-----------------------
Start of variable list:
-----------------------
Sample_ID:
G9-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-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791215
Current job name : Step_02_G9-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/8791215.1.linga

Loading required modules...


List files in scratch directory:

total 79M
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 G9-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  38M Oct 12 19:46 SRR6575899_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  41M Oct 12 19:46 SRR6575899_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575899_1.fastq <==
@SRR6575899.1 1/1
CNTGATGGCCTGGTCTGGCTTCTTCGGCCTGGCCATCTCCTCATCACTGGCACTGACGTCCAAGGCTTTGGTTTGAAAGAAGGACTCAGCTTTGGGACGC
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575899.2 2/1
CTTTTAGGAGATGACCAAATTTACAATGTTATCGTAACTGCCCATGCTTTTGTTATAATTTTCTTCATAGTAATACCAATAATAATTGGAGGCTTTGGAA
+
FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575899.3 3/1
GTCGCCCTGGTCATCCTCGAACACGACCTCCAGCGGCTTGCCCAGCACGCCGCCCGCGGCATTGATCTCCGCGACCGCGAGCTCCACGCCCTGCTTGAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575899.4 4/1
CTCTAGATAACCTCGGGCCGATCGCACGTCCCCCGTGGCGGCGACGACCCATTCGAACGTCTGCCCTATCAACTTTCGATGGTAGTCGCCGTGCCTACCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6575899.5 5/1
TCTTGGTATACGGACAACTGATGGACCCACGTTGCGAGTCCAGTAAATCAGGACGGGGATAATTGCGCGGTTTTGACTGCGGAAGGAAGCCAAGGCCCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575899_2.fastq <==
@SRR6575899.1 1/2
NCATGNAAGCAGTGCTGCGCAAGGCTGGAGGTGCAGTCTCGGGAGAGGAAAAACAGTTCTTGGAGGTCTGGGAGAAGAACCGCAAGCTCAAGAGTTTCAA
+
#8FF-#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF8FFF
@SRR6575899.2 2/2
GGTGGTAGGAGTCAAAAACTTATATTATTTATTCGTGGGAATGCTATATCTGGGGCTCCGATTATTAGTGGGACAAGTCAGTTTCCAAAGCCTCCAATTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575899.3 3/2
GTGCTCAACCTGGGCCACAAGATCGCGGACGGCGCGCCGGCCGAGGTCATGAACACGCCGGCAGTCATCGAGGCCTACCTGGGCGAACGCGTGCCCGAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-F-F
@SRR6575899.4 4/2
TGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCTGATTCCCCGTCACCCGTGGTCACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575899.5 5/2
GAATAGGTACCAAGAAAAAAACGAACCTTTGGGTTCCAGAGCTGTACGGTCGCACTGAACTCGGATAGGTCTCGGTAAAACGAAATATAGGCTTACGGTA
+
F8-F-FFFFFFF8F8FFFFFFFFFFF-F-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFF-F-F-FFF8FFFF-FF-FFFFF-FFFFF-

Starting FASTQC command


Processing SRR6575899_1.fastq

Printing command:
fastqc --outdir SRR6575899_1.fastq

Analysis complete for SRR6575899_1.fastq

Processing SRR6575899_2.fastq

Printing command:
fastqc --outdir SRR6575899_2.fastq

Analysis complete for SRR6575899_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 456M
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 G9-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 228M Oct 12 19:46 SRR6575899_1.fastq
-rw-r--r--   1 kkarri waxmanlab 228M Oct 12 19:46 SRR6575899_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:51 EDT 2018
0 hours, 0 minutes and 43 seconds elapsed.
==========================================================