-----------------------
Start of variable list:
-----------------------
Sample_ID:
K5-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 19:49:49 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791342
Current job name : Step_02_K5-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/8791342.1.linga

Loading required modules...


List files in scratch directory:

total 15M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 79 root   root       92K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:49 K5-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 7.3M Oct 12 19:49 SRR6576512_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 7.7M Oct 12 19:49 SRR6576512_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576512_1.fastq <==
@SRR6576512.1 1/1
TAAATGGCCACAGGAATAATACCATTAGGTGGTTCCCAGAGAAACTCTGAGGAGATACAGGGCCGATGGATCAGGAACCAGGGTGGACTTCCTGGAGGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576512.2 2/1
ACTTTAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAAGGATTTAAAGTGGACTCATTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF
@SRR6576512.3 3/1
GCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGTAACTAGTTAGCATGCCAGAGTCTCGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576512.4 4/1
ACGCAGAGTACATGGGAGCTATTCTTCTAAAATTAGGTAGTTACGGAATAATTCGCATCTCCATTATTCTAGACCCACTAACAAAATATATAGCATACCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFF
@SRR6576512.5 5/1
GTATCAACGCAGAGTACATGGGTACCTGGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAATATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTAC
+
FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576512_2.fastq <==
@SRR6576512.1 1/2
CCTGAACCTCAACCTTGCCAGGGTGGCCAGCTTCTGCGACCACATGTTCAACAGCAAGTAGGTCAGCTCCGGAGGAGTCCTCCTGCGGCTCCAGAGGGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576512.2 2/2
ATTCGAACGTCTGCCCTATCAACTTTCGATGGTAGTCGCCGTGCCTACCATGGTGACCACGGGTGACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576512.3 3/2
GTTATTCCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCTTTGGGTTCCGGGGGGAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFF-FFFFFFF-FFFF8
@SRR6576512.4 4/2
GTAATGAATAATTCTCCTATTAGATTGATTGAAGGGGGTAGAGCTAGATTAGCTAGACTTGCTATCAGTCATCATGTGGCTATAAGTGGGAAGACCATTT
+
FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576512.5 5/2
CTCCAATGGATCCTCGTTAAAGGATTTAAAGTGGACTCATTCCAATTACAGGGCCTCGAAAGAGTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGG
+
FFFFFFFFFFFFFFFFFFF88FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF88FFFF

Starting FASTQC command


Processing SRR6576512_1.fastq

Printing command:
fastqc --outdir SRR6576512_1.fastq

Analysis complete for SRR6576512_1.fastq

Processing SRR6576512_2.fastq

Printing command:
fastqc --outdir SRR6576512_2.fastq

Analysis complete for SRR6576512_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 82M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 79 root   root       92K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:50 K5-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  41M Oct 12 19:49 SRR6576512_1.fastq
-rw-r--r--   1 kkarri waxmanlab  41M Oct 12 19:49 SRR6576512_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:07 EDT 2018
0 hours, 0 minutes and 18 seconds elapsed.
==========================================================