-----------------------
Start of variable list:
-----------------------
Sample_ID:
A2-MAA100039-3_11_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-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790922
Current job name : Step_02_A2-MAA100039-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790922.1.linga

Loading required modules...


List files in scratch directory:

total 83M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 50 root   root      112K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A2-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  45M Oct 12 19:42 SRR6576787_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  39M Oct 12 19:42 SRR6576787_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576787_1.fastq <==
@SRR6576787.1 1/1
GGCCTGGAGGCAGCGATTGGCATTGGATAGGTCAATGATATTTTCTCTAAGGATTCCATGCTTCTCACATCGTTGTGCAAACCTTTCCTTGATGTCTGAA
+
FF--F8F-FFF-FF8FFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFF-FFF-F-FFFFFFF-FFFF-FFFFFF-FFFFFF-
@SRR6576787.2 2/1
TGGGGGTCCTGTGTGGCCTTTGCAGCTCAGCATGGCTAGGACAGCAGTGGCGCTAAATATCCTGGTGTTGCTGGGCCTGTGCTGGTCCCTGGCTGTTGCC
+
-FFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576787.3 3/1
GCGAGCAGATCTTGACTTGTCCAGGCCACTTTTCACCACTGCCGCACTACTCTCAGCATGCAAAATTCTAAAGATAAAGGTGGATAAAACCAAAATGATA
+
FFFFFF-FFFFFFFFFFFFFF8FFFFFFFFF8FFFFFFFFFF8FFFFFFFFF-FFFFFFFFFFFFFFF-F-F--FF--FFFFFF-FFFFFFFFFFFFFFF
@SRR6576787.4 4/1
GAGCAAGAAAGAGCAGGAGCTGTCCAGCGCTGAGAAACACGAAAGGTGACCATGGCTAAGGAGTGGGGCTACGCCAGCCACAATGGTCCTGATCACTGGC
+
F8FFFFFFFFFFFFFFFFFFFFF8F8FFFFFF8FFFFFFFFFFFFFFFFFFFF-F-F-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFF
@SRR6576787.5 5/1
GGAAGAGGAAGAAATTCATGAAAAATTGTCATGGGTATATCAAAGAGAAATTTAATGAAGTCTTTGATTCTTGTTGAGGTATCCTAGGTAACATCAGGAT
+
FF-FF8FFFFF-FF8FFFFFFFFFFFFFFFF8FFFFFF8FF-FFF-F----FFFF-F---F-F-FF---FF-F--FFFFFF-FFFF-FF--FFF---F--

==> SRR6576787_2.fastq <==
@SRR6576787.1 1/2
CTATGGCCGAGAACCAGATTTGAGTTCAGACATCAAGGAAAGGTTTGCACAACTATGTGAGAAGCATGGAATCCTTAGAGAAAATATCATTGACCTATCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576787.2 2/2
CCTTTAAAGAACAGCATGGTCCCATTGTGATCCATGGTCGCAGCATCAAAGCTCCAGGTATCCAAGCAGTGTTCGGGTACATCTGAATCTGGCTTGGTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576787.3 3/2
GTCTGAGCTTTGGCAGCATTTTCCAAAATCTTCCTTTTCCATTCTTCATAATCCTGTGTCAGATCTTCATCTTTAGGTAGTTTATGAAGGGTTTCTATTA
+
FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-8FFFFFFFF
@SRR6576787.4 4/2
CTTCAGAGCCTCTCCAAAGGTGTTATACTTTGGATTCCAGTGAACCAGGTGAAGCTCAGCAGCGTATTTTACTCCGTCCACGGTGTGCTCAGAGCCGTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF8FFF
@SRR6576787.5 5/2
CTATGATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAACCAGATTTGAGTTCAGAC
+
F8FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFF-8F

Starting FASTQC command


Processing SRR6576787_1.fastq

Printing command:
fastqc --outdir SRR6576787_1.fastq

Analysis complete for SRR6576787_1.fastq

Processing SRR6576787_2.fastq

Printing command:
fastqc --outdir SRR6576787_2.fastq

Analysis complete for SRR6576787_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 419M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 50 root   root      112K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:43 A2-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 210M Oct 12 19:42 SRR6576787_1.fastq
-rw-r--r--   1 kkarri waxmanlab 210M Oct 12 19:42 SRR6576787_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:01 EDT 2018
0 hours, 0 minutes and 42 seconds elapsed.
==========================================================