-----------------------
Start of variable list:
-----------------------
Sample_ID:
B7-MAA100041-3_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 19:42:19 EDT 2018
Running on node : scc-yf3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790994
Current job name : Step_02_B7-MAA100041-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790994.1.y

Loading required modules...


List files in scratch directory:

total 59M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 27 root   root      4.0K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B7-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  29M Oct 12 19:42 SRR6575344_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  31M Oct 12 19:42 SRR6575344_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575344_1.fastq <==
@SRR6575344.1 1/1
CNTCTGGGTCGCGGTAGGGAAGCGCTGTAGCCTGGCTGTGCGAGAGACGGGGAGAGCCCAGCGCCACAGCGACCTGGAGAAGGATGGCGGCCACCGGGAC
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575344.2 2/1
TCCATACAGCATCCCCAGTATAAATTCTGTGATCTGCATTCCATCCTGTCTCACTGAGAAGTCCAATTCCAGTCTATCCACATGTTACCTAGGATACCTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575344.3 3/1
GTGAGACAGGATGGAATGCAGATCACAGAATTTATACTGGGGATGCTGTATGGATAGGAAGGGATGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCAAC
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575344.4 4/1
GACTCAAGCTATGATGAGAAGAGATACACCATGGGTGACGCTCCCGACTTTGACAGAAGCCAGTGGCTGAATGAGAAGTTCAAGCTGGGCCTGGACTTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF
@SRR6575344.5 5/1
GTCACGATCCCGACCATATCCATCTCTATCACCGTAGCCTCTTGATGGATAGTCATCACGGGAACTGGAATGACTGTAATCACGGTAAGTATAATCTCTT
+
FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFF8-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFF-F-FFFFFF--FF-FFFFFF-FFF

==> SRR6575344_2.fastq <==
@SRR6575344.1 1/2
NCTCCNTCCGCTCTTGGTGGAAAAACTGGCAGTTATCTGGAACTAGCAGGACATCACTTACAAATTCACCCACAAGACACTTGAATGGTATAACAATGTG
+
#FFFF#FFFF8FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF8-FFFFFFFFFFFFFF-FFFF
@SRR6575344.2 2/2
NTCATTTATTGAACAGGAAGAGGAAGAAATTCATGAAAAATTGTCATGGGTATATCAAAGAGAAATTTAAAGAAGTCTTTGATTCTTGATGAGGTATCCT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575344.3 3/2
ATGATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAACCAGATTTGAGTTCAGACAT
+
FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575344.4 4/2
CAGGATCCCCAGTGTGGACAGGTCCTCCTAGTGAGTGCCCGTGTAGCAAGGGCCTACTTGTTACTCCAGTGGACCATCTTTGAAAATATAGGTGTTGCGA
+
FFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFF-FFFFFFFFFFF--FFFFFFFF-FF--FFFFFFF
@SRR6575344.5 5/2
GTATGGACGAATAGTGGAAATACTTTTGATGAAAGACCGGGAAACCAACAAATCAAGAGGAATTGATTATGTTACATTCGAAAGCCCAGCAGAAGCTAAA
+
-FFF-FFF-F8FFFFF8FFFFFF8--FFFFFF-FFFF-FF-F-FFFFFFFFF-FFFFFFFF---F--F-FF-FFF-FFFFFFF-F-FF--F8F--F8FFF

Starting FASTQC command


Processing SRR6575344_1.fastq

Printing command:
fastqc --outdir SRR6575344_1.fastq

Analysis complete for SRR6575344_1.fastq

Processing SRR6575344_2.fastq

Printing command:
fastqc --outdir SRR6575344_2.fastq

Analysis complete for SRR6575344_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 315M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 27 root   root      4.0K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B7-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 158M Oct 12 19:42 SRR6575344_1.fastq
-rw-r--r--   1 kkarri waxmanlab 158M Oct 12 19:42 SRR6575344_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:36 EDT 2018
0 hours, 0 minutes and 17 seconds elapsed.
==========================================================