-----------------------
Start of variable list:
-----------------------
Sample_ID:
F7-MAA100138-3_56_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 19:46:08 EDT 2018
Running on node : scc-ka5
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791174
Current job name : Step_02_F7-MAA100138-3_56_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791174.1.linga

Loading required modules...


List files in scratch directory:

total 88M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 96 root   root      128K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F7-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  43M Oct 12 19:46 SRR6575868_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  46M Oct 12 19:46 SRR6575868_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575868_1.fastq <==
@SRR6575868.1 1/1
TNTTCCTGGTACTTGGTGAGGCCAGCACAGAAGGTGTGCTCGTTCAAGATAGGCTGGACCCCAACGGGACTCGTCAAGTTTNTCTTCTCGGGCACTGTAC
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFFFF
@SRR6575868.2 2/1
GATGTATATAGAGATCCATATGCAGACTCTGTCCCAGAGCCCTGGACAGAATCATGAGAACTTGGTGAGCTTTAGGTCTACTTGGGGTTATTGACTTTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575868.3 3/1
CCCAAAGACTTTGGTTTCCCGGAAGCTGCCCGGCGGGTCATGGGAATAACGCCGCCGCATCGCCAGTCGGCATCGTTTATGGTCGGAACTACGACGGTAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFF
@SRR6575868.4 4/1
CTTAAAGAAGTCCTCAGCAGCATCGAGAGCAATGAGCCGGTCCACAACCAAGAGGTACCTCTCGGAGAGCTCCCAGCTGGCGGGGAAGATAGAGGTCTCT
+
FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6575868.5 5/1
CTTGGATCAGTGGGAAGTGCTCACGCGCGGAGCCCACTGGGCGAACAGCAACGTTATAACGGCCACTCAGTGGTTCGCCACGCGCAGCCCCGGGTTCGTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575868_2.fastq <==
@SRR6575868.1 1/2
NGCTCNACGTGGGGAAAAACCAGCTGGTGGAGATTGAGAAGGTCGTTCTCCACCCCAACCACTCCGTGGTGGATATCGGGCTAATCAAACTCAAGCAGAG
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF
@SRR6575868.2 2/2
TCACACAAGTGCTCAGAGTATCCTCTTTATGGCCAAAGTCAATAACCCCAAGTAGACCTAAAGCTCACCAAGTTCTCATGATTCTGTCCAGGGCTCTGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575868.3 3/2
GTTAAAAAGCTCGTAGTTGGATCTTGGGAGCGGGCGGGCGGTCCGCCGCGAGGCGAGTCACCGCCCGTCCCCGCCCCTTGCCTCTCGGCGCCCCCTCGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFF
@SRR6575868.4 4/2
GCAGGGAAGTGAGGAACCGATGGAGACGAATCTTAGAGGACTTGGGCTTTCAAAGGGAAGCCGACTCTCTGTTGTCAGTGACCAAACTCAGCACCATGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575868.5 5/2
ATATGATGTTGCTCTGCAAGAACCTTTAGGCTAGGCCTTATTAACCTCTCTCTCCTACATTTGCTATGCGTCTCAAGATAAGGATATTATCTCATATGGC
+
FFFFFF--FFFFFFFFFFFFFFFFF-FF-FFFFFFFF-FFF-FFFFFFFFFF-FFFFFF-FFFFF-FFFFFFFFF-FFFFFFF-FF-FFFFFFFFF8-FF

Starting FASTQC command


Processing SRR6575868_1.fastq

Printing command:
fastqc --outdir SRR6575868_1.fastq

Analysis complete for SRR6575868_1.fastq

Processing SRR6575868_2.fastq

Printing command:
fastqc --outdir SRR6575868_2.fastq

Analysis complete for SRR6575868_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 482M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 96 root   root      128K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F7-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 241M Oct 12 19:46 SRR6575868_1.fastq
-rw-r--r--   1 kkarri waxmanlab 241M Oct 12 19:46 SRR6575868_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:51 EDT 2018
0 hours, 0 minutes and 43 seconds elapsed.
==========================================================