-----------------------
Start of variable list:
-----------------------
Sample_ID:
G8-MAA100039-3_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 19:46:08 EDT 2018
Running on node : scc-tm1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791211
Current job name : Step_02_G8-MAA100039-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791211.1.linga

Loading required modules...


List files in scratch directory:

total 78M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 47 root   root       20K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G8-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  38M Oct 12 19:46 SRR6576954_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  40M Oct 12 19:46 SRR6576954_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576954_1.fastq <==
@SRR6576954.1 1/1
GNAATTCCAGCTCCAATAGCGTATATTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTTGGATCTTGGGAGCGGGCGGGCGGTCCGCCGCGAGGCGAGTCAC
+
F#FFF-FFFFFFFFFFF8FFFFFFFFF8F8FFFFFFFFFFFFFFFFFF--F-FFF-FFFF-FF--FFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF
@SRR6576954.2 2/1
TCTCCAGTCCGCCGAGGGCGCACCACCGGCCCGTCTCGCCCGCCGCGCCGGGGAGGTGGAGCACGAGCGTACGCGTTAGGACCCGAAAGATGGTGAACTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576954.3 3/1
TATTTAAACAGTTTGAAAAAGGAAATGAGGAGAAAAGTATTTGTACTGTATAATGGAGGCTGACCAGAGCAGTTTAGGAGATTGTAAAGGGAGGTTTTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF
@SRR6576954.4 4/1
GTGAAGGTGCCCATGATGACCCTCTCGGGCATGCTTGACGTGCACCATTGCAGCACGCTCTCCAGCTGGGTGCTGCTGATGGATTACGCGGGCAACGCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6576954.5 5/1
GTGCCAGAGTGAAGGCGTCCTTTTCTTCCAAGGTAACCGCAAGTGGTTCTGGGACTTTGCCACAAGAACCCAAAAGGAACGTTCCTGGTCAACTGTTGGG
+
-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576954_2.fastq <==
@SRR6576954.1 1/2
NCCCCCGGCCGTCCCTCTTAATCATGGCCTCAGTTCCGAAAACCAACAAAATAGAACCGCGGTCCTATTCCAGGATTCCTAGCTGCGGTATCCAGGCGGC
+
#FFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFF-FFFFF-F-FF-FFFFFFF-FFFFF-FFFFF-FFF-F-F--FFFF-FFFF-FFFFFFFFFFFFFFFF
@SRR6576954.2 2/2
GTATCAACGCAGAGTACATGGGAAAAAAAAAAGAGCGAGAGCGCCAGCTATCCTGAGGGAAACTTCGGAGGGAACCAGCTACTAGATGGTTCGATTAGTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576954.3 3/2
AACTAGAACCTTTTAGAACTTCACAAAACCTCCCTTTACAATCTCCTAAACTGCTCTGGTCAGCCTCCATTATACAGTACAAATACTTTTCTCCTCATTT
+
FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FF-F--FF-FFFFFFF-F-F8-FF-F-8--FFFFFF
@SRR6576954.4 4/2
GGACTCATGAGTGTCTCCAAGTTATAGTTTCCAGAGATGGACAGTCTGGGGATATGGATCTGGGCTAACCTTCTGCGCCTGTTTAGCAGGAACTTAGAGA
+
FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF
@SRR6576954.5 5/2
ATCCAGAGGGTATCTGGGAGGCACCTCTCCTGTGACAGGGTTGAATCGCAGGAACTTGTTACCCTGGAAGCAGTAGTAGCGTTCAAGCCACCTCAAGGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576954_1.fastq

Printing command:
fastqc --outdir SRR6576954_1.fastq

Analysis complete for SRR6576954_1.fastq

Processing SRR6576954_2.fastq

Printing command:
fastqc --outdir SRR6576954_2.fastq

Analysis complete for SRR6576954_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 445M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 44 root   root       20K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G8-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 223M Oct 12 19:46 SRR6576954_1.fastq
-rw-r--r--   1 kkarri waxmanlab 223M Oct 12 19:46 SRR6576954_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:35 EDT 2018
0 hours, 0 minutes and 27 seconds elapsed.
==========================================================