-----------------------
Start of variable list:
-----------------------
Sample_ID:
D6-MAA100140-3_57_F-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-tk1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791087
Current job name : Step_02_D6-MAA100140-3_57_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791087.1.linga

Loading required modules...


List files in scratch directory:

total 122M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 44 root   root       36K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 D6-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  59M Oct 12 19:44 SRR6576026_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  64M Oct 12 19:44 SRR6576026_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576026_1.fastq <==
@SRR6576026.1 1/1
CCCCCCGTGGCGGCGACGACCCATTCGAACGTCTGCCCTATCAACTTTCGATGGTAGTCGCCGTGCCTACCATGGTGACCACGGGTGACGGGGAATCAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576026.2 2/1
GCCCGAAGCGTTTACTTTGAAAAAATTAGAGTGTTCAAAGCAGGCCCGAGCCGCCTGGATACCGCAGCTAGGAATAATGGAATAGGACCGCGGTTCTATT
+
FFFFFFFFFFFFF-FFF8FFFFFFFFFFF8FFFFFFFFFFFF8F-FFFFFF-FFFFFFFFFFFFFFF-FFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576026.3 3/1
GGCTGGGGGACAGGCTGCTGGCTGCAGGTTCAGTGGCTGTCAGAGTTAAAGCGAGATGGGAAACAGGTACATGCACAGGTTGGGAAGGTGTCTAGAGGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576026.4 4/1
ATATTAAGACAGAATAGTCATTTTTCCAAGGCGCAGAGCTTGATGCCCCACATAACCTCCGTAAAATGGTGGTTTGCCCTACACTTTCATTTTCCTTGTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FF-FFF-FFFFFFFFFFFF
@SRR6576026.5 5/1
CTCCAATAGCGTATATTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTTGGATCTTGGGAGCGGGCGGGCGGTCCGCCGCGAGGCGAGTCACCGCCCGTCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576026_2.fastq <==
@SRR6576026.1 1/2
NAATTACAGGGCCTCGAAAGAGTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATG
+
#FFFFFFFFFFFFFFFFF-FFFFFFFF-F--FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576026.2 2/2
NCTAAGGGCAGCACCGACCGGTTATTGCTCAATCTCGGGTGGCTGAACGCCACGTGTCCCGCGAAGAAGTGGGGGGACGCCGACCGCTGGGGGGTCGCGT
+
#-F-FFFF-FF-FF8FFFFFF8-FF-FFFFF-FFFFF--F--FF-FFFFFFF--FF-F-F---F-FFF-F-FFF-FFFF-FF-FF-FF-FFFFF-F-8FF
@SRR6576026.3 3/2
NAACCCACGTTTCTGGCCAAACCCAAAGGTGTTTGACCCCTCTAGATTTGCACCAGATTCTTCTCACCATAGCCATGCTTATCTGCCATTCTCAGGAGGA
+
#F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF8
@SRR6576026.4 4/2
TGGCCCATTAGGTCTCATACCAAAGAGGGCTGGGACACCTCTGAGTGGGAATTCACCAGGACTACAGCCTTAATAACATGTAGGAGAGATGCAGGGCAGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576026.5 5/2
AACTAAGAACGGCCATGCACCACCACCCACGGAATCGAGAAAGAGCTATCAATCAGTCAATCCTGTCCGTGTCCGGGCCGGGTGAGGTTTCCCGTGTTGG
+
-FFFFFF-FFFFF8FF8FFFFFFF-FFFFFFF---FFFFFFFFFFFFF-FFFFF-F-FF--FFF-FFF-FF-FFF-FFFFFFFFF-FFFF--FFFF88FF

Starting FASTQC command


Processing SRR6576026_1.fastq

Printing command:
fastqc --outdir SRR6576026_1.fastq

Analysis complete for SRR6576026_1.fastq

Processing SRR6576026_2.fastq

Printing command:
fastqc --outdir SRR6576026_2.fastq

Analysis complete for SRR6576026_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 668M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 44 root   root       36K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 D6-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 334M Oct 12 19:44 SRR6576026_1.fastq
-rw-r--r--   1 kkarri waxmanlab 334M Oct 12 19:44 SRR6576026_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:06 EDT 2018
0 hours, 0 minutes and 37 seconds elapsed.
==========================================================