-----------------------
Start of variable list:
-----------------------
Sample_ID:
C4-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 19:44:29 EDT 2018
Running on node : scc-tm3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791029
Current job name : Step_02_C4-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/8791029.1.linga

Loading required modules...


List files in scratch directory:

total 49M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 41 root   root       36K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C4-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  25M Oct 12 19:44 SRR6575782_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  25M Oct 12 19:44 SRR6575782_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575782_1.fastq <==
@SRR6575782.1 1/1
CTCATTGTACTGCTCAGCATAGTAAAGAAGTTCTGGGGCATAGAAATAAGGATGTCTTCTGGCAACTTCATGCAAATAGTGTCCCATAAAGGTGGTTGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575782.2 2/1
GGTGTAGGGTTTGTGCTCATTAAGTGCTGATGGCAAGCAGTGGAAAGTGATTTACAAGCAAGGTGTGTCATCACATGCAGCACTCATGCTTCTGTCTCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575782.3 3/1
GGCATAAGATTCCATGCCTAGATGTGATACACGTTTCTAGAAACTGCCTCGTCATGCGACTGTTCCCCGGGGTCAGGGCCGCTGGTATTTGCTGTAAAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575782.4 4/1
CGTCTACACGTTGTATAAAATAAAATTAAAATTAAAAATGAATTCAAGCTCAAGAAAATGAGGTCATTTATCTAGTTTTAAATGTGAACACGAAGACCTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575782.5 5/1
TGTTTGTCCTGTCTCCCTACACTTCCCTGAGGGCTTCTTCCTACCAAAGTGTCCCCTCACCAGTCTGCCTAGAGCATCACTGGAACCCGCACTAAACAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575782_2.fastq <==
@SRR6575782.1 1/2
NTACTTGGGATCTCCAGAAATGCTCATACGATGAGCATGCCAAATTAGTGCAGGAAGTAACAGACTTTGCAAAGACGTGTGTTGCCGATGAGTCTGCCGC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575782.2 2/2
ACTCAGTTGAGGGTGCAGGAAAAGACAAGCCAAATAACCGAAAGGAGCGTCTGCCCAAGCAGCTGATTAGACGAGGCAGGCGTGGGCAAGGAGTGGCCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF
@SRR6575782.3 3/2
CTTCCTCAGACGCTGCCCTAACTGCGCAGTTAATAATTCTGGCAATTCGTCTCCACACTAGAAGTCGACGAACAACGAAGAGCGACGATGCCCGTTTCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575782.4 4/2
AAGTAGAATGTTCAATGTAACTAAAACTAAAATTGCATGTCAAAGAGACCTCGGTTCTTTCTTTCTTTCTTTCTCTCTTTCTTTCAGTTTGCTTTTGGTT
+
FFFFFFFFFFFFF8FFFFFF8FFFFF--FFF-FFF-FFFFFF-FFFFFFFF-FFF-FFFFFF-FFFFFFFFFFFFFFFF-FFFFFF-FFF--FFFF-F-F
@SRR6575782.5 5/2
AGCCAAAGCTCCGAGGACCTGGGCACCCTGTCCATTGTGCACAGTGGCTGTGGCTGCTGTAGACAGTCCCTGGTCAACCTTGGACTTGGTCATCACACGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575782_1.fastq

Printing command:
fastqc --outdir SRR6575782_1.fastq

Analysis complete for SRR6575782_1.fastq

Processing SRR6575782_2.fastq

Printing command:
fastqc --outdir SRR6575782_2.fastq

Analysis complete for SRR6575782_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 264M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 41 root   root       36K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C4-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 132M Oct 12 19:44 SRR6575782_1.fastq
-rw-r--r--   1 kkarri waxmanlab 132M Oct 12 19:44 SRR6575782_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:49 EDT 2018
0 hours, 0 minutes and 20 seconds elapsed.
==========================================================