-----------------------
Start of variable list:
-----------------------
Sample_ID:
B6-MAA100138-3_56_F-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-wg1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790988
Current job name : Step_02_B6-MAA100138-3_56_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790988.1.w

Loading required modules...


List files in scratch directory:

total 49M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 24 root   root       68K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B6-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  24M Oct 12 19:42 SRR6575760_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  25M Oct 12 19:42 SRR6575760_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575760_1.fastq <==
@SRR6575760.1 1/1
GGAAAAGGGAAGGTAGAAGAGCTGAAGGCACTCGTGGAAGAGCTTGAAGCTGATCTCCTCATCTTTAATGATGAACTGTCGCCAAGTCAGCTGAAGTCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575760.2 2/1
TACTAGTGCTACTGCTGCTGTTGGCCAGCTCCCCATTAGCTCTGGGGATCCCCATGTATTCCATCATTACTCCCAATGTCCTACGGCTGGAGAGCGAAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575760.3 3/1
CTTCCAGAAACTTCTCCACCAGCTTCAGGTCATTGTTGACAAAGAGGCCATTGCCTGTGCTCAGCTGCAGCTCACTGTCTGGTCTGTTGAGGGTTTGGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF--FFFFFFFFFFFFF-F
@SRR6575760.4 4/1
TGCTTGATGTGCATCATTGCAGCATGCTGTCCAGCTGGGTGCTGCTGATGGATTACGCAGGCAACACCACTGCTGTCTTCCTCCTGCCCGATGATGGGAA
+
-8FFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575760.5 5/1
GTCGTAGTTCCGACCATAAACGATGCCGACTGGCGATGCGGCGGCGTTATTCCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCTTTGGGTTCCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575760_2.fastq <==
@SRR6575760.1 1/2
NTTCTCGCCCGCTTTGCAAAAATATCTAATATCAATTGCGTGCGGTCAATCATCTTCACTTCAATTGCTGTTGCCAATGACTTCAGCTGACTTGGCGACA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575760.2 2/2
GTCTTCTCACTGGTCAGCACTTGCCTCTTTAGGAAGTCTTGCACAGTGACTGTGACTGGGATGTCACCCTGAGCATCGTGGGCCTCCAGTACGATGGTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575760.3 3/2
CAGTCCAACACTTCCAACATCTTCTTCTCCCCAGTGAGCATTGCCACAGCCTTTGCTATGCTCTCCCTAGGGAGCAAGGGTGACACTCACACGCAGATCC
+
FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575760.4 4/2
GCCTTGCTGAGCTTCAGGGGAGCATTCTCCTCTGTGATTCCGGAGAGGTCAGCCCCATTGTTGAAGATCCGGGTGATGCCCAGTGGACTCATGAGTGTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFF
@SRR6575760.5 5/2
ACTAAGAACGGCCATGCACCACCACCCACGGAATCGAGAAAGAGCTATCAATCTGTCAATCCTGTCCGTGTCCGGGCCGGGTGAGGTTTCCCGTGTTGTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575760_1.fastq

Printing command:
fastqc --outdir SRR6575760_1.fastq

Analysis complete for SRR6575760_1.fastq

Processing SRR6575760_2.fastq

Printing command:
fastqc --outdir SRR6575760_2.fastq

Analysis complete for SRR6575760_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 284M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 24 root   root       68K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B6-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 142M Oct 12 19:42 SRR6575760_1.fastq
-rw-r--r--   1 kkarri waxmanlab 142M Oct 12 19:42 SRR6575760_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:36 EDT 2018
0 hours, 0 minutes and 17 seconds elapsed.
==========================================================