-----------------------
Start of variable list:
-----------------------
Sample_ID:
B4-MAA100040-3_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 19:42:19 EDT 2018
Running on node : scc-tm4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790979
Current job name : Step_02_B4-MAA100040-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790979.1.linga

Loading required modules...


List files in scratch directory:

total 62M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 38 root   root       20K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B4-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  30M Oct 12 19:42 SRR6577022_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  32M Oct 12 19:42 SRR6577022_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6577022_1.fastq <==
@SRR6577022.1 1/1
GCCTTTTCTGTTTGTTCACCAATCGCAGTCATTTCGGTGCACTCTTCATTTACAATTAAATGGAATTTAAAGACTAAGGAATTCTCCAAGACAGTGATGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577022.2 2/1
ATATACTGCTGACCGGGGCGCTGCAGTTCGGCTACTGTCTCCTCGTGGGCACCTTCCCCTTCAACTCTTTCCTCTCTGGCTTCATCTCTTGTGTGGGCAG
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFF
@SRR6577022.3 3/1
GTACATGGGGACTACGAAGTTCCGGCTCAGGTCGCCTACCTCGAGTTTGTGCGTCTGTAGTGTCGGAGTCGGCTGAAGCTGGTCAGGATGATCACGGACG
+
FF8FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577022.4 4/1
GGACGAACATGAACCCTAATAATTGTTTCCCTAATCATATTTATTGGATCAACAACTCTCCTAGGCCTTTTACCACATACATTTACACCTACTACCCAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577022.5 5/1
TCTTGAAGGCGTGGTCTGTCTGAGTTATCTTTTCCTTCTGGTGGAGGTGGGCATCCAAGTTTATCTGTCTTATGGGTATGATGATGATCCCTGGATCCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6577022_2.fastq <==
@SRR6577022.1 1/2
GAACTGACTTTAGTCTGTATCCATGCAGAAGAATCTAGTTCTATGGAAAGGAACTTTAATGTAGAACAGATTAGTGGGTATTGGTTTTCTATTGCTGAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF
@SRR6577022.2 2/2
GTGCAGGATCGTGCTGGCAAAGAGGAAGTCAGCAAAGGCTCGCTCCGGAGAGATGCCTTGGAAGTCCGCCTTGTTCTGGGGGTTGATCTGTATTCTCAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF
@SRR6577022.3 3/2
CCCCTATACTGGGCCCTATTCAGTGGCAGCTTCTTGCTCCATAGGGTTAAGGAAGACTTTGAGGAAATAAAAGTTGTTTGGAAAAATCCAGGTGTAGTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF
@SRR6577022.4 4/2
CTGTTGGTGGGCTAATATTTATTAATACTAGAGTAGCTCCTCCGATTAGGTGTATTAATAAGTGTCCTGCAGTAATGTTAGCTGTAAGCCGGACTGCTAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF--F
@SRR6577022.5 5/2
CTTTCAGAGTGGAACGGGCAGAACGGGTTATAAGAGCGAGAGGAGGGGAAAGAACCAATTACTATGTGGAATTCTCCATGAGGAACTGTTCCACACAGCA
+
FFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFF-FFFFFFFFFFFFFFFFF8FFFFFFFFFFF8FFF

Starting FASTQC command


Processing SRR6577022_1.fastq

Printing command:
fastqc --outdir SRR6577022_1.fastq

Analysis complete for SRR6577022_1.fastq

Processing SRR6577022_2.fastq

Printing command:
fastqc --outdir SRR6577022_2.fastq

Analysis complete for SRR6577022_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 345M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 38 root   root       20K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B4-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 173M Oct 12 19:42 SRR6577022_1.fastq
-rw-r--r--   1 kkarri waxmanlab 173M Oct 12 19:42 SRR6577022_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:42 EDT 2018
0 hours, 0 minutes and 23 seconds elapsed.
==========================================================