-----------------------
Start of variable list:
-----------------------
Sample_ID:
A1-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 19:42:18 EDT 2018
Running on node : scc-tk2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790918
Current job name : Step_02_A1-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/8790918.1.linga

Loading required modules...


List files in scratch directory:

total 5.9M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 37 root   root       36K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 2.9M Oct 12 19:42 SRR6575437_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 3.0M Oct 12 19:42 SRR6575437_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575437_1.fastq <==
@SRR6575437.1 1/1
ATAATGGAGGCTGACCAGAGCAGTTTAGGAGATTGTAAAGGGAGGTTTTGTGAAGTTCTAAAAGGTTCTAGTTTGAAGGTCGGCCTTGTAGATTAAAACG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575437.2 2/1
TCTGTACACAGACCTGGCAGGAGAAGCACCGAACCCACAAAAAACAGGAGGCCCATTTTTCTAACTGGGGTCTCTCTGAGCTGGGTCCTAGCAGGAGAAA
+
8FFFFFF--FFFFF8-FF888F8FFF8FFF8FFFFF8FFFF-F-FF-F-F-FF-FF---FFF--F-F----FFF-FFFFF-F---F-FFF--FFFF-FF-
@SRR6575437.3 3/1
GACTTTACACATAGATCTGTAAAAGCCAAAGGACAAAAGATGAAAGGACTGGTGTCTCCCCCAGTTGTTTTTGTTTATTTTTTTTGTTTCTTGCCTGTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFF-FFF-FFFF-FFF-FF------FF
@SRR6575437.4 4/1
GACTTAAAGGGAGTAACAGGATTATGTTTCTCAAAATGTGAGATCAAGTAAACAATCTTTAACTCTAAATTTTCCAGTTGACTCTTCCATTACAAGCTCT
+
FFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFF88FFFF8FFFFF-FFFFFF-FF-FFFFFF-FFFFFFFFFF-FFFFFFF-FFF-F--FFFF-F-F
@SRR6575437.5 5/1
ATCATAGGCATAGATATTTGCATCGGGGGAGTATTCAGGGTTGTCAATTTCTGGGTGTATCCAGGTACCCTTGTAATCTGGGTTGTCAATTTGACGTGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575437_2.fastq <==
@SRR6575437.1 1/2
GATTAAAGGCGTGCGCCACCATCGCCCGGCTAGCCTAACACTTCCATCTTCCCTGTTTCCAACTCATGCCTTCAAACGTACATGCGCCAGTCGAAGGATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575437.2 2/2
CTTTAAGGCAGTTTTGTGTATCCACTAAAAGGACATCTACCTCTAAAACATTGATCAAATGTAAAACTTTAATGGAGTAATTAAACACCTACTAAAAATC
+
--F-FF---F8F88FF8F-8FFF8F---F--FFFFFFFFF---F--F-F---F-F----FF----F--FFFF--FFFF-FF-FFFFFFF---F-8--FF-
@SRR6575437.3 3/2
AGACTGGAGTTTGCCTGCTGCTGAATAATTAATTACCAAGGCATCACTAATGAATACTTACCACAGCTTACTCTGAGATGTGTCAAGTCTTGGCAAAAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF
@SRR6575437.4 4/2
ACGCAGAGTACATGGGACCAAACACCAAGCTCATTTTTGAAGTGGAATTAGTAGACATTGACTGAAACCAGTACTTCAGATCGGACATCAGCAAACATAA
+
FFFFFFFFFFFFF8FFFFFFFF-FFFFFFFFFFFF-FFFFF--FFFF--FFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFF
@SRR6575437.5 5/2
GAAGATAAAGGACCCTGATGCTGCCAAGCCGGAAGACTGGGATGAACGAGCCAAGATCGATGACCCCACAGATTCCAAGCCTGAGGACTGGGACAAGCCA
+
FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575437_1.fastq

Printing command:
fastqc --outdir SRR6575437_1.fastq

Analysis complete for SRR6575437_1.fastq

Processing SRR6575437_2.fastq

Printing command:
fastqc --outdir SRR6575437_2.fastq

Analysis complete for SRR6575437_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 32M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 38 root   root       36K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  16M Oct 12 19:42 SRR6575437_1.fastq
-rw-r--r--   1 kkarri waxmanlab  16M Oct 12 19:42 SRR6575437_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:28 EDT 2018
0 hours, 0 minutes and 10 seconds elapsed.
==========================================================