-----------------------
Start of variable list:
-----------------------
Sample_ID:
B1-MAA100040-3_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 19:42:19 EDT 2018
Running on node : scc-tm1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790966
Current job name : Step_02_B1-MAA100040-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790966.1.linga

Loading required modules...


List files in scratch directory:

total 68M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 48 root   root       20K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B1-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  33M Oct 12 19:42 SRR6577016_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  36M Oct 12 19:42 SRR6577016_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6577016_1.fastq <==
@SRR6577016.1 1/1
GGCAAATTACATTCTCTTTAAAGGCAAATGGAAGAAGCCATTCGATCCTGAGAACACTAAGCAAGCTGAGTTCCACGTGGACGAGTCCACCACGGTGAAG
+
FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577016.2 2/1
CCCGTGGTCACCATGGTAGGCACGGAGACTACCATCGAAAGTTGATAGGGCAGACGTTCGAATGGGTCGTCGCCGCCACGGGTGGCGTGCGATCGGCCCG
+
8FFFF--FFFF-FFF-FFF8FFFF88FFFFFFFFFF8FFFFFFFFFFFFF-F-F-FFFF--FF-FFFFFFF-FFFFFF-FFF--F-FFFFFFFFFFFFFF
@SRR6577016.3 3/1
GTATTTATGTTCCTTTTTGGTGGATTTTTAATGACTCTCTTTGGTTTGTTTGTGAGCTTAGTTTTTTTAGGCCAGGCCTTTACAATAATGCTGGTCTACG
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577016.4 4/1
CTGCAGGAGAGCGCGCGCCAGAAGCTGCAGGAGCTGCAAGGGAGACTGTCCCCTGTGGCTGAGGAATTTCGCGACCGCATGCGCACACACGTAGACTCTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577016.5 5/1
CCTCTAGGCGGTCACGGGCCTGGTTGCCCACTTCCTCCAGCCGCCCTCGGATGCGGTCACCAAAAGCCTGGGCGCGATCGCGCAGAGGCTGGGCGGCCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6577016_2.fastq <==
@SRR6577016.1 1/2
NTGTTCCTGTCTCATCGATGGTCAGCACGGCCTTATGCACAGCCTGGCTGAGCTTCAGGGGAGCATTCTCCTCTGTGATTCCGGAGAGGTCAGCCCCACT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFF-
@SRR6577016.2 2/2
NCTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCCGACGGGCTCTGACCCCCCTTCCCGGGGGGGGATGCGTGCATTTATAAGATCAAAACCAACC
+
#-F-FFFFFFFFFFFF8FFFFFFFFFF-FFF-FFFF-F-FFFF-----FFFF-FFFFF-FF-F----FF-FFFFFF--FF-FFF-FFFFFFFFF-FF-F8
@SRR6577016.3 3/2
NTCCACACGTAGACCAGCATTATTGTAAAGGCCTGGCCTAAAAAAACTAAGCTCACAAACAAACCAAAGAGAGTCATTAAAAATCCACCAAAAAGGAACA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577016.4 4/2
GGGGTGGGGAGTGGAAGCGGGCACCTCACTGGGCAGTCAGAGTCTCGCTGGCCTTGTCGATCACACTCTGGACTTGGGTCTTAAGCGTCTCCAGCATGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577016.5 5/2
GTGTGAGTGCCATCCGTGAGCGCCTGGGGCCTCTGGTGGAGCAAGGTCGCCAGCGCACTGCCAACCTAGGCGCTGGGGCCGCCCAGCCTCTGCGCGATCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6577016_1.fastq

Printing command:
fastqc --outdir SRR6577016_1.fastq

Analysis complete for SRR6577016_1.fastq

Processing SRR6577016_2.fastq

Printing command:
fastqc --outdir SRR6577016_2.fastq

Analysis complete for SRR6577016_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 362M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 48 root   root       20K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B1-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 181M Oct 12 19:42 SRR6577016_1.fastq
-rw-r--r--   1 kkarri waxmanlab 181M Oct 12 19:42 SRR6577016_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:42 EDT 2018
0 hours, 0 minutes and 23 seconds elapsed.
==========================================================