java:160) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:834) 16:13:29.203 [pool-2-thread-1] ERROR edu.harvard.channing.compass.core.ann.SAMAnnotator - Error opening file: /gpfs/ysm/project/neugebauer/da498/20210303coilRNAseq/2_pipeline/8_COMPSRA/NT3_Aligned/NT3_Aligned_UnMapped.bam htsjdk.samtools.util.RuntimeIOException: Error opening file: /gpfs/ysm/project/neugebauer/da498/20210303coilRNAseq/2_pipeline/8_COMPSRA/NT3_Aligned/NT3_Aligned_UnMapped.bam at htsjdk.samtools.SAMFileWriterFactory.makeBAMWriter(SAMFileWriterFactory.java:246) at htsjdk.samtools.SAMFileWriterFactory.makeBAMWriter(SAMFileWriterFactory.java:215) at edu.harvard.channing.compass.core.ann.SAMAnnotator.Annotate(SAMAnnotator.java:60) at edu.harvard.channing.compass.core.ann.SAMAnnotator.call(SAMAnnotator.java:160) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:834) 16:13:29.204 [pool-2-thread-1] ERROR edu.harvard.channing.compass.core.ann.SAMAnnotator - java.io.FileNotFoundException: /gpfs/ysm/project/neugebauer/da498/20210303coilRNAseq/2_pipeline/1_STAR (Is a directory) htsjdk.samtools.util.RuntimeIOException: java.io.FileNotFoundException: /gpfs/ysm/project/neugebauer/da498/20210303coilRNAseq/2_pipeline/1_STAR (Is a directory) at htsjdk.samtools.FileInputResource$1.make(SamInputResource.java:198) at htsjdk.samtools.FileInputResource$1.make(SamInputResource.java:192) at htsjdk.samtools.util.Lazy.get(Lazy.java:24) at htsjdk.samtools.FileInputResource.asUnbufferedSeekableStream(SamInputResource.java:230) at htsjdk.samtools.FileInputResource.asUnbufferedInputStream(SamInputResource.java:235) at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:282) at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:145) at edu.harvard.channing.compass.core.ann.SAMAnnotator.Annotate(SAMAnnotator.java:59) at edu.harvard.channing.compass.core.ann.SAMAnnotator.call(SAMAnnotator.java:160) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:834) Caused by: java.io.FileNotFoundException: /gpfs/ysm/project/neugebauer/da498/20210303coilRNAseq/2_pipeline/1_STAR (Is a directory) at java.base/java.io.RandomAccessFile.open0(Native Method) at java.base/java.io.RandomAccessFile.open(RandomAccessFile.java:345) at java.base/java.io.RandomAccessFile.(RandomAccessFile.java:259) at java.base/java.io.RandomAccessFile.(RandomAccessFile.java:214) at htsjdk.samtools.seekablestream.SeekableFileStream.(SeekableFileStream.java:47) at htsjdk.samtools.FileInputResource$1.make(SamInputResource.java:196) ... 12 more

Thanks in advance for your help!

cougarlj commented 3 years ago

Dear DAE-113,

It seems that COMPSRA fails to open the bam file listed in the file. Could you run COMPSRA with "-in" and just take one bam file as an example? If it does work, there may be a potential bug for the "-inf" function.

Best Wishes, Jiang Li

DAE-113 commented 3 years ago

Hello,

Thanks for your help! I tried to run only one of the bam files and it continues giving me the same error in opening the file. The directory it is listing is not where I have the original STAR bam file, but instead seems to be a directory/file made by COMPSRA itself?

sagarutturkar commented 3 years ago

I am having the similar issue! I did use the find command to search for "*_UnMapped.bam" files, but could not find any. Below are my commands:


java -jar COMPSRA.jar -ref hg38 -qc -ra AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC \
-rb 4 -rh 20 -rt 20 -rr 20 -rlh 8,17 \
-in /raw_data/BC-1_.fastq \
-out ./BC1/

java -jar COMPSRA.jar -ref hg38 -aln -mt star \
-in /3_COMPSRA/BC1/BC-1_S11_L001_R1_001/BC-1_S11_L001_R1_001_17to76_FitRead.fastq.gz \
/3_COMPSRA/BC1/BC-1_S11_L001_R1_001/BC-1_S11_L001_R1_001_17to76_FitRead/

java -jar COMPSRA.jar -ref hg38 -ann -ac 1,2,3,4,5,6 \
-in /3_COMPSRA/output/BC-1_S11_L001_R1_001_17to76_FitRead/BC-1_S11_L001_R1_001_17to76_FitRead_STAR_Aligned.out.bam \
-out /3_COMPSRA/output/BC-1_S11_L001_R1_001_17to76_FitRead/
cougarlj commented 3 years ago

Are there any bug messages?

On Mon, Jun 14, 2021 at 12:09 PM sutturka @.***> wrote:

I am having the similar issue! I did use the find command to search for "*_UnMapped.bam" files, but could not find any. Below are my commands:

java -jar COMPSRA.jar -ref hg38 -qc -ra AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC \ -rb 4 -rh 20 -rt 20 -rr 20 -rlh 8,17 \ -in /rawdata/BC-1.fastq \ -out ./BC1/

java -jar COMPSRA.jar -ref hg38 -aln -mt star \ -in /3_COMPSRA/BC1/BC-1_S11_L001_R1_001/BC-1_S11_L001_R1_001_17to76_FitRead.fastq.gz \ /3_COMPSRA/BC1/BC-1_S11_L001_R1_001/BC-1_S11_L001_R1_001_17to76_FitRead/

java -jar COMPSRA.jar -ref hg38 -ann -ac 1,2,3,4,5,6 \ -in /3_COMPSRA/output/BC-1_S11_L001_R1_001_17to76_FitRead/BC-1_S11_L001_R1_001_17to76_FitRead_STAR_Aligned.out.bam \ -out /3_COMPSRA/output/BC-1_S11_L001_R1_001_17to76_FitRead/

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