-----------------------
Start of variable list:
-----------------------
Sample_ID:
E4-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 19:44:32 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791119
Current job name : Step_02_E4-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/8791119.1.linga

Loading required modules...


List files in scratch directory:

total 99M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 86 root   root       92K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E4-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  48M Oct 12 19:44 SRR6575835_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  52M Oct 12 19:44 SRR6575835_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575835_1.fastq <==
@SRR6575835.1 1/1
TNCCATGCTCCTCGCATAGTTTTGCAAACTTTTCCTTGATGTCTAAACTCAAATCTGGTTCTCGGCCATAGAGCCTGTCTCNTATACACATCTCCGAGCC
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF#FFFFFFFFFFFFFFFFFF
@SRR6575835.2 2/1
GNGCAGGTATCTCTGAAGCTGATGGTGCAGCAGCCCAGACATCAGCAGATGGCTCCCAGACTCAGAACGTGGAGTCCCGGANTATAATTCGGGGCAAGAG
+
F#FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF8FFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFFFFFFF-FFF-F#F-FFF--FFFFFFFFF-F
@SRR6575835.3 3/1
GAGTGAGAAAGATCGAATGGAGCTACTAGAAATAGCAAAAGCCAACGCAGCAAAAGCTCTGGGAACAGCCAACTTCGACTTGCCAGCAAGTCTCCGAGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF
@SRR6575835.4 4/1
TTATTAGGGATTTTATTATGGTTAAGCCTCTAGGAACGAGGGCAAAAAGCCCATCAAGCCTCCTCAGATATCATAGTGAACCACGGGCTCAGGCTCTTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6575835.5 5/1
GTCTGTGTCCATGCAGAAGAAGCTAGTTCTACGGGAAGGAACTTTAATGTAGAAAAGATTAATGGGGAATGGCATACTATTATCCTGGCCTCTGACAAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-

==> SRR6575835_2.fastq <==
@SRR6575835.1 1/2
NCTCTNTGGCCGAGAACCAGATTTGAGTTTAGACATCAAGGAAAAGTTTGCAAAACTATGCGAGGAGCATGGAACTGTCTCTTATACACATCTGACGCTG
+
#FFFF#FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575835.2 2/2
NCTGTNGATGACACTGGTTATATGAGGCACGAGAGTTGGTGGAGTAACGCAGAAATGGTGTGGGTCGTAAGATATGACTGGCAGTTGTAATTGGCCAGTC
+
#8F-F#F--8F-F8F-8-F888F8-FF-F-F-FFFF-F--F----F-F---F---F---FF--F-FFFFFF---FFFFFFFFF--F----FFF-FF8FFF
@SRR6575835.3 3/2
NATCTATTTTTGGTGATCCTGAAGACTTCTCTTCAACAACAGCTTTAGTTGTTTTCTGCAGTGGCTTTGCTACGGAATTATTGGAGCTGAAGGCTATGTT
+
#FFFFFFF-FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575835.4 4/2
NCATGAGAGGGATCCGTGGTATCAGTGGGACCACTCAGAACTCAGGATGAACTGGGGTGAACCGATACACTGGGACCTAGACATGTACATCAGGAATCGT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFF
@SRR6575835.5 5/2
GGCCTGGAGGCAGCGATTGGCATTGGATAGGTCAATGATATTTTCTCTAAGGATTCCATGCTCCTCACATAGTTGTGCAAACCTTTCCTTGATGTCTGAA
+
FFFF-FFFFFFFFFFFFFFFFF-FFFFF--FFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFF-FFFFFF

Starting FASTQC command


Processing SRR6575835_1.fastq

Printing command:
fastqc --outdir SRR6575835_1.fastq

Analysis complete for SRR6575835_1.fastq

Processing SRR6575835_2.fastq

Printing command:
fastqc --outdir SRR6575835_2.fastq

Analysis complete for SRR6575835_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 549M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 86 root   root       92K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 E4-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 275M Oct 12 19:44 SRR6575835_1.fastq
-rw-r--r--   1 kkarri waxmanlab 275M Oct 12 19:44 SRR6575835_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:23 EDT 2018
0 hours, 0 minutes and 51 seconds elapsed.
==========================================================