-----------------------
Start of variable list:
-----------------------
Sample_ID:
H2-MAA100041-3_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-kb6
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791236
Current job name : Step_02_H2-MAA100041-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791236.1.linga

Loading required modules...


List files in scratch directory:

total 31M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 97 root   root       84K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H2-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  15M Oct 12 19:46 SRR6575494_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  16M Oct 12 19:46 SRR6575494_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575494_1.fastq <==
@SRR6575494.1 1/1
GTGGGAGTCCCTGGAGCCTGCTCCCCGTCTGCTCCCTTCAGGACGACATCCGGGCCCTTTCCTATAAGGCCAAGGTGTTTGGCCTTTTCCAGGTGCTGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFF
@SRR6575494.2 2/1
AGGCTACCCGGATCGATGACGCGAATTGGGGACATTCAAATGAGCATCCTAGTCACCGCGTTTAAAATGAACCTGCCGGCTGATCGTTTTTAGGATATTG
+
FF88FFFFFF-FFFFFFFF8FFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFF-F--FF-FFFFF-FFFFFFFFFFFFFFF
@SRR6575494.3 3/1
AGCCTCCAGTGTTGAGTGGAGACTTCTCACCAGGACTCCACCATCATCCCTTCCTATCCATACAGCATCCCCAGTATAAATTCTGTGATCTGCATTCCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575494.4 4/1
CCAATGGATCCTCGTTAAAGGATTTAAAGTGGACTCATTCCAATTACAGGGCCTCGAAAGAGTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTC
+
FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFF-FFFFFFFFFF-FFFFFFF-F
@SRR6575494.5 5/1
GAATTGCACCATGTTTCCTTGCATATTCGGAGTTGGTCCCCTCATTATTTGTGCTGGTCCCGGCATGACATTGGATTGGTTCTGAGAGTTAAATTGCGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575494_2.fastq <==
@SRR6575494.1 1/2
ATCCAGGCAATTTTTACACAGAAAACCAAGCGCGTGTCTGACCCACTGGACACTCGATGCTGGCAGGGCTTCCGTCTGGAGGATTATCTGATAGGGCAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF
@SRR6575494.2 2/2
CTGTTGATACCGTCTGCGATAGGCTAGTTCATAAACGAGGGGCGATGCCCGGGCTCAGAATCCAAGGAGCAAAACTGCGTCGGTTTAGCTGAGATTGCAC
+
FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFF-FFFF-FFFFFF-8FFFFFFFF
@SRR6575494.3 3/2
GGGGTATAAATTTTTTTAAAGGAAAATGAAAAAAATAAATAAAAATATTAATAGGTGTATAAAAAAAAAAAATAAAAAAAAATTTTATTTTTTATTATTT
+
FFF-----F8F-8F8-8F-F88-F----F--F-F--FFF-FFFFF-F-F-F---F--F--FFFF-FF-FF--F-FFFFFF----FF-FF-F-F-8F-8-8
@SRR6575494.4 4/2
CAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATG
+
FFFFFFFFFFFFFF8FFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575494.5 5/2
GGGCCAAATGGCCCAGCAACAAGGAACTTTGAACCCTCAAAATCCTATGATCCTTTCAAGGGCCCAGCTTATGCCACAGGGCCAGATGATGGTGAACGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF

Starting FASTQC command


Processing SRR6575494_1.fastq

Printing command:
fastqc --outdir SRR6575494_1.fastq

Analysis complete for SRR6575494_1.fastq

Processing SRR6575494_2.fastq

Printing command:
fastqc --outdir SRR6575494_2.fastq

Analysis complete for SRR6575494_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 180M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 89 root   root       84K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H2-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  90M Oct 12 19:46 SRR6575494_1.fastq
-rw-r--r--   1 kkarri waxmanlab  90M Oct 12 19:46 SRR6575494_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:42 EDT 2018
0 hours, 0 minutes and 32 seconds elapsed.
==========================================================