-----------------------
Start of variable list:
-----------------------
Sample_ID:
A11-MAA100041-3_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 19:42:18 EDT 2018
Running on node : scc-tl4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790911
Current job name : Step_02_A11-MAA100041-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790911.1.linga

Loading required modules...


List files in scratch directory:

total 50M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 43 root   root       40K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A11-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  25M Oct 12 19:42 SRR6575327_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  26M Oct 12 19:42 SRR6575327_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575327_1.fastq <==
@SRR6575327.1 1/1
GNAAGGGTGGCTGGCGGAGCATATGCTGATCCTGGGCATAACTAACCACGAAGGCAAGAAGAAATACCTGGCCGCAGCCTTCCCTAGTGCCTGTGGGAAG
+
F#F-FFFFF-FF--FF-FFFFFFFFFFFF88F88FFFFFFFF8FFFF-FFFF-FFFF-FF-FFFFFFFFF-F-FFF-FFF-F--FFFFFFFFFFF-FFFF
@SRR6575327.2 2/1
GGAACACCGTCGGGGCCCACCAGGAACTTCTCAAAGTTCCAGGCAATGTCGTTGCGGCACACCGGAGACCAAATGATGTACTTGGGGTCGGTCATGAGCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575327.3 3/1
CCACTTGTCCCTCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGTAACGAGTTAGCATGCCAGAGTCTCGTTCGTTATCGGAATTAACCAGACA
+
FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575327.4 4/1
GTACATGGGTACCTGGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF
@SRR6575327.5 5/1
CACCAAGAATTATCTCTCTATGGTTGGATCCTGCTGTACTTCTGCAAACCCAACTGTATGCTTTGTGAAGGAGAGACTCCAGATGAAGCATTTGTCACTT
+
FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF

==> SRR6575327_2.fastq <==
@SRR6575327.1 1/2
NATCATGGCCAAGTTAGTCTTCCCACAGGCACTAGGGAAGGCTGCGGCCAGGTATTTCTTCTTGCCTTCTGGGTTAGTTATGCCAAGGATCAGCATATGA
+
#FFFFFFF-FFF8FFFFFFFF8F8F-F--F-FFF---FF---F-F-FF-----FF-F-----F-FF--F-F--FFFF--FFF-F-FF-----FF88F---
@SRR6575327.2 2/2
NTGCGAAGTGAATGGTGAGAAGGCTCACCCGCTCTTTACCTTCCTGCGGAATGCCTTGCCAACACCCAGTGACGACCCCACTGCGCTCATGACCGACCCC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575327.3 3/2
NTCCCGCGGGGCCCGAAGCGTTTACTTTGAAAAAATTAGAGTGTTCAAAGCAGGCCCGAGCCGCCTGGATACCGCAGCTAGGAATAATGGAATAGGACCG
+
#FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFF--FF-FFFFFFFFFFFF
@SRR6575327.4 4/2
TTCTCAGGCTCCCTCTCCGGAATCGAACCCTGATTCCCCGTCACCCGTGGTCACCATGGTAGGCACGGCGACTACCATCGAAAGTTGATAGGGCAGACGT
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFF-FFFFFFFF-F-FFFFFFFFF-FFFF-
@SRR6575327.5 5/2
CTCTTCAAACTTAGAATTCTTTTTGGATAAGTTTTGACAGATTTTTATTGTGTGCTCAGGCAGCTCACTGGCCATGCAATCCTCTGAGGTAGACTCACAA
+
F8FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FF-FFFFFFF

Starting FASTQC command


Processing SRR6575327_1.fastq

Printing command:
fastqc --outdir SRR6575327_1.fastq

Analysis complete for SRR6575327_1.fastq

Processing SRR6575327_2.fastq

Printing command:
fastqc --outdir SRR6575327_2.fastq

Analysis complete for SRR6575327_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 275M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 43 root   root       40K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A11-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 138M Oct 12 19:42 SRR6575327_1.fastq
-rw-r--r--   1 kkarri waxmanlab 138M Oct 12 19:42 SRR6575327_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:39 EDT 2018
0 hours, 0 minutes and 21 seconds elapsed.
==========================================================