-----------------------
Start of variable list:
-----------------------
Sample_ID:
F1-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 19:49:50 EDT 2018
Running on node : scc-tk3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791374
Current job name : Step_02_F1-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/8791374.1.linga

Loading required modules...


List files in scratch directory:

total 20M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 22 root   root       20K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:49 F1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 9.7M Oct 12 19:49 SRR6576308_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  11M Oct 12 19:49 SRR6576308_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576308_1.fastq <==
@SRR6576308.1 1/1
GTTGTGACGTCCAGGAGGAGTGCCAGGACTCAAGACTTTGGCTGTTGGAGATAGTCAGCAGGCTAGTTCTGAGAAATTGTCCAGCGTGGACAGGGGTGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576308.2 2/1
GAGTACATGGGTGGGGGAGTCAGCACCAGGGATTCTGGGCACATGTCTGTCCGCAGCTCGCAGTGGTCCTTCAGCACCATCAGCAGCAGCACACAGCGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF
@SRR6576308.3 3/1
GTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGGTTTTAACCCCCAGTAACAGTTTAATTTAAAAAAAAACAAGCCCACAAAAACATTTTTGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF888-F8-----FFF------F-------FF-FFF-FFF-------F--------------F-F
@SRR6576308.4 4/1
GAGCAGACAGCAGGAAAGAAGAAACCCTTTGTCTATACCCAGGGTCAGGCGGTCTTAAACCGAGCCTTTTTCCCTTGCTTTGACACTCCAGCAGTGAAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576308.5 5/1
ATACTATTCCCACCATGGGGAGCGAAAACGTTAAAAAAAAAAGAAAAAAATCACAAGGAATTGCCCAATGTAAGCAGACTTTGCCTTTTCACAAAGGTGG
+
FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF

==> SRR6576308_2.fastq <==
@SRR6576308.1 1/2
CCTGGGGACCACAGCCTATCAGGAGAACACAGGCATCAAGCCGGACGTGGGTCTGGCACCAGCTTCTCCCTTCCTACCACACCGAGGACTTCTGTCTCGG
+
FFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFF8FFFFF
@SRR6576308.2 2/2
CTGTGGACACGTGGAGGTGACCTGAGGCCTTGGATCACTGGTGAGCCACTGGCCAGTTGCAGCTCACTTCTCAAAGTAGGGCAGGTAGAAGAATTGGAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-F8--FFFFFFFFFFFFF
@SRR6576308.3 3/2
GTACATGGGGGTATCAACGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATACAAGTAAATTAAAAAAAAATAAACCAACCCACAAATTATTGGGG
+
FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--F---------F-FFFFFFF---F------8-F------F------
@SRR6576308.4 4/2
GTATTCCTCCTTGGCAGCTTCAATCAGGCAGGGCTCCGCCCACACCCGGCTCCTGGGTCCAACCTCAGCTGAAGCCAGATCTCCAATGGCCAAAGCTATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF
@SRR6576308.5 5/2
TCTTAATACAGTCTACATAAATTTGAACTGGTATTTATTTGGGTTCAGTTATAACATAGCATAAAAAAAATCAAAGCACTGGTTGTCTGAAATAAAGCAA
+
FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFF-FF--FFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFF

Starting FASTQC command


Processing SRR6576308_1.fastq

Printing command:
fastqc --outdir SRR6576308_1.fastq

Analysis complete for SRR6576308_1.fastq

Processing SRR6576308_2.fastq

Printing command:
fastqc --outdir SRR6576308_2.fastq

Analysis complete for SRR6576308_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 104M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 22 root   root       20K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:50 F1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  52M Oct 12 19:49 SRR6576308_1.fastq
-rw-r--r--   1 kkarri waxmanlab  52M Oct 12 19:49 SRR6576308_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:03 EDT 2018
0 hours, 0 minutes and 13 seconds elapsed.
==========================================================