-----------------------
Start of variable list:
-----------------------
Sample_ID:
B8-MAA000377-3_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-yi2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790996
Current job name : Step_02_B8-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790996.1.y

Loading required modules...


List files in scratch directory:

total 56M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 34 root   root      4.0K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B8-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  27M Oct 12 19:42 SRR6576269_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  29M Oct 12 19:42 SRR6576269_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576269_1.fastq <==
@SRR6576269.1 1/1
GGGCAGACGTTCGAATGGGTCGTCGCCGCCACGGGGGGCGTGCGATCGGCCCGAGGTTATCTAGAGTCACCAAAGCCGCCGGCGCCCGACCCCCGGCCGG
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576269.2 2/1
ACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAATATACATTTGCGAAGCAACACCCACAGTTAAAGTACATTTAGTAATTGGATCCCCA
+
FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF8F--F8-F-F-FF--F--FF--FFFF-F---FFF--F--FFFF--FFF-F-F----FF
@SRR6576269.3 3/1
ACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAATAAACATTGGCGCACAAAACCCCAAAGTTAAAGGAATTTTAGGAATTGTAACGCCA
+
FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F88F---8---------F--FF--FF---F-F-FFF---F-FF----FF-----F--FF-
@SRR6576269.4 4/1
CCATAATAATCTCTTACTGCAGTAAATGGCAAACTTTAATCATCCAGAATATCTTCATCCAGATTAATGTCTGTTGTGTCAATATCCTCTAATTCCAAGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576269.5 5/1
ATCTAAGAGTGAGCAACGACGCGCAATCGGGAGAAACAAGCGAGATAGGAATGTCTTACACGCGGGGCAAGACAGTTACTGATACGGGCAGACACAGAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576269_2.fastq <==
@SRR6576269.1 1/2
NCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCTACTTGGATAACTGTGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF88FFFFFFFFF-FF
@SRR6576269.2 2/2
GGTCAAAGTGTTTGGCCCAGGCGTGGAGAGGAGTGGTCTGAAGGCAAATGAGCCTACTCACTTTACAGTGGATTGCACGGAGGCCGGGAAGGTGATGTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFF-FF8F-F
@SRR6576269.3 3/2
GGTCAAAGTGTTTGGCCCAGGCGTGGAGAGGAGTGGTCTGAAGGCAAATGAGCCTACTCACTTTACAGTGGATTGCACGGAGGCCGGGAAGGTGATGTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576269.4 4/2
GCCAAGCAGTACCCTCTTGTCACGCCAAATGAAGAGAGAAATGTTATGGAAGAGGCAAAAGGCTTTCAGCCCTCAAGACCCACAGCCCAGCAGGAACCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576269.5 5/2
TTTTTTGGGGAGGTGGAGAGTCCCGAGTACTTCACTCCTGTCTGTGGTGTCCAAGTGTTCATGCCACGTGCCTCCCGAGTGCACTTTTTTTTTGTGGCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FF--8F

Starting FASTQC command


Processing SRR6576269_1.fastq

Printing command:
fastqc --outdir SRR6576269_1.fastq

Analysis complete for SRR6576269_1.fastq

Processing SRR6576269_2.fastq

Printing command:
fastqc --outdir SRR6576269_2.fastq

Analysis complete for SRR6576269_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 291M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 34 root   root      4.0K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B8-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 146M Oct 12 19:42 SRR6576269_1.fastq
-rw-r--r--   1 kkarri waxmanlab 146M Oct 12 19:42 SRR6576269_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:36 EDT 2018
0 hours, 0 minutes and 17 seconds elapsed.
==========================================================