-----------------------
Start of variable list:
-----------------------
Sample_ID:
F11-MAA000377-3_9_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 19:44:29 EDT 2018
Running on node : scc-wb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791139
Current job name : Step_02_F11-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791139.1.w-long

Loading required modules...


List files in scratch directory:

total 60M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 27 root   root       36K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F11-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  30M Oct 12 19:44 SRR6575703_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  30M Oct 12 19:44 SRR6575703_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575703_1.fastq <==
@SRR6575703.1 1/1
TNCTCCGAGAGTGCAATCAACTATGAAATTATAATCATAGATGATGGAAGCCCAGACGGGACAAGAGAAGTTGCTGAACAACTGGCAGAGATCTATGGGC
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF
@SRR6575703.2 2/1
GTTTTCGGAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGGTGAAATTCTTGGACCGGCGCAAGACGGACCAGAGC
+
F-FFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575703.3 3/1
GGTTGGAGCGGAGACCAGTCACGCGGCCCAGGAAAGGGAAGCGGTCCACCTTTAGGGCCTGTGCCCGAGAGATGAGGTATGGGAGGTCAAAGTTCTGAAT
+
-F-FFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFF-F-
@SRR6575703.4 4/1
GTCCCTTACAACAGGAAACACTATCGTGATAACTTTGGAGGAGACTACAATGAGCTGTTGCTGAAATCAGAGCAGGAGCAGACGCTGTTGCAGCTGGTGG
+
F-FFFFFFFFFFFFFFFFFFFF8F8FFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575703.5 5/1
TATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTATATTTTGTACAAGGCCAGGATAATAGTTTGCCATTACCCAATTATATTTTCTAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFF-F-FFF--F-----F-F-FF--FF-F-FF--FFF---FFFF-F-F---FFF--F--

==> SRR6575703_2.fastq <==
@SRR6575703.1 1/2
NTCCAGGTCTCAGCAGAATTTGAGTTATAAAATTGGCCCCACGGCTGATTATCTTTCTTTTCAAATCCCATCCATAAACACCCCCATTCCCCTTGTATCG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575703.2 2/2
GCCCCGGACATCTAAGGGCATCACAGACCTGTTATTGCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTAAGAAGTTGGGGGACGCCGACCGCTCG
+
FFFFFFFFFFFF8FFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFF-FFFFF-FFFFFFFFFFF-F-FFFFF
@SRR6575703.3 3/2
TTGCACCCCTGCGTGTGCTTAGCTTCGACATCGAGTGTGCTGGCCGAAAAGGCATCTTCCCTGAGCCTGAGCGTGACCCCGTGATCCAGATCTGTTCTCT
+
FFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FF-FFFFFF8F-8FF
@SRR6575703.4 4/2
CATGATTATATCTCCATTTGGTCATGAGCGTGTCAATGTCCAGAAGTGAGGTCAGCAGCTGGAAAGGGACCTGGAATCGAGGCTCCTCCCTGTAAAAATA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6575703.5 5/2
CATGGGAATCCTATTCCCTACCAAAATGAAGATGCTGCTGCTGCTGTGTTTGGGACTGACCCTAGTCTGTGTCCATGCAGAAGAAGCTAGTTCTACGGGA
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFF-FFFFF8FFFF8FFFF

Starting FASTQC command


Processing SRR6575703_1.fastq

Printing command:
fastqc --outdir SRR6575703_1.fastq

Analysis complete for SRR6575703_1.fastq

Processing SRR6575703_2.fastq

Printing command:
fastqc --outdir SRR6575703_2.fastq

Analysis complete for SRR6575703_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 290M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 27 root   root       36K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F11-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 145M Oct 12 19:44 SRR6575703_1.fastq
-rw-r--r--   1 kkarri waxmanlab 145M Oct 12 19:44 SRR6575703_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:47 EDT 2018
0 hours, 0 minutes and 18 seconds elapsed.
==========================================================