-----------------------
Start of variable list:
-----------------------
Sample_ID:
A9-MAA100042-3_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 19:42:19 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790949
Current job name : Step_02_A9-MAA100042-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790949.1.linga

Loading required modules...


List files in scratch directory:

total 67M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 95 root   root       92K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A9-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  33M Oct 12 19:42 SRR6575531_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  35M Oct 12 19:42 SRR6575531_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575531_1.fastq <==
@SRR6575531.1 1/1
GNCTTGGAGAATTCCTTAGTCTTTAAATTCCATTTAATTGTAAATGAAGAGTGCACCGAAATGACTGCGATTGGTGAANAANCAGAAAAGGCTGGCATAT
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FF#FFFFFFFFFFFFFFFFFF
@SRR6575531.2 2/1
ACTGTACCGTATGCGAATCTTTGCACCCAACCATGTGGTGGCCAAGTCCCGCTTCTGGTACTTTGTGTCACAGCTGAAGAAGATGAAGAAGTCATCCGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF
@SRR6575531.3 3/1
AATGTAGATAGACTGGAATTGGACTTCTCAGTGAGACAGGATGGAATGCAGATCACAGAATTTATACTGGGGATGCTGTATGGATAGGAAGGGATGATGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575531.4 4/1
AAATTAGAGTGTTCAAAGCAGGCCCGAACCGCCTGGATACCGCAGCTAGGAATAATGGAATAGGACCGCGGTTCTATTTTGTTGGTTTTCGGAACTGAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575531.5 5/1
GTATCTCTCAGGGAGCAAGGAACTCCAATTCACAAACTGTAACAAGTGGCTAGATTCCATGGGTACATGTTGGTTGAGAAGCATGGCTTTTTCCAGGCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575531_2.fastq <==
@SRR6575531.1 1/2
NCATANAGCTNCANCAGCTGGAAGGTTTTCCCATCCTTTTTGTTAATGAGATGAATCATAATATAATTATCATAGTCTGTCTTAAGAATACTAAATGTAT
+
#FFFF#FFFF#FF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6575531.2 2/2
NCCTCTTGGTGGTGAAGCGTGGCTTGTGCTGGCGCCGCAACACACGGTGGGGCAGTGGGAATTTGATCTTGGAGTCGTGGAACTGCTTGACAGCTGGCCG
+
#FFFFFFFF8FFF8FFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFF--FFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF8F
@SRR6575531.3 3/2
NATGTGAGGAGCATGGAATCCTTAGAGAAAATATCATTGACCTATCCAATGCCAATCGCTGCCTCCAGGCCCGAGAATGAAGAATGGCCTGAGCCTCCAG
+
#FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575531.4 4/2
ACCATACTCCCCCCGGAACCCAAAGACTTTGGTTTCCCGGAAGCTGCCCGGCGGGTCATGGGAATAACGCCGCCGCATCGCCAGTCGGCATCGTTTATGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6575531.5 5/2
GTGTTTGGGGAGTGCTGCTCACTTCTCCTATGACACTCTATCGAGATGGACAGCCCATAAACTTGATGCTGTTGTTGTGTCAACTGACTATGGCTTAGCC
+
FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFF

Starting FASTQC command


Processing SRR6575531_1.fastq

Printing command:
fastqc --outdir SRR6575531_1.fastq

Analysis complete for SRR6575531_1.fastq

Processing SRR6575531_2.fastq

Printing command:
fastqc --outdir SRR6575531_2.fastq

Analysis complete for SRR6575531_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 410M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 95 root   root       92K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:43 A9-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 205M Oct 12 19:42 SRR6575531_1.fastq
-rw-r--r--   1 kkarri waxmanlab 205M Oct 12 19:42 SRR6575531_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:02 EDT 2018
0 hours, 0 minutes and 43 seconds elapsed.
==========================================================