-----------------------
Start of variable list:
-----------------------
Sample_ID:
A4-MAA100041-3_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-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790932
Current job name : Step_02_A4-MAA100041-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790932.1.linga

Loading required modules...


List files in scratch directory:

total 33M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 89 root   root      108K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A4-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  16M Oct 12 19:42 SRR6575311_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  17M Oct 12 19:42 SRR6575311_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575311_1.fastq <==
@SRR6575311.1 1/1
ACTTAAGACAGACTATGATAATTATATTATGATTCATCTCATTAACAAAAAGGATGGAGAAACCTTCCAGCTGATGGAGCTCTATGGCCGAGAACCAGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF
@SRR6575311.2 2/1
TATCAAGAAGGAGTTTGACAAGAAGTACAACCCTACCTGGCACTGCATTGTGGGCCGAAACTTCGGTAGTTATGTGACACATGAAACCAATCACTTCATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF
@SRR6575311.3 3/1
CCATCTGCTGGTGGCTCCAGCCAAGGTGCCTCTTAGCCACTGAATTGCTATGTTATCCTTTCTCTTGTAACAAACCCACCCCAGAGATAAAGCCTTTATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF8FFFFFFFFF-FFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-F
@SRR6575311.4 4/1
TTCTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575311.5 5/1
GTCTTATGTGCATGTGGGATCACAGAGATAGTCAATGTAGCTGTCTAAGCCAACTTTGGAACAGCCAATCAGAGCTTGAATGACAGGATGTATATAGAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575311_2.fastq <==
@SRR6575311.1 1/2
ATTTAAAGAAAGACTTTGATTCTTGATGAGTTATCCTAGTAACATGCTGGAGAGACAGGGATTGCACTTCTCTGTAAGACACGATGGAAAGCAGATCACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FF8F
@SRR6575311.2 2/2
GACTTGTACAGAGAATGAAGCCCTGTACACAACACAACAGATTCAAACGAGGTGTTCCCTTAGCAAGGCTGAAGATTCAGTCTCTGGTATTTGGAATTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575311.3 3/2
GGGTAGGTAGTCTTGCACTTTGACTGGTCATATCTGTCAGTCTCTGGGAAGAGCAATGTAGACTAAACGATGGTCTCAGGAACATATATAGTTCTTTGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6575311.4 4/2
ACTCCCCCCGGAACCCAAAGACTTTGGTTTCCCGGAAGCTGCCCGGCGGGTCATGGGAATAACGCCGCCGCATCGCCAGTCGGCATCGTTTATGGTCGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFF8FFFF
@SRR6575311.5 5/2
TCCTCTTTATGGCCAAAGTCAATAACCCCAAGTAGACCTAAAGCTCACCAAGTTCTCATGATTCTGTCCAGGGCTCTGGGACAGAGTCTGCATATGGATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575311_1.fastq

Printing command:
fastqc --outdir SRR6575311_1.fastq

Analysis complete for SRR6575311_1.fastq

Processing SRR6575311_2.fastq

Printing command:
fastqc --outdir SRR6575311_2.fastq

Analysis complete for SRR6575311_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 207M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 89 root   root      108K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A4-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 104M Oct 12 19:42 SRR6575311_1.fastq
-rw-r--r--   1 kkarri waxmanlab 104M Oct 12 19:42 SRR6575311_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:48 EDT 2018
0 hours, 0 minutes and 30 seconds elapsed.
==========================================================