-----------------------
Start of variable list:
-----------------------
Sample_ID:
L7-MAA000377-3_9_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 19:46:10 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791281
Current job name : Step_02_L7-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791281.1.linga

Loading required modules...


List files in scratch directory:

total 22M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 92 root   root       92K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 L7-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  11M Oct 12 19:46 SRR6576547_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  11M Oct 12 19:46 SRR6576547_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576547_1.fastq <==
@SRR6576547.1 1/1
GATCAGACTCTCCTCGTTCGCGCAGCTCGCTCGGCTCCTTCCAGCAACCATGTCTGACAAACCCGATATGGCTGAGATCGAGAAATTCGATAAGTCGAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576547.2 2/1
GGTTAGTCCCGTCCTGAGCTTTTCCAAGCCCATGATGGAGGGTTGCTTGTTTGTGACGACATGATGCCTTTCCACCAGAGGGTTGCTTTAGGTGCAGCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF
@SRR6576547.3 3/1
ATTCTACCAGCTGTAATCCTTATCATAATTGCTCTCCCCTCTCTACGCATTCTATATATAATAGACGAAATCAACAACCCCGTATTAACCGTTAAAACCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFF
@SRR6576547.4 4/1
TCCTGGGATATTAAGTCAGCTTGGTGCTGACTGCTTTACGAGCCGGAGCTTGTTAGCTGACCAGTTCCCACGGCAAGTATTGGAGAGTAACGCGCCCCAA
+
---FFFF8FFFF88FFFFFF88FFFFFFF8F8FF8888FFFFF8--FF---F-F-FFFF--F-FFF-FFFF-FF--FF---FFF--FFFFFF-F--F---
@SRR6576547.5 5/1
ATGCTAGTGTTAGGGGTAGAAAGTTTTTTCATAGAAGATGTATAAGTTGATCGTAACGGAAGCGTGGATAATATGCTCGGATCCATAGGAATGTTGATGA
+
FF-FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF--FFFFFF-FFFFFFFFFFFFFFFFFFFF

==> SRR6576547_2.fastq <==
@SRR6576547.1 1/2
NTACAGTGCATATTGGCGGCGCTCGCCTCATTACGATTCGCCAGCTTGCTTCTCTTGTTCAATTGTTTCTTTTGTAGGCAGAGGATTTTTCTCTTGCGTT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFF-F8FFF
@SRR6576547.2 2/2
AATATTTTCACTGTTAACACTAAGAACGACTAGACAGGCAAAATCCTCTATTAAATTTAGCAATAAGTATTGTGAGCCAAGTAACTCCATGGGTGGGATA
+
FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFFF-FFF-F-
@SRR6576547.3 3/2
GAATAACCCTGGTCGGTTTGATGTTACTGTTGCTTGATTTAGTCGGCCTGGGATGGCATCAGTTTTAAGTCCTAGGGAGGGGACTGCTCATGAGTGGAGG
+
FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576547.4 4/2
GAGGTAAGGTCATGGCCAAGAATTGGACTCTGCCGGGAGAACGTCTCCTGCAGCCAGTACCATGGCAGAGAAGGCCTGTTTAGGGTGGGTGATCATGTGG
+
F-FF88FFFF888FFFF88F8F88FF888FFFFF-F--F-----F-F---FFFFFFFFF-F-FF-F-F-F-F-FF-F-F--F-F---FF-F----8--F8
@SRR6576547.5 5/2
ATTAATAAATGGATCCTACTCTCTACAAACACTTATTACAACCCAAGAACACATATGATTACTTCTGCCAGCCTGACCCATAGCCATAATATGATTTATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-

Starting FASTQC command


Processing SRR6576547_1.fastq

Printing command:
fastqc --outdir SRR6576547_1.fastq

Analysis complete for SRR6576547_1.fastq

Processing SRR6576547_2.fastq

Printing command:
fastqc --outdir SRR6576547_2.fastq

Analysis complete for SRR6576547_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 116M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 78 root   root       92K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 L7-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  58M Oct 12 19:46 SRR6576547_1.fastq
-rw-r--r--   1 kkarri waxmanlab  58M Oct 12 19:46 SRR6576547_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:31 EDT 2018
0 hours, 0 minutes and 21 seconds elapsed.
==========================================================