-----------------------
Start of variable list:
-----------------------
Sample_ID:
C6-MAA100140-3_57_F-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 19:44:28 EDT 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791036
Current job name : Step_02_C6-MAA100140-3_57_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791036.1.linga

Loading required modules...


List files in scratch directory:

total 97M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 38 root   root      112K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C6-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  48M Oct 12 19:44 SRR6575999_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  50M Oct 12 19:44 SRR6575999_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575999_1.fastq <==
@SRR6575999.1 1/1
TATAGGAAAAGGGAAGGTAGAAGAGCTGAAGGCACTCGTGGAAGAGCTTGAAGCTGATCTCCTCATCTTTAATGATGAACTGTCGCCAAGTCAGCTGAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575999.2 2/1
GATAAGAACCCTCCAGCTCGGGGCCTCAAACCGATATTCCATGTGGGCCAACTGCCATGTTGTGTCCAGTCGCTATCGGAGTAGCCGCGCTGGTGCCACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575999.3 3/1
GCTGTGTACAAGGCAGGGGCACGCGAGGGCGCCGAGCGCGGTGTGAGTGCCATCCGTGAGCGCCTGGGGCCTCTGGTGGAGCAAGGTCGCCAGCGCACTG
+
FF8-F8FF-FFFFFFF-FFFFFFFFFFFFFFFF8FFFFFFFFF--FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF
@SRR6575999.4 4/1
TCTTGGGAGCGGGCGGGCGGTCCGCCGCGAGGCGAGTCACCGCCCGTCCCCGCCCCTTGCCTCTCGGCGCCCCCTCGATGCTCTTAGCTGAGTGTCCCGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575999.5 5/1
GTCTGGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGACCCCCGAGCGGTCGGCGTCCCCCAACTTCTTAGAGGGACAAGTGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575999_2.fastq <==
@SRR6575999.1 1/2
NGTCGGTATAAAATCAGGCAGTTTTTGTTCACGTTTATTGTAAGCCGTCCGCATCGGGATATCATCTGCTTCCAGCTCCTCAAGCAGCCGAAGCTCTGTT
+
#F-FFFFFFFFF8FFFFFFFFFFFFFF-FFF-FF-F--FFFFFFFFF-F-FFFFFFFF---FFFFFFFF----FFFFFF-FFFFFFFF-FFFFF-8FFFF
@SRR6575999.2 2/2
NGGTATATGATGTTGCTCTGCAAGAACCTTTAGGCTAGGCCTTATTAACCTCTCTCTCCTACATTTGCTATGCGTCTCAAGATAAGGATATTATCTCATA
+
#8FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFF
@SRR6575999.3 3/2
GGAGAAGGATACTCATTGATTCTCCTGGGCCACTGGGGTGATGATGGGGTTGGTAGCCACAGAGGCCTGTATCTTCTCCATCAGGTTTGCCCACTGGCGA
+
-FFFFFFFF8FFFFFFFFFF88FF--FFFFFFFFFFFFFFFFFFF-FFFFFFFFFF---FFFFF-FF-FFF-FFFFFFFFFF-F-FFF-F-FFFF-8-FF
@SRR6575999.4 4/2
GGCCTGCTTTGAACACTCTAATTTTTTCAAAGTAAACGCTTCGGGCCCCGCGGGACACTCAGCTAAGAGCATCGAGGGGGCGCCGAGAGGCAAGGGGCGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF
@SRR6575999.5 5/2
ACGCAGAGTACATGGGGAATAATTGCAATCCCCGATCCCCATCACGAATGGGGTTCAACGGGTTACCCGCGCCTGCCGGCGTAGGGTAGGCACACGCTGA
+
FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575999_1.fastq

Printing command:
fastqc --outdir SRR6575999_1.fastq

Analysis complete for SRR6575999_1.fastq

Processing SRR6575999_2.fastq

Printing command:
fastqc --outdir SRR6575999_2.fastq

Analysis complete for SRR6575999_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 551M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 38 root   root      112K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 C6-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 275M Oct 12 19:44 SRR6575999_1.fastq
-rw-r--r--   1 kkarri waxmanlab 275M Oct 12 19:44 SRR6575999_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:18 EDT 2018
0 hours, 0 minutes and 50 seconds elapsed.
==========================================================