-----------------------
Start of variable list:
-----------------------
Sample_ID:
A7-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 19:42:18 EDT 2018
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790942
Current job name : Step_02_A7-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/8790942.1.linga

Loading required modules...


List files in scratch directory:

total 62M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 112 root   root      164K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 A7-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  30M Oct 12 19:42 SRR6577005_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  33M Oct 12 19:42 SRR6577005_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6577005_1.fastq <==
@SRR6577005.1 1/1
GGGTTTTTTCTGAATGGGACCAGCTCATCTAAGTGCACGGAGGAAGGAAAATGGAGCCCAGATATTCCTGCTTGTGCTCGCATCACCTGCCCGCCACCAC
+
FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577005.2 2/1
GTACATAGGCGCATCCACTGGCCTTGCAGGAAGAAGACCATGTCATCGATACTCATGGCATCACAGACAAAGTGTGCGCCCAGCAGCCCAGTATCAGAGT
+
FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFF
@SRR6577005.3 3/1
GGCTGCTGACCACGGCCAAAAACCTCTTCCTGAACCACAGCGAGACGGCGTCAGCCAAGGACATCACCCCCACCCTAACGCTCTACGTGGGGAAAAACCA
+
F8F8FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577005.4 4/1
TCATACAGCTGTGTAAATCCCAGATTCTCAAGCACCCTTCTCTAGCCAGGCGGACCTCTGCCCAAAACTGCACCTTAGCCACCACCTGGAACCGCGAGTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577005.5 5/1
GCCAGATGAGGTAGATGTGAAAGTGGATCCCAAGGATCTGCGAGTAGACACATTTCGAGCCAGAGGAGCAGGGGGGCAGCATGTTAACACCACCGACAGT
+
-88FFFF-FFFFFFFFFFFFFFF8F8FFFFFFFFFFF8FF--FFFFFFFFFF-FFFFFFF-FFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFF

==> SRR6577005_2.fastq <==
@SRR6577005.1 1/2
NCCTCATCCCTTGGTACAGCACGGTGGCTTTCTTAACGGGGAGTTTGCAAGACTCTCTACAGGTCGGCAAGAAGGACCAAGTTCCCGTCTTGGTACATTC
+
#-FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFF
@SRR6577005.2 2/2
NCCATGCAGAACGTGGTCTTTGATTACCTGCATGCGACAGCATTCCAGGGCACACCTCTAGCCCAGGCTGTGGAGGGGCCCAGTGAGAACGTCAGGAGGC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF
@SRR6577005.3 3/2
NGTAAATCTAAAGTTGGCGTTCCGCCCCCAGCCAGACACGTAGCCCACACGGCCTGGTGCTATGTAGTCTTTGGAAGGCAGGCAGATAGGCATGACTCTC
+
#FFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFF--FFFFFFFF8F-FFFFFF
@SRR6577005.4 4/2
CCCACGCTCTGCACGACTATTGGCTGCTCCAAGACTTTGGCTGTGTTCCCATAGAGGAGCCTGGCCTGGGCCAGGGCATTTGCGAAAGCAAACAGGAGCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF8FFFFF
@SRR6577005.5 5/2
GTCTTTCTCGATTATCTGTTGGTAGAGTCTGGCTCTCAACACACGCAAAGCTATTTCTTTATTTTTCAGCTGTGATCGTTCTTGTTGGCACTCTACTACC
+
-FFFFF-FFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8

Starting FASTQC command


Processing SRR6577005_1.fastq

Printing command:
fastqc --outdir SRR6577005_1.fastq

Analysis complete for SRR6577005_1.fastq

Processing SRR6577005_2.fastq

Printing command:
fastqc --outdir SRR6577005_2.fastq

Analysis complete for SRR6577005_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 349M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 112 root   root      164K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 A7-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 175M Oct 12 19:42 SRR6577005_1.fastq
-rw-r--r--    1 kkarri waxmanlab 175M Oct 12 19:42 SRR6577005_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:52 EDT 2018
0 hours, 0 minutes and 34 seconds elapsed.
==========================================================