-----------------------
Start of variable list:
-----------------------
Sample_ID:
C8-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 19:44:28 EDT 2018
Running on node : scc-tk4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791044
Current job name : Step_02_C8-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/8791044.1.linga

Loading required modules...


List files in scratch directory:

total 55M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 38 root   root       52K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C8-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  27M Oct 12 19:44 SRR6576004_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  29M Oct 12 19:44 SRR6576004_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576004_1.fastq <==
@SRR6576004.1 1/1
GGTATAGGCAAAGACAATGAAATGCAGGATCCCTCAACAAGAGCAGGAAAGTGAAACTGTACCAACGGAAGGTTCATACACGTTTTATTTCTTTTTCTGT
+
FFFF-8FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFF-FFFFFF
@SRR6576004.2 2/1
GTTCAAAGCAGGCCTGAGCCGCCTGGATACCGCAGCTAGGAATAATGGAATAGGACCGCGGTTCTATTTTGTTGGTTTTCGGAACTGAGGCCATGATTAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FF-
@SRR6576004.3 3/1
CGTTTATTGTAAGCCGTCAGCATCGGGATATCATCTGCTTCAAGCTCCTCAAGCAGCCGAAGCACTGTTTTTTTCATGTCCCGCATAATCCTCATTTGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576004.4 4/1
GTGTAGGACTCGTCGCATTGGATGACGATGCCTAGTACTGTGCGCCAATTAGGTCGTCATTGCGCCAGCTCGTCAGCGCTGGTCGTCTACCAGCTCGATA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF
@SRR6576004.5 5/1
GTCTGGGGAAGTGGATCTGGGCTAACCTTCTGGGCCTCTTTAGCAGGAACTTGGAGATGAGCTCCTTGCTGAGAGTTTGCTCCAGATGCTGCATCTTCCC
+
FF-FFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF

==> SRR6576004_2.fastq <==
@SRR6576004.1 1/2
NCACAACACATGTGAATCATAAACACAAGAGAAAAGCCAAATCAGCTTTGAAACCCAAGAATGAGCATGTCACCCAATAGTCTCTCAACACTTCCAGTTC
+
#8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF8FF8F
@SRR6576004.2 2/2
GTATCTGATCGTCTTCGAACCTCCGACTTTCGTTCTTGATTAATGAAAACATTCTTGGCAAATGCTTTCGCTCTGGTCCGTCTTGCGCCGGTCCAAGAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FF-F
@SRR6576004.3 3/2
ATTCAGGATCTTCCGACGACATTGATTGCTGCATTCCGCTCAACGCTTGAGGAAGTAAAAGAAGCGGATTTAATTCTGCATTTAATTGATTCTTCAAATG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F8
@SRR6576004.4 4/2
GATTGTCGCAGCCCGGGTCGATTATAACAACGGTGCAATCTCAGCTAAACCGACGCAGTTTTGCTCCTTGGATTCTGAGCCCGGGCATCGCCCCTCGTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576004.5 5/2
GTGACACTCACACGCAGATCCTAGAGGGCCTGCAGTTCAACCTCACACAAACATCGGAGGCTGACATCCACAAGTCCTTCCAACACCTCCGCCAAACCCT
+
FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFF-FFF--FFF-

Starting FASTQC command


Processing SRR6576004_1.fastq

Printing command:
fastqc --outdir SRR6576004_1.fastq

Analysis complete for SRR6576004_1.fastq

Processing SRR6576004_2.fastq

Printing command:
fastqc --outdir SRR6576004_2.fastq

Analysis complete for SRR6576004_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 333M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 38 root   root       52K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C8-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 167M Oct 12 19:44 SRR6576004_1.fastq
-rw-r--r--   1 kkarri waxmanlab 167M Oct 12 19:44 SRR6576004_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:51 EDT 2018
0 hours, 0 minutes and 23 seconds elapsed.
==========================================================