-----------------------
Start of variable list:
-----------------------
Sample_ID:
C4-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 19:44:28 EDT 2018
Running on node : scc-tk3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791030
Current job name : Step_02_C4-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/8791030.1.linga

Loading required modules...


List files in scratch directory:

total 76M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 24 root   root       20K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C4-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  37M Oct 12 19:44 SRR6575995_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  40M Oct 12 19:44 SRR6575995_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575995_1.fastq <==
@SRR6575995.1 1/1
AGTCTCGTTCGTTATCGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCACGGAATCGAGAAAGAGCTATCAATCTGT
+
FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575995.2 2/1
CCAGACCCTGGACGGGAGCCAGTACAACCCTGTTAAACAACAGCTAGAGCGTTATGCCACCAGTTGTTACAGCTGTTCTCCACAGCTGGCTTCTGTGTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575995.3 3/1
CCCGACCCCCGGCCGGAGCCGGGAGGGAGCTCACCGGGTTGGTTTTGATCTGATAAATGCACGCATCCCCCCCCGGGAAGGGGGGTCAGCGCCCGTCGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575995.4 4/1
TTTCTGTCCCTTTGTCCTCGTTTATGTACGAAGCTGCCAGCGGGCCATAGAAACATGACCACCAATACGGTCCCCTTGCACCCGTACTGGCCCAGGCACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575995.5 5/1
GGACATGCCCCCGCCAGGGGGCTACGGCCCCATCGACTACAAGCGGAACCTGCCCCGCCGGGGACTGTCGGGGTACAGCATGTTTGCTGTGGGCATCGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575995_2.fastq <==
@SRR6575995.1 1/2
NCCAGGAGTGGAGCCTGCGGCTTAATTTGACCCAACACGGGAAACCTCACCCGGCCCGGACACGGACAGGATTGACAGATTGATAGCTCTTTCTCGATTC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6575995.2 2/2
GGTCAGGGAGGGCTTGATGTCCACCAGGAACTCAGTCAGATGCTCCACGCGCTCTGCATACGGCTGGAGCAGCTCGGGGAGCAACTTGCTCTTCAACAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFF
@SRR6575995.3 3/2
GATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F8FFFFFFFFFFFFFFFFFFFF
@SRR6575995.4 4/2
CAGCAAACCAGCACAAGGCCAGTCGCCGCCCAGCTCCAAGTGGGACGACGGAAGCTCGGCTAGACAACAGCCACGTGATCACAATTAGGCCCCCAGAGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFF
@SRR6575995.5 5/2
GGCTTCCTCCTCCAGGTTTTCCCGGAGAATCTGCAGGGTCCTCCGGTCCTTCTCTGCCTGGAAGAGCGGCATGAGGGCGATCCTGGCCTCCAAGTCCTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FF-FFFFFFFFFFF-FFFFFFFF-FFFFFFFF8FFFFFFFFFFFFFFFF8FFF

Starting FASTQC command


Processing SRR6575995_1.fastq

Printing command:
fastqc --outdir SRR6575995_1.fastq

Analysis complete for SRR6575995_1.fastq

Processing SRR6575995_2.fastq

Printing command:
fastqc --outdir SRR6575995_2.fastq

Analysis complete for SRR6575995_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 422M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 24 root   root       20K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C4-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 211M Oct 12 19:44 SRR6575995_1.fastq
-rw-r--r--   1 kkarri waxmanlab 211M Oct 12 19:44 SRR6575995_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:54 EDT 2018
0 hours, 0 minutes and 26 seconds elapsed.
==========================================================