-----------------------
Start of variable list:
-----------------------
Sample_ID:
C1-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 19:44:28 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791018
Current job name : Step_02_C1-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/8791018.1.linga

Loading required modules...


List files in scratch directory:

total 103M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 86 root   root       92K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C1-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  50M Oct 12 19:44 SRR6575775_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  53M Oct 12 19:44 SRR6575775_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575775_1.fastq <==
@SRR6575775.1 1/1
GTGTTTCAACTTCATTCGAGTCCTGGTCTCTTACAATGCTACTCACCTCTATGCCTGTGGGACCTTTGCCTTCAGCCCTGCCTGTACCTTCATTGAACTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575775.2 2/1
GGGCAAAGAGGTGCAGGCGGCACAGGCCCGACTCGGAGCCGACATGGAGGATCTACGCAACCGACTCGGGCAGTACCGCAACGAGGTGCACACCATGCTG
+
FFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575775.3 3/1
GCACCAACCTCTTCATCAAGGTTGATGTTGGTGGAGATAAATGCGTGCACTTGAGGGTGTTTCAACCCCTCCCCCATGAAAACAAGCCTTTGACCCTGTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575775.4 4/1
GATGTGGACGAGTCCATCGCGGGACGCACCACCGATGCGGAGTTCCACACCTTCTTCAATGAGAAGACCTTCGGCCTTGGGGAGGCAGACTGTGGCCTGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575775.5 5/1
ATAGTAGCTGGCACCCCATCCAGTTGTCGCGCCCCATGATTCGACACCAAGATCCCATCCACACCATGTTTAACAGCTTCCTTGGCATCATCACCTCTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF-FFFFFFF-FFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575775_2.fastq <==
@SRR6575775.1 1/2
NCTGTGTGCTTGTGAACAGGGTCAAAGGGGCTTTGGCCCTTCCCGTCCATGACCTTGTCTATCAAGATGGGCAACAGGAGGGAATCTTGGAGTTCAATGA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575775.2 2/2
GGATGTTGTTGCAGGACAGGAGAAGGATACTCATTGATTCTCCTGGGCCACTGGGGTGATGATGGGGTTGGTAGCCACAGAGGCCTGTATCTTCTCCATC
+
FFFFFFFFFFFFFFFFF-FFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF8FF
@SRR6575775.3 3/2
TCACAACAGAAGCTGCTCAACTCCCTTCTCTCCATCACCGAGGGGGGTTTTACTACGTGGTCCCAAACACAGGTGCAAAGGAGCCCCGAATCAGAAGTAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575775.4 4/2
GTCCATGTCTCCCGAAGGTTGCCCCAGCCTGTCACCCGCCCTTTATAACCAGCCCGGAGCAAGCTGGTTACTGTCTGCTTGTCTGGCAAACACACGGGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-
@SRR6575775.5 5/2
TAGCTGATAACATCCAAGCATTTTCTAGATGGAAGCTCTAACCACGGATGCTTCGCAACGTTGCTGATATCGATCTGTCAACTTCTGTTTTAGGACAGAG
+
FFFF--FFFFFF8FFFF-FFF8F8FFFFF-FFFFFFFFFF-FFFFFF-F-FFFFFFFFF---FFFF-FF-FFFFFFFFF-FFF-F-FFFFF8F-FFFFFF

Starting FASTQC command


Processing SRR6575775_1.fastq

Printing command:
fastqc --outdir SRR6575775_1.fastq

Analysis complete for SRR6575775_1.fastq

Processing SRR6575775_2.fastq

Printing command:
fastqc --outdir SRR6575775_2.fastq

Analysis complete for SRR6575775_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 550M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 86 root   root       92K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 C1-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 275M Oct 12 19:44 SRR6575775_1.fastq
-rw-r--r--   1 kkarri waxmanlab 275M Oct 12 19:44 SRR6575775_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:18 EDT 2018
0 hours, 0 minutes and 50 seconds elapsed.
==========================================================