-----------------------
Start of variable list:
-----------------------
Sample_ID:
P5-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 19:42:18 EDT 2018
Running on node : scc-tk1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790906
Current job name : Step_02_P5-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/8790906.1.linga

Loading required modules...


List files in scratch directory:

total 10M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 50 root   root       36K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 P5-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 4.8M Oct 12 19:42 SRR6576745_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 5.2M Oct 12 19:42 SRR6576745_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576745_1.fastq <==
@SRR6576745.1 1/1
TGACAGACGTCCTGGATGGGGGGCTGGAGGGGGGGTGTTCATCACCCATTGTAAGGAAAACAAAGCACAAAGCCACTCAAACAAAGTGGCTGCAGGGAGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576745.2 2/1
AGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCC
+
FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FF
@SRR6576745.3 3/1
ATATACTACCTTAATGCATCTGCTAACTGCCAGATCACAGAATAAATTGCAATCTTTAAAAGTAACATGCATAGGAATGGATTCTGAGATGTTCCTGCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576745.4 4/1
GACTGAGGTTGGGGAAATGAACTCGGGACCAGCATCCCTCTTGATGCGCGACCCTGGGGAAGTGGCACATCCTCACTGTGCTGTCCCCAACCCTGAGTAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576745.5 5/1
CTTGTGTGTCCTCCATTGGACCACCTTCTGATTCTGTTTTGTTTTTGATTTGTCTGGTTTCAGGTCTGGTTTTGGTCCCAAGAAGTTGACTGATTATCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFF--FF-FFF

==> SRR6576745_2.fastq <==
@SRR6576745.1 1/2
CACACACACACACATCTACACGCTGACAAGAAACGAATGAATAGCAAATAAAGGACATCCACAAATCCTGGGGAGCGGTGACTTCAGTGAGCCCTCAGGA
+
FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF
@SRR6576745.2 2/2
CTATTGGAGCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAAGGATTTAAAGTGGACTCATTCCAATTACAGGGCCT
+
FFFFFFFFFFFF8FFFFFFFFFFF-FFFFF-FFF-F-FF-FFFFFFFFFFFFFFFFFFFFFFFF-FFF-FF-F-FFF-F8FFFFFFFFFFF-FFFFFF-F
@SRR6576745.3 3/2
CACCAGTGGTACATCACTAAAGACAAGGGTTTCCTTTCCCCTTCGTTAATTCTCCTGTAACCATAGCCTTAGTCAGCCAGTAAATTGGATATGCAATAGC
+
-FFF-F-FFFFFFFFFFFFF8FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576745.4 4/2
CCCCCTCTACTGCGCTGATTAATGACTTAGGCAGGGTTTCTCTTTTAGTTATTGGCATAATTTGCGAACAGAGTGAACTTCAGTATCCGTCACCCGCTAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576745.5 5/2
GTCCAAGTCCGAACACAAAGAGACACAAAAGACACACACAGAAACCGTTTTTCAGGCAACCACTATAGAATCACAGTACCACAGAAATGACAAACACAAA
+
FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F

Starting FASTQC command


Processing SRR6576745_1.fastq

Printing command:
fastqc --outdir SRR6576745_1.fastq

Analysis complete for SRR6576745_1.fastq

Processing SRR6576745_2.fastq

Printing command:
fastqc --outdir SRR6576745_2.fastq

Analysis complete for SRR6576745_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 52M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 50 root   root       36K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 P5-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  26M Oct 12 19:42 SRR6576745_1.fastq
-rw-r--r--   1 kkarri waxmanlab  26M Oct 12 19:42 SRR6576745_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:31 EDT 2018
0 hours, 0 minutes and 13 seconds elapsed.
==========================================================