-----------------------
Start of variable list:
-----------------------
Sample_ID:
B4-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 19:42:20 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790981
Current job name : Step_02_B4-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/8790981.1.linga

Loading required modules...


List files in scratch directory:

total 98M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 103 root   root      180K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 B4-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  47M Oct 12 19:42 SRR6575755_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  51M Oct 12 19:42 SRR6575755_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575755_1.fastq <==
@SRR6575755.1 1/1
ANCAAACTCCTTCTAAGTGACTGCTGTGAACTTGCCACTAGGTGGCGGTGCCTGTGTAGCTGGGGAGAAAGTCACCACCTTNATCTTTATCTGACAGTAT
+
F#FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFF-F
@SRR6575755.2 2/1
CNAGTGGACTCATGAGTGTCTTCAAGTTATATTCTCCAGAGATGGACAGTCTGGGGAAGTGGATCTGGGCTAACCTTCNGCNCCTGTTTAGCAGGAACTT
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF#-F#FFFFFFF-FFFFFFFFFF
@SRR6575755.3 3/1
CTGTGGGGAAAAGAGAAAATGAATTCTTCATAGTCACCCAGACCTGCAAGATTGCTCCAAGTAAGGCCCCCATACTGAAAGCCTATTTCCCCTGTATTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575755.4 4/1
CCCTGGAGGCTAAGGACTTGTTTCGGAAGGAGCTGACTGGCCAATCACAATTGCGAAGATGAAGGCTCTGTGGGCCGTGCTGTTGGTCACATTGCTGACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575755.5 5/1
CTACTGGCGTCTGGACTCCAGCCGTGATGGATGGCATAGCTGGCCCATTGCTCATCACTGGCCTCAGGGTCCTTCAACAGTAGATGCTGCCTTTTCCTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575755_2.fastq <==
@SRR6575755.1 1/2
NTTTTNCTGGTGTNATGTATGGGGTCTTTTTATGGTCCAAACTCTGCCTGCCACAGATTTCACTGTCTTACTGAACACTTCGTAATCCTATGTGCAATGT
+
#FFFF#FFFFFFF#FFFFFFFFFFFFFFFFFF-FFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575755.2 2/2
NGTGCNCCATNGCNGCACGCTGTCCAGCTGGGTGCTGCTGATGGATTATGCAGGCAATGCCACTGCTGTCTTCCTTCTGCCCGATGATGGGAAGATGCAG
+
#FFFF#FFFF#FF#FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575755.3 3/2
NAAGAGATTTCCTCTACATTCACCATCATCACCATTGGGAAGGGCCACGCAGTCTCCATGGAGGGAAGGAAAACGCTCCTTTGAACAATTTGTTTGCACA
+
#-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FF
@SRR6575755.4 4/2
NTCCAGCTCCTTTTTGTAAGCCTTTACTTCCGTCATAGTGTCCTCCATCAGTGCCGTCAGTTCTTGTGTGACTTGGGAGCTCTGCAGCTCTTCCTGGACC
+
#FFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575755.5 5/2
GTGTTGGGGCCAAGAGACTTGTCCAAACACAGGGCCCCATCAACTTTCTCATGGGGCCAGGAAACCTCTGTCCATGTTGCCTGGGCTCCTGACTTCAGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575755_1.fastq

Printing command:
fastqc --outdir SRR6575755_1.fastq

Analysis complete for SRR6575755_1.fastq

Processing SRR6575755_2.fastq

Printing command:
fastqc --outdir SRR6575755_2.fastq

Analysis complete for SRR6575755_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 527M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 103 root   root      180K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:43 B4-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 264M Oct 12 19:42 SRR6575755_1.fastq
-rw-r--r--    1 kkarri waxmanlab 264M Oct 12 19:42 SRR6575755_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:07 EDT 2018
0 hours, 0 minutes and 47 seconds elapsed.
==========================================================