-----------------------
Start of variable list:
-----------------------
Sample_ID:
A4-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 19:42:18 EDT 2018
Running on node : scc-tl3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790931
Current job name : Step_02_A4-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/8790931.1.linga

Loading required modules...


List files in scratch directory:

total 72M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 38 root   root      132K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A4-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  37M Oct 12 19:42 SRR6576792_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  35M Oct 12 19:42 SRR6576792_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576792_1.fastq <==
@SRR6576792.1 1/1
GTCTGTGTCCATGCAGAAGAAGCTAGTTCTACGGGAAGGAACTTTAATGTAGAAATGATTAATGGGGAATGGCATACTATTATCCTGGCCTCTGACAAAA
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFF-FFF-FFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFF-FFFFF-FFFF
@SRR6576792.2 2/1
CACCCGTGGTCACCATGGTAGGCACGGCGACTACCATCGAAAGTTGATAGGGCAGACGTTCGAATGGGTCGTCGCCGCCACGGGGGGCGTGCGATCGGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6576792.3 3/1
GTAAATGTATTGAATCCATCATACGTCACAGAATATTCACCAGCCTTTTCTGTTTTGTCAGCAACCATAGATAATTCCGAGCACTCTTCATCTCTTACAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576792.4 4/1
GTAAAGTCCTAGTATAATGGTAATTAGTAGGGCTTGATTTATGTGGTTTCGTTTACCTTCTATAAGGCTATGATGAGCTCATGTAATTGAAACACCTGAT
+
FFFFFFFFFFFFFFFFFFFF8F8FFFFFFFFF8F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6576792.5 5/1
AGCCTACACTGACATGAAGGAAGCTGGCTGGAAAGATGGAGACAAATACTTCCATGCTCGGGGGAACTATGATGCTGCCCAAAGGGGTCCCGGGGGAGTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF---FFFFFF-FFFFFFFFFFFFFFF

==> SRR6576792_2.fastq <==
@SRR6576792.1 1/2
NCCATAGATAATTCGGAGCACTCTTCATCTCTTACAGTATGGAATTTAAGAACTAAGGATTTCTCCAAGACATGGATTTGCTCCAGAAAAAGTCTAAAGT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFF
@SRR6576792.2 2/2
NTACCTGGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFF-FFFF
@SRR6576792.3 3/2
NAGACAGACAATCCTATTCCCTACCAAAATGAAGATGCTGCTGCTGCTGTGTGTGGGACTGACCCTAGTCTGTGTCCATGCAGAAGAAGCTAGTTCTACG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF
@SRR6576792.4 4/2
NTATAATTCTATTCATCGTCTCGGAAGTATTTTTCTTTGCAGGATTCTTCTGAGCGTTCTATCATTCTAGCCTCGTACCAACACATGATCTAGGAGGCTG
+
#FFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576792.5 5/2
CACATGAGAGGTATACTATGTTGCCCCAGAGAGCATCTTCAGTGTTCCTAGATAGGAAGCCCAGACCCCACCCTCAGGACCCCAACACAGCCTTCTGAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFF

Starting FASTQC command


Processing SRR6576792_1.fastq

Printing command:
fastqc --outdir SRR6576792_1.fastq

Analysis complete for SRR6576792_1.fastq

Processing SRR6576792_2.fastq

Printing command:
fastqc --outdir SRR6576792_2.fastq

Analysis complete for SRR6576792_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 406M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 38 root   root      132K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A4-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 203M Oct 12 19:42 SRR6576792_1.fastq
-rw-r--r--   1 kkarri waxmanlab 203M Oct 12 19:42 SRR6576792_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:43 EDT 2018
0 hours, 0 minutes and 25 seconds elapsed.
==========================================================