-----------------------
Start of variable list:
-----------------------
Sample_ID:
P18-MAA000377-3_9_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 19:42:18 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790899
Current job name : Step_02_P18-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790899.1.linga

Loading required modules...


List files in scratch directory:

total 29M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 95 root   root       92K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 P18-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  14M Oct 12 19:42 SRR6575348_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  15M Oct 12 19:42 SRR6575348_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575348_1.fastq <==
@SRR6575348.1 1/1
GTAAAGAACCCAGTCTAGGAAAGTCAGTAAATCTTTTGGGAGTCTCACATCTGTAAAACCAGGCTAAGGCTACACCCATCTTAAAATCTGAAGCCAGTAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF
@SRR6575348.2 2/1
ATCCTGAGTGCTAGGATTAAAGGCATATACCATCATACTTAGCTTCTTTGCTTTTTAAAATTTCTTTTCACTATGATAATATTGCAGCTAGTATAATGTT
+
FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFF-FFFFFFFFFFFFFFF-FFFF-FFF--FF--
@SRR6575348.3 3/1
GTTTGCTACTTACATGAAAAGAAGATTTTAAAAAACAATCACTGCACAAAATACAAAGGGGCAGGGTATGCTGTGGCATTGAATTCCTCCCCACGTTTTT
+
FFF8FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-F-FFF-FFFF
@SRR6575348.4 4/1
ATAATCCCCAGAGCCGAGTGGTAGAAGGAGACCCAATCCAACAACACTGCCCTCTGCCCCTCCCCTGCGCCGGCACACATGCACAAGTGTAAGAAACATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFF
@SRR6575348.5 5/1
CTACAAAGAAATGGCCCTTCTGTTTCAGGTTGATGCCACAGTCGGTGCACACATAGCATTCAGGGTGGCGATGGTGATCCCTCAGCTTCACAAACACACC
+
FFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF

==> SRR6575348_2.fastq <==
@SRR6575348.1 1/2
ATATGGTAGCACCTGTGACAGGTAACGATGCTGGAATTCGGAGAGCAGAAATTAAGCAAGGGATCCGTGAAGTTATTTTGTGTAAGGATCAAGATGGAAA
+
F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFF-FFFFFFFF-FFFFFFFF-F--FFFFFFFFFF-FF-FF8--F
@SRR6575348.2 2/2
GCGGGTCTCGTACGTGTAGTTCGCGTCGGCCCCCGCGTGGCGTGTCCCAGGGTTGGCTCCGGCGTGTGGGTCCTGTCAGCGGTGTACATGGGTGCTTGGC
+
---FF88F8FF888FFF8F88888888FFF-8FF---FFF------F-FF-F--F----FFFFF---FF---F--F--8--F-FF----F----F---F8
@SRR6575348.3 3/2
CAACAAGAAACTCACTGCTTATTTGGACCTTAACCTGGACAAGTGCTACGTGATTCCTCTGAACACTTCCATCGTTATGCCGCCCAAAAACCTGCTGGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF
@SRR6575348.4 4/2
ATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTGGTTCTATCTGGACTTTGTAAGGAGTGATGTGTGGGTAGGAAGCCTCTTGTTGCTACACATAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF--FFFF-FFF-FF-FFF-F-FF-F-FFF-F---FF8F-FFFF-FFF-FF--FFFFF-
@SRR6575348.5 5/2
TCCCTACAAGATGAATTTAGCGTCGGAACCCCAAGAAGTCCTGCACATAGGAAGTGCCCACAACCGAAGTGCCATGCCATTTACTGCCTCACCTGCTCCC
+
FFFFFFFFFFFFF8FFFFFFFF8FFFFFFFFFFFF-FFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF

Starting FASTQC command


Processing SRR6575348_1.fastq

Printing command:
fastqc --outdir SRR6575348_1.fastq

Analysis complete for SRR6575348_1.fastq

Processing SRR6575348_2.fastq

Printing command:
fastqc --outdir SRR6575348_2.fastq

Analysis complete for SRR6575348_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 146M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 95 root   root       92K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 P18-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  73M Oct 12 19:42 SRR6575348_1.fastq
-rw-r--r--   1 kkarri waxmanlab  73M Oct 12 19:42 SRR6575348_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:42 EDT 2018
0 hours, 0 minutes and 24 seconds elapsed.
==========================================================