-----------------------
Start of variable list:
-----------------------
Sample_ID:
E2-MAA100039-3_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 19:44:32 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791109
Current job name : Step_02_E2-MAA100039-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791109.1.linga

Loading required modules...


List files in scratch directory:

total 106M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 86 root   root       92K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E2-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  53M Oct 12 19:44 SRR6576894_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  54M Oct 12 19:44 SRR6576894_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576894_1.fastq <==
@SRR6576894.1 1/1
CNGTGAGACAGGATGGAATGCAGATCACAGAATTTATACTGGGGATGCTGTATGGATAGGAAGGGATGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCA
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576894.2 2/1
CCCGGAAGCTGCCCGGCGGGTCATGGGAATAACGCCGCCGCATCGCCAGTCGGCATCGTTTATGGTCGGAACTACGACGGTATCTGATCGTCTTCGAACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576894.3 3/1
ACCCACTCCTTGCTCTCTTTGGATATTGCCCACCAGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTGGAGGCAGCGATTGGCATTGGATAGGTCAATGA
+
FFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFF8F8FFFFFFFFFFFF-FF-FFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6576894.4 4/1
ATACAGCATCCAGTAAGAAGTTCTGTGATCTGCTTTCCATCGTGTCTTACAGAGAAGTGCAATCCCTGTCTCTCCAGCATGTTACTAGGATAACTCATCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576894.5 5/1
CTCCAGCGCAGGTCTGGCTTTCTCGCCAAGTGTCTTCAGGTGGGTTTTGGCCCTGGTGTGGTACTCGTTCAAGGTAGGATTGCTCTTGAGCTCAGCCAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576894_2.fastq <==
@SRR6576894.1 1/2
NGCATACTATTATCCTGGCCTCTGACAAAAGAGAAAAGATAGAAGATAATGGCAACTTTAGACTTTTTCTGGAGCAAATCCGTGTCTTGGAGAATTCCTT
+
#FFFFFFFFFF-FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FF8FF-FF
@SRR6576894.2 2/2
NAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGTTCCGACCATAAACGATGC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576894.3 3/2
NTAGAAGATAATGGCAACTTTAGACTTTTACTGGAGCAAATCCATGACTTGGAGAATTCCTTAGATCTTAAAGTCCATACTGTAAGAGATGAAGAGTGCT
+
#FF-F-FFFFFFFFFFF--FFF-FF-F-F-FFFFFFFFFFFFFFFF-FF--FFFFFF-F---FF-FFF-FFFFFFF----FFFFFFFFFFFFF-FF-FFF
@SRR6576894.4 4/2
TTGTGCAAGTGTAATCATTTATTGAACAGGAAGAGGAAGAAATTCATGGAGAATTGTCATGGGTATGTCAAAGAGAAATTTAAAGAAAGACTTTGATTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF
@SRR6576894.5 5/2
GCCCAGCGCCTGGCTGAGCTCAAGAGCAATCCTACCTTGAACGAGTACCACACCAGGGCCAAAACCCACCTGAAGACACTTGGCGAGAAAGCCAGACCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576894_1.fastq

Printing command:
fastqc --outdir SRR6576894_1.fastq

Analysis complete for SRR6576894_1.fastq

Processing SRR6576894_2.fastq

Printing command:
fastqc --outdir SRR6576894_2.fastq

Analysis complete for SRR6576894_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 605M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 86 root   root       92K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 E2-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 303M Oct 12 19:44 SRR6576894_1.fastq
-rw-r--r--   1 kkarri waxmanlab 303M Oct 12 19:44 SRR6576894_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:22 EDT 2018
0 hours, 0 minutes and 50 seconds elapsed.
==========================================================