-----------------------
Start of variable list:
-----------------------
Sample_ID:
A1-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 19:42:19 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790921
Current job name : Step_02_A1-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/8790921.1.linga

Loading required modules...


List files in scratch directory:

total 89M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 95 root   root       92K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A1-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  44M Oct 12 19:42 SRR6575935_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  46M Oct 12 19:42 SRR6575935_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575935_1.fastq <==
@SRR6575935.1 1/1
CCCCAACTCTCGTGGAGGCTGCAAGAAACCTAGGAAGAGTGGGCACCAAGTGTTGTACACTTCCTGAAGATCAGAGACTGCCTTGTGTGGAAGACTATCT
+
-FFFFFFFFFFFFF8FFFFFF8FF88FFFF8FFFFFF8FFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF--FFFFFFFF
@SRR6575935.2 2/1
CCAACTACGAGCTTTTTAACTGCAGCAACTTTAATATACGCTCTTGGAGCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCG
+
FFFFFFFFFFFFFFFFFFFF8FFFFFFFF8FFFFFFFFFFFF8FFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575935.3 3/1
GGTGAGTAGTGTTTTCTATTTCTTCCATGCACGTGGTCCCTTCTTAATCCCCAGGTCTTTATCTTCTCTCTTCACTCCACCTTCCTTCTAGCACCACTTC
+
FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575935.4 4/1
CTCAGGTAGCAGACTGTTCCTGGGATGAAACCATAAAGATCTATGACCCTGTTTGTCTCACGGTTCCTGGTTAAGACACGCTGCTCTAGTCAGAAAGAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF
@SRR6575935.5 5/1
GTTAAGTGTTGCTGAAATCAATAAAATAAAAATAATGAGAGCGGAGGTTAGGGCATTAAGTGTTCCTGATGACATGCCAAACTATTTTAGAGATGGCGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575935_2.fastq <==
@SRR6575935.1 1/2
NTTTTTCTCAGGGTAGCCTGAGAAGGTTGGGGTTGTGATGTGTTTAGGCTAAGGCGTCTTTGCATCTAGTGACAAGGTTTGGACCCTCAGTCGAGAAGCA
+
#FFFFFFF-F8FFFFF8FFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFF-FFFFFFFFF-FFFFFF-FFFFFF--F--F8-
@SRR6575935.2 2/2
NATCAAAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGCCGGGGGTCGGGCGCCGGCGGCTTTGGTGACTCTAGATAACCTCGGGCCGATCGCACGCCCC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575935.3 3/2
CCCTACACCAGAGGGGTTTACCAGGATCATACCAAAGTACACCATGAGCTTCGTGCCCATCTGATTCTGGGTTGAGCCAAGATGGGTCAAGAGGGAGGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575935.4 4/2
CACAATGTCTTTATCAGATGCCTCAAAATGTAAGTTTGAGAATTGTGAAATCTCAGTACATGTAAAGGCCTAATTTTTCCCTTTCAGTAGTTAGTGCTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575935.5 5/2
AAGCAGTTCGTGCAATTGAAAGTATTAATAAAAACACCAGGTACACACACGGCAGTGGCTCAGAAAGTTTATATCTAGCTCCTGGAGGTTCTGACGATTG
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575935_1.fastq

Printing command:
fastqc --outdir SRR6575935_1.fastq

Analysis complete for SRR6575935_1.fastq

Processing SRR6575935_2.fastq

Printing command:
fastqc --outdir SRR6575935_2.fastq

Analysis complete for SRR6575935_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 470M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 95 root   root       92K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:43 A1-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 235M Oct 12 19:42 SRR6575935_1.fastq
-rw-r--r--   1 kkarri waxmanlab 235M Oct 12 19:42 SRR6575935_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:05 EDT 2018
0 hours, 0 minutes and 46 seconds elapsed.
==========================================================