-----------------------
Start of variable list:
-----------------------
Sample_ID:
A2-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 19:42:18 EDT 2018
Running on node : scc-tl2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790925
Current job name : Step_02_A2-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/8790925.1.linga

Loading required modules...


List files in scratch directory:

total 91M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 43 root   root       36K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A2-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  46M Oct 12 19:42 SRR6575938_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  45M Oct 12 19:42 SRR6575938_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575938_1.fastq <==
@SRR6575938.1 1/1
TNCTTAGATATTGAGATAGCTTTACTCATTATCCCCACTGGGCCAAATTCCCGCCGGTTTGTGAAGACAGAAAAACATTCCNTCACTAGAACATTCTTAA
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFFFF
@SRR6575938.2 2/1
CTTTAGCACTGTTGAAACTTAATGTTTATTCCTGTGCTGTGCGGTGCGGTGCTGTGCTGTGCTGTGCAGCTAATCAGATTCTTGTTTTTTCCCACTTGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFF-FF-F-FF-FFFFFFFFFFFFFFFFFFF
@SRR6575938.3 3/1
GAAGTGGTTAAGATCAGTCAAAGTTATTTCCTTGGGATTCACACCTCCTCTGACTTGGAGCTCCCGAGCTTCCTGTGTTTGCTCTTCTGCCTCCAGAGTG
+
8FFFFFFFFFFFFFF-FFFFFF8F8F8FF8FFF88FFFFFF-F-FFFFFFFFF-F-FFF-F-FFFFF---FFF-F---FFF-FFFF---F-FF--F-FFF
@SRR6575938.4 4/1
CGCCTGCCGGCGTAGGGTAGGCACACGCTGAGCCCGTCAGTGTAGCGCGCGTGCAGCCCCGGACAGCTAAGGGCATCACAGACCTGTTATTGCTCAATCT
+
FF88FFFFFFFFFFFFFF8FFFFFFFFFFFFFFF8FFFFF-FFFFFFFFFFFFFFFFFFFFFF-F-FFFFF-FFFFFF-F--FF-FFF--FF--F--FFF
@SRR6575938.5 5/1
TCTAAGGGCATCACAGACCTGTTATTGCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575938_2.fastq <==
@SRR6575938.1 1/2
NTACANAGAGTCACACACACATCTGGAGGGAGAACACTGAGGAGTAAAATTGCTGACAGACAAGCAGGGATGAACCTGTTTTCAGCTCTCTCACTGGATA
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6575938.2 2/2
NTACAAATCATCCTATGTGAAATCACTGCGTATTAACATCAACATAATCCAAGTGGGAAAAAACAAGAATCTGATTAGCTGCACAGCACAGCACAGCACC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575938.3 3/2
ATTATTACCTGCATGCTGCCATGCTCCCTGCAACGTTGGCCATGGACTCACCATCTGTGAGCCCCCACTAAAGGCCTTCTTCTATAAGTCGTCTTGGTCA
+
8F--FF-FFFFFFFF-FFF8FFF8FF-FFFF-FFFFFFFFF-FFFF-F---FF-F-FFFFF--FFFFF-F-F-FF-FFF8F-F-FFFFFFFFFFFFFFFF
@SRR6575938.4 4/2
TCCCCGCCCCTTGCCTCTCGGCGACCCCTCGATGCTCTTAGCTGAGTGTCCCGCGGGGCCCGAAGCGTTTACTTTGAAAAAATTAGAGTGTTCAAAGCAG
+
F8FFFFFFFFF-F8FF8FF88FF8FFFFFF--FFFFF-FFFF-FFFF-FFFFF-FFF-FF-FFFFFFFFFF-FFFF-FFFFF--F-FF-F-FF-F-FFFF
@SRR6575938.5 5/2
ATTCGTATTGCGCCGCTAGAGGTGAAATTCTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575938_1.fastq

Printing command:
fastqc --outdir SRR6575938_1.fastq

Analysis complete for SRR6575938_1.fastq

Processing SRR6575938_2.fastq

Printing command:
fastqc --outdir SRR6575938_2.fastq

Analysis complete for SRR6575938_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 479M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 43 root   root       36K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A2-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 240M Oct 12 19:42 SRR6575938_1.fastq
-rw-r--r--   1 kkarri waxmanlab 240M Oct 12 19:42 SRR6575938_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:45 EDT 2018
0 hours, 0 minutes and 27 seconds elapsed.
==========================================================