-----------------------
Start of variable list:
-----------------------
Sample_ID:
H3-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 19:46:09 EDT 2018
Running on node : scc-tk2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791241
Current job name : Step_02_H3-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/8791241.1.linga

Loading required modules...


List files in scratch directory:

total 35M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 39 root   root       36K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H3-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  17M Oct 12 19:46 SRR6575496_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  18M Oct 12 19:46 SRR6575496_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575496_1.fastq <==
@SRR6575496.1 1/1
CNTCAGGAGGAGGCAGGAGATCCAGGTGGGCCTCACTCACATACACATGACAGGTGGAACAGGCCAGGGATGCTTCGCNGGNCCCTTCCAGGTCCACCCC
+
8#FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF#FF#FFFF-FF-FFFFFFFFFF
@SRR6575496.2 2/1
CNTCTAAAGAAAGCAGTGAGGTTAGAAAAGGCTTCTCTTACCTGGTAACTGCAACTACTACTGTGGGTGTTGCTTATGCGGNCAAAAATGTGGTCTCCCA
+
F#FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF#FF-F--FFFFFFFFFFFF
@SRR6575496.3 3/1
GATCCTAGAGGGCCTGCAGTTCAACCTCACACAAACATCGGAGGCTGACATCCACAAGTCCTTCCATCACCTCCTCCAAACCCTCAACAGACCAGACAGT
+
FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFF-FFFFFFFFFFFFF-FF-FFFF--FFFFFFFFFFFFF-FF
@SRR6575496.4 4/1
GTGTAGCGCGCGTGCAGCCCCGGACATCTAAGGGCATCACAGACCTGTTATTGCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTAAGAAGTTGGG
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575496.5 5/1
AGCCACGATCACAAGAAAGACGTGGTCCTGACAGACAGACAATCCTATTCCCTACCAAAATGAAGATGCTGCTGCTGCTGCTGTTTTTGGGACTGACCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575496_2.fastq <==
@SRR6575496.1 1/2
NTGTANCACGGACNAAGGAGTCTAACGCGTGCGCGAGTCAGGGGCTCGTCCGAAAGCCGCCGTGGCGCAATGAAGGTGAAGGGCCCCGCCCGGGGGCCCG
+
#FFFF#FFFFFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575496.2 2/2
NACAGNGGTTTGCCTCTCCATTTAAAAGCCATGTTCTTCCCTTCAGGGATATCAGACAACTTGATCTCGATCTTCGACATGGCCAGTACGTCAGCAGAAG
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575496.3 3/2
GATCCGGGTGATTCCCAGTGGACTCATGAGTGTCAACAAGTAATAGTCACCAGAGTAGCACAGTCTGGTGTTATGGATCTGGACAAAACTTAAGCGCCAC
+
F-F---FFF88F8FF-FFF88FF8FFF-F-F-F--F-FF-F-FFFFF--FFF--F-F--FFF---FF---FF-F-FFFFFFFF--F---F--F-------
@SRR6575496.4 4/2
GACCCAACACGGGAAACCTCACCCGGCCCGGACACGGACAGGATTGACAGATTGATAGCTCTTTCTCGATTCCGTGGGTGGTGGTGCATGGCCGTTCTTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF
@SRR6575496.5 5/2
GTATGGAATTTAAGAACTAAGGATTTCTCCAAGACATGGATTTGCTCCAGAAAAAGTCTAAAGTTGCCATTATCTTCTATCTTTTCTCTTTTGTCAGAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F-FFF

Starting FASTQC command


Processing SRR6575496_1.fastq

Printing command:
fastqc --outdir SRR6575496_1.fastq

Analysis complete for SRR6575496_1.fastq

Processing SRR6575496_2.fastq

Printing command:
fastqc --outdir SRR6575496_2.fastq

Analysis complete for SRR6575496_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 205M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 39 root   root       36K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H3-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 103M Oct 12 19:46 SRR6575496_1.fastq
-rw-r--r--   1 kkarri waxmanlab 103M Oct 12 19:46 SRR6575496_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:27 EDT 2018
0 hours, 0 minutes and 18 seconds elapsed.
==========================================================