-----------------------
Start of variable list:
-----------------------
Sample_ID:
M7-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 19:41:28 EDT 2018
Running on node : scc-yf4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790864
Current job name : Step_02_M7-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/8790864.1.y

Loading required modules...


List files in scratch directory:

total 38M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 34 root   root      4.0K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 M7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  19M Oct 12 19:41 SRR6576606_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  20M Oct 12 19:41 SRR6576606_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576606_1.fastq <==
@SRR6576606.1 1/1
CCACGAAGGGTCCTAAAAGAATATTTGGTACTGTTCTCTTTGTCTCGAAAGTGCTCGAGGAACCTAAGAATGTTTCCTGTGAAACCCGAGACTTTAAGAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576606.2 2/1
GCCCCGGAGTGGTACATAGGAGATCAAAATCCAATGCTAAACTCAGAGGGCAAAGTGACAGTGGTTGCTCTTCTTCAAGCCAGCTGATACTTGTGTCTTC
+
FFF8FFFFFF-FFF8F-8FFFFFFFFFFFFF8FFFF8FFFF-FFFF-F--FFFF-FFFFFFFF-FFFFFF-FFFFFFF-FF--FF-FFFFFFFFFFFFFF
@SRR6576606.3 3/1
TGCTACAAATGAAAACAATTGAATTACAGACCACCTCTGCTGTCATAAAGATTAGAAGACATGTTAAGTTTAAAACTGAATACTCAGGCTACCAATCCTC
+
F-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576606.4 4/1
CAATAATTCATGCCATCTTTTGTAGGGTGGTAAATCAAGATTTATGGTGTGCCACGGAACTGGTCCTCTATAGGTTGGTCCAGAAGGAGGATACGTTGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6576606.5 5/1
GTGTAATTACAGAAGGTGCACTGGAATCAGCAGCGAGGGTGCATGCTGCTCTTGCATAGGGCCTGAGTTCCCAGCCCAGGGCATATTGTCCGGCAGCTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF

==> SRR6576606_2.fastq <==
@SRR6576606.1 1/2
CTATGGGTCAGGTTAAAATTAATGTTGACACTTCTTTTCCTTAGTTGGTTTTCAGCTGTGAGAGTAAAGTTATACATTTCCTGTGAGCCTTCAGTGATTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-8FFFFFFFFFFFFF8F
@SRR6576606.2 2/2
ACATATGGGAATGTGAGGAATGAGTAAGGCAAAACAAGGTGATACACAAGACGGCCACATCTGTCATAGATGAGGAAGTCATCTTTGTTTCCATTTAAGA
+
F--F-FF-FFFFFFFFF-FF88FF-FFFFFFFF-FFFF-FFFFFFFFFF-FFF--FFFFF-FFF-FFFFFF--FFFF-F-FF-F8F-FF---FFF8F-F8
@SRR6576606.3 3/2
AATTAGGGGACACATGGTAAGAAAAAGTCCATCTAGTAGGGGACTACAGAGAAATGGGCTCGGTTTTTAAGGGTTCTGTTAATGTCACAATTTGAAACGC
+
FFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFF-FFF8FFFF
@SRR6576606.4 4/2
AACGCAGAGTACATGGGGAGCTGCTGCTAGAGTCCCTCGGAGCGGCGCTTGCAGCTGGGAAGATGCGGGGCCAAAGTCTTCTCACCTGGGTCCTAGCCGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576606.5 5/2
CTTTTCCTCTCCCTTTTTTATTTTGGAAAGTGTGTGTGTGCATGTGTGAGCTCCCATGTGTGTGTCTGTGCAAGCACACACACATACACATACACACATG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576606_1.fastq

Printing command:
fastqc --outdir SRR6576606_1.fastq

Analysis complete for SRR6576606_1.fastq

Processing SRR6576606_2.fastq

Printing command:
fastqc --outdir SRR6576606_2.fastq

Analysis complete for SRR6576606_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 196M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 34 root   root      4.0K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 M7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  98M Oct 12 19:41 SRR6576606_1.fastq
-rw-r--r--   1 kkarri waxmanlab  98M Oct 12 19:41 SRR6576606_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:40 EDT 2018
0 hours, 0 minutes and 12 seconds elapsed.
==========================================================