-----------------------
Start of variable list:
-----------------------
Sample_ID:
C1-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 19:44:28 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791015
Current job name : Step_02_C1-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/8791015.1.linga

Loading required modules...


List files in scratch directory:

total 8.7M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 86 root   root       92K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 4.1M Oct 12 19:44 SRR6576175_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 4.5M Oct 12 19:44 SRR6576175_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576175_1.fastq <==
@SRR6576175.1 1/1
TGCATGCACTGCCTCAGTGACCAGTAAAGTCACGTGGCTTTGGGGAAGTCAGCTTAGCTCTCATCACCGTGTCCCAGGGTGTGCTTGTCAAAGAGATATT
+
FFFFFFFFFFF-FFFFFFFFFFFFFFFF8FFFFFFFF8FFF-FFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFF-
@SRR6576175.2 2/1
CCTCGAAAGAGTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576175.3 3/1
AATAATCGGAGCCCCAGATATAGCATTCCCACGAATAAATAATATAAGTTTTTGACTCCTACCACCATCATTTCTCCTTCTCCTAGCATCATCAATAGTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576175.4 4/1
GGGGTGGTCCTTCTAGCCAGGAGCTCTCTCGTCTTGGCTTCTATCTCTCCCAGCAGCGTCTCGGGACTAGCGCTGGTCTTCTCCTCCTCCAGGCTGTACG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576175.5 5/1
GTATAGGGGTCCTAGGAAGATAATAGTTGTTAGGGCGTTTATTAGAATAATGTTAGTGTACTCTGCTATAAAGAATAACGCGAATGGGCCGGCTGCGTAT
+
FFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FF

==> SRR6576175_2.fastq <==
@SRR6576175.1 1/2
CCGCCACCATGACCACCGCGTCTCCCTCGCAAGTGCGCCAGAACTACCACCAGGACGCGGAGGCTGCCATCAACCGCAAGATCAACCTGGAGTTGTATGC
+
FFFFFFF-FFFFFFFFFFF8FFFFFFFF-FFF-F-F---F--FFFF--F--FFFFFFFFFFFFFFFF-FFFFFFFFF-FFFF-F8-FF-FF8FFFF-F8F
@SRR6576175.2 2/2
CCGTGGCGGCGACGACCCATTCGAACGTCTGCCCTATCAACTTTCGATGGTAGTCGCCGTGCCTACCATGGTGACCACGGGTGACGGGGAATCAGGGTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFF
@SRR6576175.3 3/2
TGATAATAGTGGTAATAAAATTAATTTCACCTAAAATAGATGACACTCCAGCTAAATGAAGGGAGAAAATTGTTAGGTCTACTGATGCTCCTGCATGGGC
+
FFFFFFF-FFFF888FFFFF8FFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF--F-FFFFFF-FF
@SRR6576175.4 4/2
GTATCCTGCTGTGGTGGAGTTTGCTCCATTCCAGAAGATTGCCAAAAAGAAGCTTAAGAAAAAAGATGCCAAGACCGGAAGCATTGAAGATGACCCAGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFF
@SRR6576175.5 5/2
GGATGAGCCTCAAACTCCAAATACTCACTATTCGGAGCTTTACGAGCCGTAGCCCAAACAATTTCATATGAAGTAACCATAGCTATTATCCTTTTATCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF8FFF8

Starting FASTQC command


Processing SRR6576175_1.fastq

Printing command:
fastqc --outdir SRR6576175_1.fastq

Analysis complete for SRR6576175_1.fastq

Processing SRR6576175_2.fastq

Printing command:
fastqc --outdir SRR6576175_2.fastq

Analysis complete for SRR6576175_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 43M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 86 root   root       92K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  22M Oct 12 19:44 SRR6576175_1.fastq
-rw-r--r--   1 kkarri waxmanlab  22M Oct 12 19:44 SRR6576175_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:48 EDT 2018
0 hours, 0 minutes and 20 seconds elapsed.
==========================================================