-----------------------
Start of variable list:
-----------------------
Sample_ID:
A7-MAA100138-3_56_F-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 19:42:19 EDT 2018
Running on node : scc-ka4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790944
Current job name : Step_02_A7-MAA100138-3_56_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790944.1.linga

Loading required modules...


List files in scratch directory:

total 92M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 117 root   root       84K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 A7-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  44M Oct 12 19:42 SRR6575735_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  48M Oct 12 19:42 SRR6575735_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575735_1.fastq <==
@SRR6575735.1 1/1
TNCCAACTAAGAGACCACCTGTCCTCCGAGCAGGAGTCAATACAGTCACCACCTTGGTGGAGAACAAGAAGGCTCAGCTGGNGGTGATTGCCCATGACGT
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFFFF
@SRR6575735.2 2/1
TNGCTCCTCTATTTGGCTGGAAAACAAAGTTTTCCTCCATTTCCTCAGGGTCTCTGGTTGTAAGCTGGCTTCCACCTGCTGNATCCTGCCTTGGTCAGGG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFFF-
@SRR6575735.3 3/1
AAGATGATGTTCATGAGCTCTGCGACCGCATTCCAGAGGATAACCAACAAGGTTTTTGCCAACCCAGAAGACTGCGCTGGCTTTGGCAAGGGAGAGAATG
+
FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6575735.4 4/1
ACCTAAGACAGACTATGATAACTTCCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAACCAGAT
+
FFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF-FF8F-F8FFFFFF-FFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575735.5 5/1
ATGATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAACCAGATTTGAGTTCAGACAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575735_2.fastq <==
@SRR6575735.1 1/2
NACTTNGGACCCAGGACGTTGCCTCCCCAGTGGCGACGGATCTCGTCATATCTGTCATTATAATTGGTCCTAATAGCTTCCACCAGCTTAGCCAGAGCAC
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF
@SRR6575735.2 2/2
NTGCCNTGTTTATTGAAAAGGACCTGCAGATCCTGGCAGAATTCCATGAGAAGACAAGGGCTCTGTACCAGACTGAGGCCTTCACAGCAGACTTCCAGCA
+
#FF-F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF
@SRR6575735.3 3/2
NAAAGTAACTCCATAGCCAACAAAAAATGCCAAGCCCCTGTTTGGCTGAGGAAGGGGAGTCAAGTAAGCAATGGTGTGGTAGATCCGAGCACCTACAAAG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6575735.4 4/2
NGTAACATGTGGATAGACTGGAATTGGACTTCTCAGTGAGACAGGATGGAATGCAGATCACAGAATTTATACTGGGGATGCTGTATGGATAGGAAGGGAT
+
#FFFFFFFFFFFFFFFFF-F8FFFFFFFFFFFFFFF--FFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF8FF88FFFF
@SRR6575735.5 5/2
NATGTGGATAGACTGGAATTGGACTTCTCAGTGAGACAGGATGGAATGCAGATCACAGAATTTATACTGGGGATGCTGTATGGATAGGAAGGGATGATGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF

Starting FASTQC command


Processing SRR6575735_1.fastq

Printing command:
fastqc --outdir SRR6575735_1.fastq

Analysis complete for SRR6575735_1.fastq

Processing SRR6575735_2.fastq

Printing command:
fastqc --outdir SRR6575735_2.fastq

Analysis complete for SRR6575735_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 506M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 117 root   root       84K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:43 A7-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 253M Oct 12 19:42 SRR6575735_1.fastq
-rw-r--r--    1 kkarri waxmanlab 253M Oct 12 19:42 SRR6575735_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:05 EDT 2018
0 hours, 0 minutes and 46 seconds elapsed.
==========================================================