-----------------------
Start of variable list:
-----------------------
Sample_ID:
H7-MAA100039-3_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 19:46:11 EDT 2018
Running on node : scc-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791251
Current job name : Step_02_H7-MAA100039-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791251.1.linga

Loading required modules...


List files in scratch directory:

total 62M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 89 root   root      108K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H7-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  30M Oct 12 19:46 SRR6576978_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  32M Oct 12 19:46 SRR6576978_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576978_1.fastq <==
@SRR6576978.1 1/1
CCCAAGAACCGTGAGGACAGAGCCGCCCTACTCCGAACCTTCAGCTTTCTTGGCTTTGAGATTGTGAGACCCGGGCATCCCCTTGTCCCCAAGAGACCCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576978.2 2/1
CATTAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGTTCCGACCATAAACGATGCCGACTGGCGATGCGGCGGCGTTATTCCC
+
FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF
@SRR6576978.3 3/1
GTGTGACATTTCTCCTTGGGGGGACTAGAGAAGAAACAGATTTCCATAGTTGACCAGGAATTAGTGCCTCACACTCAATTACCTGCATCAGTTTCTCACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576978.4 4/1
CTCTGAGTGTGTTCTTCAAATATTATGAAAAGGAAAGGGTGATCGAAGCGCACGATAGGGGGCATAGAATAAGGAACGGCTAGTAAGACTGTAGCTGCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576978.5 5/1
TTCTCAGGCTCCCTCTCCGGAATCGAACCCTGATTCCCCGTCACCCGTGGTCACCATGGTAGGCACGGCGACTACCATCGAAAGTTGATAGGGCAGACGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576978_2.fastq <==
@SRR6576978.1 1/2
NTCCAGAGTGTAGACCATGAAGCAAGCGTCGGGTCTCTTGGGGACAAGGGGATGCCCGGGTCTCACAATCTCAAAGCCAAGAAAGCTGAAGGTTCGGAGT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576978.2 2/2
NACCTGTTATTGCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGTAACTAGTTAGCATAC
+
#FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFF--FFFFFFF
@SRR6576978.3 3/2
NTCTTAAGCTCTGACCATAATTCTTGTATTTTATTTGGGAAGAAAAGAACTGTTTCTGATGGCATAAAATGAACATTTTTAAAGTTTTTTTTTTAAACTT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576978.4 4/2
NTCAGCAAGGAGCTCATCTCCAAGTTCCTGCTAAAGAGGCCCAGAAGGTTAGCCCAGATCCACTTCCCCAGACTGTCCATCTCTGGAGAATATAACTTGA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFF
@SRR6576978.5 5/2
TATCAACGCAGAGTACATGGGTCGCTCGCTCCTCTCCTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCCGACGGGCGCTGACCCCCCTTCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576978_1.fastq

Printing command:
fastqc --outdir SRR6576978_1.fastq

Analysis complete for SRR6576978_1.fastq

Processing SRR6576978_2.fastq

Printing command:
fastqc --outdir SRR6576978_2.fastq

Analysis complete for SRR6576978_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 333M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 80 root   root      108K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H7-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 167M Oct 12 19:46 SRR6576978_1.fastq
-rw-r--r--   1 kkarri waxmanlab 167M Oct 12 19:46 SRR6576978_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:47 EDT 2018
0 hours, 0 minutes and 36 seconds elapsed.
==========================================================