-----------------------
Start of variable list:
-----------------------
Sample_ID:
M10-MAA000377-3_9_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 19:46:09 EDT 2018
Running on node : scc-tm1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791282
Current job name : Step_02_M10-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791282.1.linga

Loading required modules...


List files in scratch directory:

total 16M
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 M10-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 8.0M Oct 12 19:46 SRR6576669_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 7.8M Oct 12 19:46 SRR6576669_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576669_1.fastq <==
@SRR6576669.1 1/1
TTATATCTCAGTAAGAGTAAACAAAAAAGTGGGGAAATTCAAGATAAATACACAGTAATGCAAGTCAAAGATGGTCTTAAGCATAGGAAATGGCCATAGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F---FFFFFFF-FFFF-FFFFFFFF
@SRR6576669.2 2/1
GCCTAGAGCCATGCTAGAGGACTGGATATATGTGCTGGGCAGATGGTGGAATCTCAGAGAATCTCAAAGGAAAGTGGAAATTGTACTCTGGTTGGGGTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576669.3 3/1
AAGTTATATAATTTAAGCTCCATAGGGTCTTCTCGTCTTATTATTATATTTCAGCCTCTTCACTGAAAGGTCAATTTCACTGATTAAAGATAAGAGACAG
+
FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF88FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFF
@SRR6576669.4 4/1
ACCCTGTCTTAAGGTGGAGAACAATGAAAGGGATGCCTGACATCTCTGGTCTCCCCTATGTGCACACATGCAAGGGTATACATGCAGGTGTGTGGGTGTT
+
FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFF-F-FFFFFFFF-FFFFF
@SRR6576669.5 5/1
AGCCAGGGACCTGGGAAAGCCAGGCTACCTGCCACTGGAATCAGAGAAGCAGACATGGCGGCCTCCCACAAAGCTCCTCTCTTACCGGGTTACCATGGCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576669_2.fastq <==
@SRR6576669.1 1/2
NATATATGCTATGAACCTAAATAATTGCCCTTAGCCAAATATAATGTATGTTAAAAACACATAGAATAAAAACAGGGGCATGAAAACTTGTTTGTACTGA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576669.2 2/2
CATTACATCTTTAGCACCCTCAGTGGCCAGCTAGAGTGGGTGATGGGCAAGACACTATCCCTCCTTGAGAGGCCATCTGCTGCTTCATAAAAGTAGGCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576669.3 3/2
ATCAAAAAGTAAGTTTAGATTATAGCCAAAAGAGGGACAGCTCTTCTGGAACGGAAAAAACCTTTAATAGTGAATAATTAACAAAACAGCTTTTAACCAT
+
8FFFFFFFFFFFFF8F8F8FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF
@SRR6576669.4 4/2
TTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAGTGCTGGGATGAAAGGTGTGCGCCACACACACACTTTATAAAGTGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF88-FFF-F
@SRR6576669.5 5/2
GATCTCATCCCGGTGAAGCAATGTCTGCTGATTATCCTCATCTTGGCTTCTCTGGCCACCATCTTCCTCGTGTGCACAGTGGTGCTGGCGGTCCGTCTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FF

Starting FASTQC command


Processing SRR6576669_1.fastq

Printing command:
fastqc --outdir SRR6576669_1.fastq

Analysis complete for SRR6576669_1.fastq

Processing SRR6576669_2.fastq

Printing command:
fastqc --outdir SRR6576669_2.fastq

Analysis complete for SRR6576669_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 83M
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 M10-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  42M Oct 12 19:46 SRR6576669_1.fastq
-rw-r--r--   1 kkarri waxmanlab  42M Oct 12 19:46 SRR6576669_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:22 EDT 2018
0 hours, 0 minutes and 13 seconds elapsed.
==========================================================