-----------------------
Start of variable list:
-----------------------
Sample_ID:
H12-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 19:41:31 EDT 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790797
Current job name : Step_02_H12-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/8790797.1.linga

Loading required modules...


List files in scratch directory:

total 240M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 41 root   root      112K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 H12-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 121M Oct 12 19:41 SRR6575720_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 119M Oct 12 19:41 SRR6575720_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575720_1.fastq <==
@SRR6575720.1 1/1
TNACAGGGCCTCGAAAGAGTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGG
+
F#FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFF-FFFFFFFFFFF
@SRR6575720.2 2/1
GNGTGTTGATTTTACACCAACAGAAAAGATGAGTCCTGAGTCTTCATGTCTTTTTTTCTCAGGGTAGCCTGAGAAGGTTGTNGTTGTGATGTGTTTAGGC
+
F#FFF-FFFFFFFFFFFFF8FFFFFFFF8FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF#FFFFFFF-FFFFFFFFFF
@SRR6575720.3 3/1
AATACATGCCGACGGGCGCTGACCCCCCTTCCCGGGGGGGGATGCGTGCATTTATCAGATCAAAACCAGCCCGGTGAGCTCCCTCCCGGCTCCGGCCGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6575720.4 4/1
AGATAATTCGGAGCACTCTTCATCTCTTACAGTATGGAATTTAAGAACTAAGGAATTCTCCAAGACATGGATTTGCTCCAGAAAAAGTCTAAAGTTGTCA
+
F8-FFFFFFFFFFFFFFFF8FFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFF-FFFFFFFFFFFF-F-FFF-FFFF-F-F
@SRR6575720.5 5/1
CGGGAAGGAACTTTAATGTAGAAAAGATTAATGGGGAATGGCATACTATTATCCTGGCCTCTGACAAAAGAGAAAAGATAGAAGATAATGGCAACTTTAG
+
FFFFF8FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF

==> SRR6575720_2.fastq <==
@SRR6575720.1 1/2
NCCCGNGGGGGGATGCGTGCATTTATCAGATCAAAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGCCGGGGGTCGGGCGCCGGCGGCTTTGGTGACTCT
+
#FFFF#FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575720.2 2/2
NGCTANAGCGGAGCAACTGAAGACTGTCATGGATGACTTTGCACAGTTCCTGGATACATGTTGCAAGGCTGCTGACAAGGACACCTGCTTCTCGACTGAG
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575720.3 3/2
NGGCCTCGAAAGAGTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF
@SRR6575720.4 4/2
NTGTTTGGGACTGACCCTAGTCTGTGTCCATGCAGAAGAAGCTAGTTCTACGGGAAGGAACTTTAATGTAGAAAAGATTAATGGGGAATGGCATACTATT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF
@SRR6575720.5 5/2
NCCTTTTCGTTAATGAGATGAGCCATAAGAAAGTTATCATAGTCTGTCTTAGGTATAGTAAATGTATTGAATCCATCATACGTCACAGAATATTCACCAG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575720_1.fastq

Printing command:
fastqc --outdir SRR6575720_1.fastq

Analysis complete for SRR6575720_1.fastq

Processing SRR6575720_2.fastq

Printing command:
fastqc --outdir SRR6575720_2.fastq

Analysis complete for SRR6575720_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 1.4G
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 50 root   root      112K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:43 H12-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 699M Oct 12 19:41 SRR6575720_1.fastq
-rw-r--r--   1 kkarri waxmanlab 699M Oct 12 19:41 SRR6575720_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:12 EDT 2018
0 hours, 1 minutes and 41 seconds elapsed.
==========================================================