-----------------------
Start of variable list:
-----------------------
Sample_ID:
E3-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 19:44:31 EDT 2018
Running on node : scc-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791113
Current job name : Step_02_E3-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/8791113.1.linga

Loading required modules...


List files in scratch directory:

total 93M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 79 root   root      108K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E3-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  46M Oct 12 19:44 SRR6576896_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  47M Oct 12 19:44 SRR6576896_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576896_1.fastq <==
@SRR6576896.1 1/1
GGGTTTGTGGAGCAAGCTGGAGCTCTGAAGGCCAAGGGAGCGCAGGTGGTGGCCTGTCTGAGCGTTAATGACGTCTTTGTGATTGAAGAGTGGGGTCGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576896.2 2/1
CCGCGCGCCCAGTTCGCAAGGACGTGAAACCCGCCAGAGAGCTGGCGTGTGGCCGGGGCATCCAGACCTCCGGCACGGATCGGCCCAACCGTCCTCGGCC
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576896.3 3/1
GTTACCAAGTGCTGTAGTGGATCCCTGGTGGAAAGGCGGCCATGCTTCTCTGCTCTGACAGTTGATGAAACATATGTCCCCAAAGAGTTTAAAGCTGAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFFFF
@SRR6576896.4 4/1
AGTCAGTATTCCCCTGGCCGGCTTCCCAGATGCCCTGGACGGCACTCTGTTCCTTAAAGTCCAGTTCCACCCTGACGTCCACAGAGGCAGCACGGAGTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF
@SRR6576896.5 5/1
ACCTAAGACAGACTATGATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAACCAGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576896_2.fastq <==
@SRR6576896.1 1/2
NCCAAAGGCTCCAGTGGGGTCAGCCAGGAGCCGAACCTTGCCTTCTGCCTGGTGGGCTCGACCCCACTCTTCAATCACAAAGACGTCATTAACGCTCAGA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF8FFFFFFFF
@SRR6576896.2 2/2
NAGCCGGTCCTACCGCATCGATCGGCTCGGAGAGGAGGTGGCCCTTCAGGCCCGCAGTAAGGGCGACTTCGCGGTGCTTGAAGCGGCCTGCCCGGCAATC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFF
@SRR6576896.3 3/2
NCCTTAGGGTGTTGATTTTACACCAACAGAAAAGATGAGTCCTGAGTCTTCATGTCTTTTTTTCTCAGGGTAGCCTGAGAAGGTTGTGGTTGTGATGTGT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF8FFFFFF-F
@SRR6576896.4 4/2
CTATAAAACTGAAGACTCTAACATCTCAATCCCAGACCTGGTAGGAGCTGCCGACCTTTATTTGGGAACAACTGTGGTCAGCTTTCACTATTTCACTGGT
+
F-FFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFF-FFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFF-8
@SRR6576896.5 5/2
GGTATATCAAAGAGAAATTTAAAGAAGTCTTTGATTCTTAATGAGGTATCCTAGATAACATGTGGATAGACTGGAATTGGACTTCTCAGTGAGACAGGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF

Starting FASTQC command


Processing SRR6576896_1.fastq

Printing command:
fastqc --outdir SRR6576896_1.fastq

Analysis complete for SRR6576896_1.fastq

Processing SRR6576896_2.fastq

Printing command:
fastqc --outdir SRR6576896_2.fastq

Analysis complete for SRR6576896_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 518M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 79 root   root      108K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 E3-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 259M Oct 12 19:44 SRR6576896_1.fastq
-rw-r--r--   1 kkarri waxmanlab 259M Oct 12 19:44 SRR6576896_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:20 EDT 2018
0 hours, 0 minutes and 49 seconds elapsed.
==========================================================