-----------------------
Start of variable list:
-----------------------
Sample_ID:
H7-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-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791382
Current job name : Step_02_H7-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/8791382.1.linga

Loading required modules...


List files in scratch directory:

total 49M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 102 root   root      164K Oct 12 19:49 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:49 H7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  25M Oct 12 19:49 SRR6576401_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  25M Oct 12 19:49 SRR6576401_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

@SRR6576401.1 1/1
ACCCGCGCCTGCCGGCGTAGGGTAGGCACACGCTGAGCCAGTCAGTGTAGCGCGCGTGCAGCCCCGGACATCTAAGGGCATCACAGACCTGTTATTGCTC
+
FFFFFF-FFFFFFFFFF8FFFFFF88FFFFF8FFFFFFFFFFF-F-FF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF--FFF-FFFFFFF-F
@SRR6576401.2 2/1
TCTGTTTTCCGTGCGCACGTGAAGCACCGTAAGGGCGCCGCGCGCCTACGTGCTGTGGACTTCGCGGAGTCCACAGCAACATTAAAGGCATCGTAAAGGA
+
-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576401.3 3/1
AGGATTGCAGTGAGTTCCAGGCCAGAGAGAGATACAAAGAGATGACCAGTTTCCAAACACAAAACACAATGAAAACCCCAAAGCCCACACAGGGCTGCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576401.4 4/1
CACATCCAGAGGATAGTAGCCGGCAATGCTGCAGACGAGGGAAGGCAGAGGATCCTTGTTTGCCAAGTGCAGTTGTATTTTGGGGGGAGCCAGGATGTTA
+
FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576401.5 5/1
AAGTAAACGCTTCGGGCCCCGCGGGACACTCAGCTAAGAGCATCGAGGGGGCGCCGAGAGGCAAGGGGCGGGGACGGGCGGTGACTCGCCTCGCGGCGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576401_1.fastq

Printing command:
fastqc --outdir SRR6576401_1.fastq

Analysis complete for SRR6576401_1.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 159M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 101 root   root      164K Oct 12 19:49 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:50 H7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 134M Oct 12 19:49 SRR6576401_1.fastq
-rw-r--r--    1 kkarri waxmanlab  25M Oct 12 19:49 SRR6576401_2.fastq.gz
==========================================================
Finished on : Fri Oct 12 19:50:06 EDT 2018
0 hours, 0 minutes and 16 seconds elapsed.
==========================================================