-----------------------
Start of variable list:
-----------------------
Sample_ID:
C3-MAA000907-3_11_M-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 19:41:27 EDT 2018
Running on node : scc-tm3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790744
Current job name : Step_02_C3-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790744.1.linga

Loading required modules...


List files in scratch directory:

total 25M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 41 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 C3-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  12M Oct 12 19:41 SRR6576179_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  13M Oct 12 19:41 SRR6576179_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576179_1.fastq <==
@SRR6576179.1 1/1
GCATGGGCCTGACTGAGGGGTCAGTCTTGTGGGGTAAAGTTACTCCATAGGACTCTCTGTTCTTACTCCTTAATTCCTCATATGTAACACCTTTTCTTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF
@SRR6576179.2 2/1
GTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAAATAAATTGCTTTATTTATTACTTAATTATTGGGAGTATCAGGCAATTCTTATCATGATAACATAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F8-F8FF-F8--FFF-F---F--F---FF---FFFF-FF--F--FFF---F----F----FF---FF
@SRR6576179.3 3/1
CTCCTAAGGCAACAGAAACTACTGGGGCGAGTATTCCCAATGTATGGTCAGAATATCCCACAGGGATATTGAATATACTTTTCAAGGTTTTAATAGCGTT
+
8FFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFF-F-FFFFF
@SRR6576179.4 4/1
CCTCTCGAGTTATCAGAAAAAAACTTCCAGCTCAACCAGGACAAGATGAACTTTTCCACGCTGAGGAACATCCAGGGTCTGTTTGCTCCCCTGAAGTTAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576179.5 5/1
GGATGAACCCCAGCGGGAAACACTCAAAGCCATCCATATGGCGTTGGACTGCTGTGGCATAGCTGGTCCTTTGGAGCAGTTTATCTCGGACACCTGCCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576179_2.fastq <==
@SRR6576179.1 1/2
ATTCCTAAACTTCTATTCGCTTGTATCGTGGGGTACTTCGCTGGAAAGCTTTCTTACGTGAAAACGTGCCAAGAGAAGTTCAAGAAGCTTGAAAACTCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFF
@SRR6576179.2 2/2
ATTAGATGCTCTGAACAAAAATTGGCGGTATATTGTGCCCATGATTACGGTGGATGGGAAGAGGGTTCCCAGAGATGCTGGACACCCTCTGTATCCCTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576179.3 3/2
GTACTTTTTTTTTTTTTTTTTTTGGCCTGATTTAAAATTGCCTCTGGTGATTTAACCTTTTATCCCTTATTAGAAAAAGTGGCAAAAAACAGGCAAGCCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFF----FFF-FF--F-FF---FF-F-FFFFF---FFFF--F-FFFFF--FFFFF-F-F-FFFFF--F8F-F88-FF
@SRR6576179.4 4/2
TCATTAAGAATATCCTCAAAACCAATGGTCTCATCGTTGCCCCTCAAAATATCCAGTGAGAGGTTTGAGCTCGGGAGAAACGGGAGACGGTGAACCTGCT
+
FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF
@SRR6576179.5 5/2
ATATAGTACCTTTCATTGCAGGATTTTTGCTTAACATAACAAGCAAAAATAAACAACCAAAAAAAAAAATCAAAATAAATTGAACCCCCGGATCACTAAA
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFF-FFFFFFFF-FFFF-FFFFFFFFFF-FFFFFFFFFFFFFF-FFFFF-FFFFFFFF-F--FF

Starting FASTQC command


Processing SRR6576179_1.fastq

Printing command:
fastqc --outdir SRR6576179_1.fastq

Analysis complete for SRR6576179_1.fastq

Processing SRR6576179_2.fastq

Printing command:
fastqc --outdir SRR6576179_2.fastq

Analysis complete for SRR6576179_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 131M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 41 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 C3-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  66M Oct 12 19:41 SRR6576179_1.fastq
-rw-r--r--   1 kkarri waxmanlab  66M Oct 12 19:41 SRR6576179_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:42 EDT 2018
0 hours, 0 minutes and 15 seconds elapsed.
==========================================================