-----------------------
Start of variable list:
-----------------------
Sample_ID:
N2-MAA000907-3_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 19:41:28 EDT 2018
Running on node : scc-yi3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790875
Current job name : Step_02_N2-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790875.1.y

Loading required modules...


List files in scratch directory:

total 38M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 27 root   root      4.0K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 N2-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  18M Oct 12 19:41 SRR6576641_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  20M Oct 12 19:41 SRR6576641_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576641_1.fastq <==
@SRR6576641.1 1/1
GTGTGTGTGTGTGTGTGTGTGTATGTATGTGTGTGTACAACAGTTAATGAGAAAAGAGGCCATGTATTTGAAATTGGAACATAACAAAGAAGGGTTTAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFF-FFFFFF-
@SRR6576641.2 2/1
AGCAACAACAGGGAAGGAACAGCAACTCAAGGAAATGAGGCTGAGGGGATAAACCCTGTAGGCTTCCTCATTTAAGACTTGAGGGGCTTCAGAGGATCGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576641.3 3/1
GTCCAACTGTAGGTGACTGGTTATCACATCTTCACTGGCCCCTGTGGCCCTGCATGTAGTAGGGGAGGCTTCAGTCAGCCCCTCACTGTGGTCCAAGAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576641.4 4/1
GCTACCAACCCTGGGTCTCATTAGCACCCATCCTGCCTCAAATGCAGGCTGCATTGCTTTCACCCCAGCTCAGCCTCTTTAAGAAGGAACCGCAGTAGTT
+
F8F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFF
@SRR6576641.5 5/1
TATCAACGCAGAGTACATGGGATCTTCCAGGACTCTGATAATCTGAGGTTTGGGGATACTATTATGCCATATAAGGTAGGGTTTTTCCTTTTGTTTTGTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF

==> SRR6576641_2.fastq <==
@SRR6576641.1 1/2
NCGAGATCCTGTGAATGGAACCTGGTCTATTCAGTCACTTTGCCAGAGCCTGAGGGAAAGATGTCCTCAAGGAGATGACATTCTTAGCATCCTGACTGGC
+
#FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576641.2 2/2
NTCTATCCTCTGTGCGGGCTGAGGCCTTCTGGTAGGTGGGATCAGTCTCTGAGGTCACAGTTCTAGCCAAATTCCCAGCAGACACCAGGTGCCTGTTCTC
+
#-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF
@SRR6576641.3 3/2
GCTAGACAGAGGCATTATTTTTAAGATCTTTTAAAAATATGTTGACTTTCGTTTCCCTTCCACACTCACTTTTAAATTGATCTGATGAGGTCCTCAACGT
+
FFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF-FFF-FFFFFFFF-F88
@SRR6576641.4 4/2
TTGCTGTATGGTTTGTGCCCATTCTTGGCGTGGCTATGGCTCTACAGAGGCCATTGTTCCTTGAGGAATATGAGGGGGTGTCTTTGTCCAAAGTGACAAA
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFF
@SRR6576641.5 5/2
GTGTGTGTATGTGTACACACGAACACGTGCTCATAAAGCCAGGTAGTGGTGGTGCTTGCCTTTAATCCTAGCACTTGGTAGGCAGAGGCAAGCAGATCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576641_1.fastq

Printing command:
fastqc --outdir SRR6576641_1.fastq

Analysis complete for SRR6576641_1.fastq

Processing SRR6576641_2.fastq

Printing command:
fastqc --outdir SRR6576641_2.fastq

Analysis complete for SRR6576641_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 196M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 27 root   root      4.0K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 N2-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  98M Oct 12 19:41 SRR6576641_1.fastq
-rw-r--r--   1 kkarri waxmanlab  98M Oct 12 19:41 SRR6576641_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:41 EDT 2018
0 hours, 0 minutes and 13 seconds elapsed.
==========================================================