-----------------------
Start of variable list:
-----------------------
Sample_ID:
B7-MAA100040-3_11_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 19:42:19 EDT 2018
Running on node : scc-yf3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790993
Current job name : Step_02_B7-MAA100040-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790993.1.y

Loading required modules...


List files in scratch directory:

total 67M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 27 root   root      4.0K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B7-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  32M Oct 12 19:42 SRR6577029_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  35M Oct 12 19:42 SRR6577029_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6577029_1.fastq <==
@SRR6577029.1 1/1
TATCAACGCAGAGTACAGGGCCTATGTTCATTAATCGTTGATTATTCTCAACCAATCACAAAGATATCGGAACCCTCTATCTACTATTCGGAGCCTGAGC
+
FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6577029.2 2/1
TNCTTCTGGTTGGCAGTAGCCTTGGCTGGACGGGCTCGATAGCCCCCTCCACTGATAGGAGGAGGGGCAGGTCTTAGGCTAGGAGGCTCTTCCTTTCTCC
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577029.3 3/1
CTGTAAGAGATGAAGAGTGCTCCGAATTATCTATGGTTGCTGACAAAACAGAAAAGGCTGGTGAATAATCTGTGACGTATGATGGATTCAATACATTTAC
+
F-FFFFFFFFFFFFFFFFFFFFFFFFF8FFFFF8FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF--FFFF-FFFFFFFFFF-FF-FFFFFFFF-FFFF
@SRR6577029.4 4/1
GCCTACACTGACATGAAGGAAGCTGGCTGGAAAGATGGAGACAAATACTTCCATGCTCGGGGGAACTATGATGCTGCCCAAAGGGGTCCCGGGGGAGTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577029.5 5/1
GTACATGGGACACCGCGCTTTGTACCGTCCTCCGGTCCACGCTCGCAGTCTCTCCGCCACCATGCCTATGTTCATCGTGAACACCAATGTTCCCCGCGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6577029_2.fastq <==
@SRR6577029.1 1/2
NTAGGAGAAGGAGAAATGATGGTGGTAGGAGTCAAAATCTTATATTATTAAAACGAGGGAATGCTATATCTGGGGCTCCGATTATTAGTGGGACAAGTCA
+
#FFFF--FFFFFFFFFFFFFFF-FF-F-FFFFFFFFF-FFFFFFFFFFF-F-FF--FFFF-F-FFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577029.2 2/2
NAGGGCAACTGCTCGGAATTTCGGAAACTCTGAAACCATGAGGCATCTATGGCTGCTGCTGCTATTGTGTGTTTTCTCAGTTCAAACTCAAGCTGCCGAT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF
@SRR6577029.3 3/2
GGGTAATCATTTAATGAACAGGAAGAGGAAGAAATTCATGAAAAATTTACATGGGTGTATCAAATAGAAAATTAAAGAAGTCTTTGATACTTGAAGAGGT
+
-FFF-FFFF8F-88FF8FFF8FFF-FFFFFFFF-FFFFFFFFFFF--F-FF-FFFFFFFFFFFF-FF-FF-F--FFFFFFFFFF-FFF-FFFFF-FFFFF
@SRR6577029.4 4/2
GAGGTATACTATGTTGCCCCAGAGAGCATCTTCAGTGTTCCTAGATAGGAAGCCCAGACCCCACCCTCTGGACCCCAACACAGCCTTCTGAACTAATAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF
@SRR6577029.5 5/2
GTCCGGGACCACGTGCACTGCGATGTACTGTGCGGGCTTGCCGGTGGCCTGCGCCAGCTGCTGGGTGAGCTCCGACAGAAACCCCTCTGGCACGGAGGCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF8FF

Starting FASTQC command


Processing SRR6577029_1.fastq

Printing command:
fastqc --outdir SRR6577029_1.fastq

Analysis complete for SRR6577029_1.fastq

Processing SRR6577029_2.fastq

Printing command:
fastqc --outdir SRR6577029_2.fastq

Analysis complete for SRR6577029_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 364M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 27 root   root      4.0K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B7-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 182M Oct 12 19:42 SRR6577029_1.fastq
-rw-r--r--   1 kkarri waxmanlab 182M Oct 12 19:42 SRR6577029_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:36 EDT 2018
0 hours, 0 minutes and 17 seconds elapsed.
==========================================================