-----------------------
Start of variable list:
-----------------------
Sample_ID:
D4-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 19:41:27 EDT 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790753
Current job name : Step_02_D4-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/8790753.1.linga

Loading required modules...


List files in scratch directory:

total 35M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 41 root   root      112K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 D4-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  17M Oct 12 19:41 SRR6576228_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  18M Oct 12 19:41 SRR6576228_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576228_1.fastq <==
@SRR6576228.1 1/1
TTCGAGGTCTCGTAGTAGAGATCGTATTTATTCTAGAGATTATCGTCGAGATTACAGGAATAATAGAGGAATGAGACGACCTTATGGGTACAGAGGAAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576228.2 2/1
CTAGTGAGCTGGATCTGCTGAAGGCAGTGGACCAGTGGAGCACAGAAACCATTGCCTCACACGAGGATATAGAGCGCCTGGTGGAACAGGTCCGCTTCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576228.3 3/1
GTACTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTAACAATAAATGAGTAAATTACTCCAAATGCAGGGCACAAATTCCAATATATTTAAAAT
+
FFFFF-FF-FF-FF8FF8FFF8F8FFFFF8FFFFFF888F-F8--F-FF-----F--FFF--F--F------F---F---F-----FF---FFFF-F-F-
@SRR6576228.4 4/1
ATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAAGGATTTAAAGTGGACTCATTCCAATTAC
+
FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FF
@SRR6576228.5 5/1
TCTTCAAGACTCGTGAGATTGCAGTTTCCGCACCTCTCCTCACAGTAAGCGATCTTAATGGCTTCTTCAACATATGGGAATGTGAGGAAGGAGTAAGGCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF

==> SRR6576228_2.fastq <==
@SRR6576228.1 1/2
GGACTATATCGACTCGACCCATTTCCAACAGAGCCAGATCCAGACCTCTCAGGACTGTGCTGAATGGAATGTGAATGCTGAGAAGGGGTATTTTTGGCAG
+
FF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFF--FFFF-F-F
@SRR6576228.2 2/2
GCGTATGACCACACGGAAGCTGCTAAAGGCCCCTGAGGCACAGGGAAAGAGGGAGGGAGTCTTGGAACTATTGGTGTCCAGGGCAGTGGGACGAGGGGCC
+
FFFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF--FF8FFFF
@SRR6576228.3 3/2
GACCTAGTAGTGTCAGATGACCCAACTTCAGTTGAACACTGTGAGAACAACAGAACATGTGAAATTCAAAGCAAAGCAGGTTCTGAAGTAGAAAACCTTC
+
8FFF--F-FFFFFFF-8FFFFFF8-FFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFF--FF--FFFFFFFFFFFFFFFFF-FFFF--FFFFFFF--F
@SRR6576228.4 4/2
CCCCGTGGCGGCGACGACCCATTCGAACGTCTGCCCTATCAACTTTCGATGGTAGTCGCCGTGCCTACCATGGTGACCACGGGTGACGGGGAATTAGGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFF
@SRR6576228.5 5/2
CTCTTACATTGTTGTTAACCATCAAGGATCTCCTTCCCAATTAAAACACTCACATCTTAAAAAGCAGGTGTCAGAACACATCGCAGTGTACAGACAAGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFF-FF

Starting FASTQC command


Processing SRR6576228_1.fastq

Printing command:
fastqc --outdir SRR6576228_1.fastq

Analysis complete for SRR6576228_1.fastq

Processing SRR6576228_2.fastq

Printing command:
fastqc --outdir SRR6576228_2.fastq

Analysis complete for SRR6576228_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 175M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 41 root   root      112K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 D4-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  88M Oct 12 19:41 SRR6576228_1.fastq
-rw-r--r--   1 kkarri waxmanlab  88M Oct 12 19:41 SRR6576228_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:55 EDT 2018
0 hours, 0 minutes and 28 seconds elapsed.
==========================================================