I am trying to run salmon and it keeps giving me 2 java exceptions:
java.io.EOFException
at java.util.zip.GZIPInputStream.readUByte(GZIPInputStream.java:268)
at java.util.zip.GZIPInputStream.readUShort(GZIPInputStream.java:258)
at java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:164)
at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:79)
at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:91)
at uk.ac.babraham.FastQC.Utilities.MultiMemberGZIPInputStream.<init>(MultiMemberGZIPInputStream.java:37)
and
java.lang.ArrayIndexOutOfBoundsException: -1
at uk.ac.babraham.FastQC.Modules.SequenceLengthDistribution.calculateDistribution(SequenceLengthDistribution.java:100)
at uk.ac.babraham.FastQC.Modules.SequenceLengthDistribution.raisesError(SequenceLengthDistribution.java:184)
at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:336)
at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:155)
at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:110)
at java.lang.Thread.run(Thread.java:745)
at uk.ac.babraham.FastQC.Sequence.FastQFile.<init>(FastQFile.java:80)
at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:106)
at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62)
at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:129)
at uk.ac.babraham.FastQC.Analysis.OfflineRunner.<init>(OfflineRunner.java:102)
at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:316)
I installed `salmon` using `Anaconda`s' `conda install -c bioconda salmon` and all other necessary packages in the same way. I thought that it could be a problem with `fastqc`, so I uninstalled it and then installed it manually (through the fastqc`.zip` file), but the output remained the same.
I am using `Java8`:
java -version
openjdk version "1.8.0_92"
OpenJDK Runtime Environment (Zulu 8.15.0.1-linux64) (build 1.8.0_92-b15)
OpenJDK 64-Bit Server VM (Zulu 8.15.0.1-linux64) (build 25.92-b15, mixed mode)
I am running the script on a cluster with `SLURM`. Locally on my laptop the script is running without any issues. I am really stuck and do not know what to try, so any suggestions would be greatly appreciated.
`Update`
Another issue that I just found is the following (the last command that `salmon` is trying to execute):
Exception : [Failed to read 8 bytes from input stream! Read 0]
salmon quant was invoked improperly.
Then I searched online for the issue and found the following thread:
https://github.com/COMBINE-lab/salmon/issues/129
However, updating `salmon` to the newest `0.9.1` version did not solve the issue.
`Edit`
The command I am running is the following one:
python "$path/salmon_rna_seq.py" -L 'IU' -E "$path/jyvo_experiment-
metadata.yaml" -T 'gencode_mouse_m13' -C "$path/salmon_rna_seq.yaml" -I
"$path_to_fastq/$name-lec_1_r1.fq.gz" "$path_to_fastq/$name-
lec_1_r2.fq.gz" -O "$path/res/$name-lec_1" -S "$name-lec_1" -P '6' -X 'True'
The command is run by `Pypiper`: https://github.com/epigen/pypiper
Inside of `salmon_rna_seq.py` I am also running commands to treat the data, the `salmon` part looks the following way:
def salmon(self):
cmd = "salmon quant -i " + self.indexed_transcriptome
cmd += " -l " + self.lib_type
if self.trim:
cmd += " -1 " + self.sample_files['r1']['fastq']['trimmed_paired']
cmd += " -2 " + self.sample_files['r2']['fastq']['trimmed_paired']
else:
cmd += " -1 " + self.sample_files['r1']['fastq']['chastity']
cmd += " -2 " + self.sample_files['r2']['fastq']['chastity']
cmd += " -o " + self.sample_dirs['salmon']['base']
cmd += " --numBootstraps=30"
self.pipe_manager.run(cmd, self.sample_files['salmon'])
Commands that the `Pypiper` runs are the following ones (`_commands.sh` `Pypiper` file):
zcat -c $PATH/res/old-lec_1/fastq/merged/old-lec_1_r1.fq.gz | grep -A 3
'^@.*[^:]*:N:[^:]*:' | grep -v '^\-\-$' | gzip -c > $PATH/res/old-lec_1/fastq
/chastity/old-lec_1_r1.fq.gz
zcat -c $PATH/res/old-lec_1/fastq/merged/old-lec_1_r2.fq.gz | grep -A 3
'^@.*[^:]*:N:[^:]*:' | grep -v '^\-\-$' | gzip -c > $PATH/res/old-lec_1/fastq
/chastity/old-lec_1_r2.fq.gz
java -jar $HOME/anaconda2/share/trimmomatic-0.36-5
/trimmomatic.jar PE -threads 6 -phred33 $PATH/res/old-lec_1/fastq/chastity/old-
lec_1_r1.fq.gz $PATH/res/old-lec_1/fastq/chastity/old-lec_1_r2.fq.gz $PATH/res/old-
lec_1/fastq/trimmed/old-lec_1_r1.fq.gz $PATH/res/old-lec_1/fastq/trimmed/unpaired
/old-lec_1_r1.fq.gz $PATH/res/old-lec_1/fastq/trimmed/old-lec_1_r2.fq.gz $PATH/res/old-
lec_1/fastq/trimmed/unpaired/old-lec_1_r2.fq.gz ILLUMINACLIP:$HOME/anaconda2/share/trimmomatic-0.36-5/adapters
/Small_List_Of_Adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15
MINLEN:36
fastqc $PATH/res/old-lec_1/fastq/merged/old-lec_1_r1.fq.gz --outdir $PATH/res/old-
lec_1/fastqc/merged
fastqc $PATH/res/old-lec_1/fastq/chastity/old-lec_1_r1.fq.gz --outdir $PATH/res/old-
lec_1/fastqc/chastity
fastqc $PATH/res/old-lec_1/fastq/merged/old-lec_1_r2.fq.gz --outdir $PATH/res/old-
lec_1/fastqc/merged
fastqc $PATH/res/old-lec_1/fastq/chastity/old-lec_1_r2.fq.gz --outdir $PATH/res/old-
lec_1/fastqc/chastity
fastqc $PATH/res/old-lec_1/fastq/trimmed/old-lec_1_r1.fq.gz --outdir $PATH/res/old-
lec_1/fastqc/trimmed
fastqc $PATH/res/old-lec_1/fastq/trimmed/old-lec_1_r2.fq.gz --outdir $PATH/res/old-
lec_1/fastqc/trimmed
salmon quant -i $HOME/Genomes/mouse/salmon
/gencode.vM13.transcripts.fa.sidx -l IU -1 $PATH/res/old-lec_1/fastq/trimmed
/old-lec_1_r1.fq.gz -2 $PATH/res/old-lec_1/fastq/trimmed/old-
lec_1_r2.fq.gz -o $PATH/res/old-lec_1/quantification --numBootstraps=30
`Edit`
After running manually `gzip -t` on a file:
-bash-4.2$ gzip -t old-lec_1_r1.fq.gz
gzip: old-lec_1_r1.fq.gz: unexpected end of file
So, I guess the file is corrupted and the issue is with some library that is generating the file. However, reinstalling manually other libraries do not help.