-----------------------
Start of variable list:
-----------------------
Sample_ID:
M15-MAA000377-3_9_M-1-1
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/SRR
OUTPUT_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Oct 12 19:49:50 EDT 2018
Running on node : scc-tl1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791386
Current job name : Step_02_M15-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791386.1.linga

Loading required modules...


List files in scratch directory:

total 21M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 35 root   root       20K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:49 M15-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 9.9M Oct 12 19:49 SRR6576691_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  11M Oct 12 19:49 SRR6576691_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576691_1.fastq <==
@SRR6576691.1 1/1
ACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGGGAAAGGGTTTATATGTAAAGCCCGGGCGGTACAGGGAAACAAATTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-8FFFFF------F--FFFF-F------F--FF--F---F------F---F--FF-F
@SRR6576691.2 2/1
TCTTTAGCCTTTGCTTTTTCCAGCTTGGCAATTCGAGCCACAGACTTAGGACCCAGGACGTTGCCTCCCCAGTGGCGACGGATCTCGTCATATCTGTCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576691.3 3/1
GCTTATTGCTCTGATACCTTTTAAATGCTACTTTTAATATCTTTTTCAAAATCTGAAGGAAAGAGTTTACCTTGATCTGCAAGACATCAAGTGGAACAGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFF8FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFF-
@SRR6576691.4 4/1
GTCTAGGACTGTGTACGGCTGTCGAGCATCTGTTATGACTTTAGGAAAGCTGGAGGGCAGGAAACCATGGGGAGTAGTCTATTTCTGTGGTGTGTTTCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576691.5 5/1
ACTTATACTAAATAACTCTATAACCATCAACTCAATCTCACTTCTATGAAATAAAACTCCAGCAATACTAACTATAATCTCACTGATATTACTATCCCTA
+
FFFFFFFFFFFFFFFFF8FFF8FF8FFFFFFFFFFFFFFFF88FFFFFFFF-FFFF--FFFFFFF-FF-FFFFF-FFFFF-FFFFFFFFFFF-FFF-FFF

==> SRR6576691_2.fastq <==
@SRR6576691.1 1/2
NGAGATGGGGTATCCACTGGGTACTGGGGATCGCAGTCCTGTCTATATGGTAAGTGCCTCACCAAAGAGTAAAGAAGGGAAGCCCCAGGCCCTTGGCAGT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576691.2 2/2
NCATTAACCAGTTCACCCAGGCCCTGGACAGGCAGACAGCTACTCAGCTGCTTAAGCTTGCCCACAAGTACAGGCCAGAGACAAAGCAAGAGAAGAAGCA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFF
@SRR6576691.3 3/2
ATGCTATGTTATTACCATATTTTAAGTAGCAAGTTTTCAGATACTTGGTGCAGTGGAGTGATGTAATAAATGTGTATGCATTGATAATTGGTCACACGCT
+
FFFF8F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-8F
@SRR6576691.4 4/2
ACATATGCTGTTTTGTAACTGACTCAAGAGATAGCTGTAACATGTGCCACTCAATAATCCCAATAAAGTCTCTGCTTGCTGATACAGTGAAAACCTGCTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFF
@SRR6576691.5 5/2
GCTTATGATAGCTAGGGTGGAAAATATTAGGTTGGGTTTAGTTTTTGTTTGGTGAGTTATTATTTTTGAGTTATTGTTGGTTGGAAATATTGTTAGTGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF-FFF-FF-FFFFFF-FFFFFFFFFFFFFFFFFF-FFFFF-FF-FFFFFFFFFFFFFFFFFFF-F

Starting FASTQC command


Processing SRR6576691_1.fastq

Printing command:
fastqc --outdir SRR6576691_1.fastq

Analysis complete for SRR6576691_1.fastq

Processing SRR6576691_2.fastq

Printing command:
fastqc --outdir SRR6576691_2.fastq

Analysis complete for SRR6576691_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 106M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 35 root   root       20K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:50 M15-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  53M Oct 12 19:49 SRR6576691_1.fastq
-rw-r--r--   1 kkarri waxmanlab  53M Oct 12 19:49 SRR6576691_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:02 EDT 2018
0 hours, 0 minutes and 12 seconds elapsed.
==========================================================