-----------------------
Start of variable list:
-----------------------
Sample_ID:
L4-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 19:41:28 EDT 2018
Running on node : scc-yi2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790850
Current job name : Step_02_L4-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/8790850.1.y

Loading required modules...


List files in scratch directory:

total 32M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 33 root   root      4.0K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 L4-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  16M Oct 12 19:41 SRR6576552_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  17M Oct 12 19:41 SRR6576552_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576552_1.fastq <==
@SRR6576552.1 1/1
CNTCAGTAAAGAATCTCAGGCTGAAGGCCGAACAGTCCCAGCAGCTGTCACCAATCTGAGGATCACAGAGAACTCCAGTAGATACCTGTCCTTCGGCTGG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576552.2 2/1
GCAATATCCTTCTCGATGTTGTACTTCTCCAACGCCTGGGTAGCGCACTCCACCGAGTCCTGTTGCATCTCTTCCGACATGTCTGCATTTTTGATCACCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576552.3 3/1
GGGACGGTCGGAATGGCGCTGCAGGATCTTGGAGAAAACTTGCAGCCTTGGTGTCCGCTGGGTCTCAGCCTCGAATGGGTGAAGACCGTGTGGGACCTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576552.4 4/1
CTGTGAGATAGTGTGCTCTCATGGCGTTCTTCTGTACTAGAAATGTGAATAACACATACGGAACAAACTAATGGTTTGTGGTAATGATGCTCTGTGGAAT
+
FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576552.5 5/1
GGTTCTGCCTCAGGAGTACTGGGATGAAAGGTATGGCCAAGCACACAGTGCCTATATTTATAAATGTTTTGACCAAGTTCAGGAGCTGGTCAGATGAAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFF8FFF8FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFF

==> SRR6576552_2.fastq <==
@SRR6576552.1 1/2
NCCGANTATAAATGACTCATTGGACAGCTCCCCACTGTGAGTGACAATCACCATCTTGTACATTCTGCCTTGTAGCAAGTTCTGGAAAGAGAAGCTCTGG
+
#FFFF#FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF8FFFF
@SRR6576552.2 2/2
NTACATGGGGGGTGATGCGCCACGGCTTCGGTAGCGACCGGCTGTCTTCTGCTGCTTGAGCGGCGCCCGCACCTTCCCTAGGAGCTCGCAGCAGCCGGCT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576552.3 3/2
CGCCTACTATGCTGGGGTCCAAAGGCTCAATCTCCGTGAAGTCCAGGTCCCACACGGTCTTCACCCATTCGAGGCTGAGACCCAGCGGACACCAAGGCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF
@SRR6576552.4 4/2
CTGTCAAGGTGCTGGTGAAGAACACAGATTCACAGCGCCCCCCCCCCCCGTCATGGGGCCTATAAAATAAAAATGGCTAAACACTGTGACTATTTTGTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FF-FFFF----FF--FFF-FFF---FFFF-F-F-------FF---F-F
@SRR6576552.5 5/2
AATCTTGGATGAACACTTTTAATTGCTAAAAAGGTAAGGGAACAATAAACACGGGAAATATAAATGAATAAAGTGTTCGGAGTCAAGCTGCTTTCAAGGC
+
-FFFFFFFFF8FFFFFFFFFFF-F-FFFFFFFFFFFFF-FF-FFFFFFFFFFF----FF---FF-FF-FFFFFFF-FFFFFF--FFF-FFF8FFFFF-FF

Starting FASTQC command


Processing SRR6576552_1.fastq

Printing command:
fastqc --outdir SRR6576552_1.fastq

Analysis complete for SRR6576552_1.fastq

Processing SRR6576552_2.fastq

Printing command:
fastqc --outdir SRR6576552_2.fastq

Analysis complete for SRR6576552_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 168M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 33 root   root      4.0K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 L4-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  84M Oct 12 19:41 SRR6576552_1.fastq
-rw-r--r--   1 kkarri waxmanlab  84M Oct 12 19:41 SRR6576552_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:40 EDT 2018
0 hours, 0 minutes and 12 seconds elapsed.
==========================================================