-----------------------
Start of variable list:
-----------------------
Sample_ID:
E3-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 19:44:31 EDT 2018
Running on node : scc-ka4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791116
Current job name : Step_02_E3-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/8791116.1.linga

Loading required modules...


List files in scratch directory:

total 134M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root       84K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:44 E3-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  67M Oct 12 19:44 SRR6576046_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  68M Oct 12 19:44 SRR6576046_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576046_1.fastq <==
@SRR6576046.1 1/1
GTCCACGAGGGAAATGCCCAGTGCCCTCAGCATCCTTCTCCTTGGCGTGGCTTACTTCAAGGGGCAGTGGGTAACCAAGTTTGACTCGAGAAAGACGACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576046.2 2/1
TTCTGCAACTATGAAGAGAGCAGAGGTAACTACCTAGTGGACGTGGACGGCAACCGCATGTTGGACCTGTATTCTCAGATCTCCTCTGTGCCCATAGGTT
+
FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576046.3 3/1
GTTGGAGAGATGCTTCAGTGTCTCGTTTTCTGATACACACAAGTCCAAATCATTAAACCGGAGCAGAAAAGTATTCCAATCCTCAGCCATTTCTGGGGAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576046.4 4/1
TCATACAAGAACGTGCCCAGGAAGACATCCTTGGCCTCAGCATAGTTCTTGCACACTTCCTGGTCCTCAACAAAATCAGCAGCAATGGCAGGCAGATCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576046.5 5/1
GTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576046_2.fastq <==
@SRR6576046.1 1/2
NTCATGGTCAAGTTCTGGGTCACGGTCAGGGGCAGGAAGAAGATGATGCTCATACTTCCTGTCAAGGGCAGCTGGGCAATCTTGCAGTTGAGATCAGAGT
+
#-FFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF
@SRR6576046.2 2/2
NTCCGGTACCACATGAAGATGGTCTTGAATGCATTCTCATTGGAGCAGGAGCCACAGGCCATGGTGATGAGCTGGGACATGCCCCTGGGCGCCACCGACA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576046.3 3/2
NTCTGGTACAAGATCTTCACAACTGCCAGAGATGCCAACACGAAATATGCTCAAGACTACAATCCTTTCTGGTGTTATAAGGGTGCCATTGGGAAAGTCT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFF-
@SRR6576046.4 4/2
NAATGAAGTGCTCCAGTATGCAGAAGTTTGGAGAGAGAGCTTTTAAAGCATGGGCAGTAGCTCGTCTGAGCCAGACATTCCCCAATGCTGACTTTGCAGA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576046.5 5/2
NAGTACATGGGGGCCGATCGCACGCCCCCCGTGGCGGCGACGACCCATTCGAACGTCTGCCCTATCAACTTTCGATGGTAATCGCCGTGCCTACCATGGT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFF

Starting FASTQC command


Processing SRR6576046_1.fastq

Printing command:
fastqc --outdir SRR6576046_1.fastq

Analysis complete for SRR6576046_1.fastq

Processing SRR6576046_2.fastq

Printing command:
fastqc --outdir SRR6576046_2.fastq

Analysis complete for SRR6576046_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 751M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root       84K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:45 E3-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 376M Oct 12 19:44 SRR6576046_1.fastq
-rw-r--r--    1 kkarri waxmanlab 376M Oct 12 19:44 SRR6576046_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:33 EDT 2018
0 hours, 1 minutes and 2 seconds elapsed.
==========================================================