-----------------------
Start of variable list:
-----------------------
Sample_ID:
C9-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 19:44:28 EDT 2018
Running on node : scc-kb6
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791048
Current job name : Step_02_C9-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/8791048.1.linga

Loading required modules...


List files in scratch directory:

total 46M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 89 root   root       84K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C9-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  23M Oct 12 19:44 SRR6575584_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  23M Oct 12 19:44 SRR6575584_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575584_1.fastq <==
@SRR6575584.1 1/1
CNCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCTTTGCAACCATACTCCCCCCGGAACCCAAAGACTTTGGATNCCCGGAAGCTGCCCGGCG
+
8#F8FFFFFFFFF-8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--F-FFFFFF-F#FFFFFFFFFFFFFFFFFF
@SRR6575584.2 2/1
ATGCCGACTGGCGATGCGGCGGCGTTATTCCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCTTTGGGTTCCGGGGGGAGTATGGTTGCAAAGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF
@SRR6575584.3 3/1
AAAAGGAACCGGCCTATGAGCAAGTGCAGATATGGACTGAGGGGGTGGGTGTGGCCTGAAGCTTACAAAGGAGCCGCTGTCAGAACAGAAACAGCAGGTT
+
FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF88FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575584.4 4/1
GAGTCAGGGGAAACACCCTCTTCCTACTTACACTTGTCTCGCCCACCCCCCATTCTCTCCTTGGTTTCTTGGCCCTTTACTGTGGCTGTACTTCAGATCA
+
FF--FFFFFFFFFFFFFFFFFFFF8FFFFFFFFF8FFFF8F-FFFFFF-FF--F---FFF--FFFFF-FFFF-FFFFFFFFFFFFF-FF--FFF-FFFFF
@SRR6575584.5 5/1
CCCTGGATTCAGTCATTTGAAGACTGAGACCAAGATTGGAAGCATGGCCGACCTCAGGCAGCTCATGGACAATGAGGTGTTGATGGCCTTTACCTCCTAT
+
FFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575584_2.fastq <==
@SRR6575584.1 1/2
NATTANAGTTGCTGCAGTTAAAAAGCTCGTAGTTGGATCTTGGGAGCGGGCGGGCGGTCCGCCGCGAGGCGAGTCACCGCCCGTCCCCGCCCCTTGCCTC
+
#8FFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFF8FF-FFFFFFFFFFF-FFFFF
@SRR6575584.2 2/2
NGTTTCCCGTGTTGGGTCAAATTAAGCCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCTTTGCAACCATACTCCCCCCG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575584.3 3/2
NTGTGAGTTGATGCCGGTTCTCAAGCCGCAGAGCCTGGCTCTCAGAAGCCACGTTAGCGTCTCTCTCTCCTGCTGATCGCTCGACACAGCACCTTTTCTA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575584.4 4/2
TCTCAGGACCATGTGCAGGTACAGCAGCTGTGAGGCAAAAGGCCAGATCAAAGTTGTGGCTGAGGGGACTAGCTCCAAGGGCCTTTAAATCACTGTTCCT
+
FF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFF-FFFFF-FFFFF-FFFFFFF8FFFFFFF-
@SRR6575584.5 5/2
GGTGGGCTCTGCGCACGCGTTCCACCTTCTCGTCAGTGCGAACAAACTTCTTGGCATTCTCTCCCTTGCCAAAGCCAGCGCAGTCTTCTGGGTTGGCAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575584_1.fastq

Printing command:
fastqc --outdir SRR6575584_1.fastq

Analysis complete for SRR6575584_1.fastq

Processing SRR6575584_2.fastq

Printing command:
fastqc --outdir SRR6575584_2.fastq

Analysis complete for SRR6575584_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 266M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 89 root   root       84K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 C9-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 133M Oct 12 19:44 SRR6575584_1.fastq
-rw-r--r--   1 kkarri waxmanlab 133M Oct 12 19:44 SRR6575584_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:01 EDT 2018
0 hours, 0 minutes and 33 seconds elapsed.
==========================================================