-----------------------
Start of variable list:
-----------------------
Sample_ID:
D1-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 19:44:31 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791064
Current job name : Step_02_D1-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/8791064.1.linga

Loading required modules...


List files in scratch directory:

total 58M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 94 root   root      180K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 D1-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  28M Oct 12 19:44 SRR6575594_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  30M Oct 12 19:44 SRR6575594_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575594_1.fastq <==
@SRR6575594.1 1/1
CCCCAAATACAATATTAATGGGAAAAAGGCAGAAGGGATCCCTGAGTTCTATGATTATGATGTGGCCCTAGTCAAGCTCAAGAACAAGCTCAAGTATGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575594.2 2/1
CCATTATTCCTAGCTGCGGTATCCAGGCGGCTCGGGCCTGCTTTGAACACTCTAATTTTTTCAAAGTAAACGCTTCGGGCCCCGCGGGACACTCAGCTAA
+
FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-
@SRR6575594.3 3/1
CAGTGAGACAGGATGGAATGCAGATCACAGAATTTATACTGGGGATGCTGTATGGATAGGAAGGGATGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575594.4 4/1
ACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAATTTGAATTTTAAAAATTTTTTTTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF-8-FFFFFFFFFFFFFFFFFFFFFFFFFF-FF----------F---F-----F-F---F
@SRR6575594.5 5/1
ATGCAGAAGAAGCTAGTTCTACGGGAAGGAACTTTAATGTAGAAAAGATTAATGGGGAATGGCATACTATTATCCTGGCCTCTGACAAAAGAGAAAAGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575594_2.fastq <==
@SRR6575594.1 1/2
NCATAGGGATCCACCCCTCCTGTGCAGAGGAACCGTGGAGTGACCACCTCAGAGGCATCTTTGACCTTCTCATAGCCTTGGGCCTTTGTAGCATCTCTCT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFF8
@SRR6575594.2 2/2
NATCAAAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGCCGGGGGTCGGGCGCCGGCGGCTTTGGTGACTATAGATAACCTCGGGCCGATCGCACGCCCC
+
#8-FFFFFFFF-8FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFF-F--F-FFFFFF8FFF-FFFF-FFFF-FFFFFF
@SRR6575594.3 3/2
GTGACGTATGATGGATTCAATACATTTACTATACCTAAGACAGACTATGATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF
@SRR6575594.4 4/2
CACCAGGACTCCAGGATCAGTCCTTCCTATCCATACAGCATCCAGTAAGAAGTTCTGTGATCTGCTTTCCATCGTGTCTTACAGAGAAGTGCAATCCCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6575594.5 5/2
TGTGGATAGACTGGAATTGAACGTCTCAGTGAGACAGGATGGAATGCAGATCACAGAATTTATACTGGGGATGCTGTATGGATAGGAAGGGATGATGGTG
+
FFFFFFF-FFFFFFFF8FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFF-FFFFFFF-FFFF

Starting FASTQC command


Processing SRR6575594_1.fastq

Printing command:
fastqc --outdir SRR6575594_1.fastq

Analysis complete for SRR6575594_1.fastq

Processing SRR6575594_2.fastq

Printing command:
fastqc --outdir SRR6575594_2.fastq

Analysis complete for SRR6575594_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 350M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 94 root   root      180K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 D1-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 175M Oct 12 19:44 SRR6575594_1.fastq
-rw-r--r--   1 kkarri waxmanlab 175M Oct 12 19:44 SRR6575594_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:11 EDT 2018
0 hours, 0 minutes and 40 seconds elapsed.
==========================================================