/var/spool/slurm/d/job358962/slurm_script: line 22: fg: no job control
Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_2.fq.gz' does not exist, please respecify!

Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/strigg/data/Pgenr/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181011'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz
Supplied filename '/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_2.fq.gz' does not exist, please respecify!

/var/spool/slurm/d/job358962/slurm_script: line 39: fg: no job control
cat: /gscratch/srlab/strigg/analyses/20181011/*PE_report.txt: No such file or directory
cat: /gscratch/srlab/strigg/analyses/20181011/*.deduplication_report.txt: No such file or directory