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So, I guess the file is corrupted and the issue is with some library that is generating the 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.

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.

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