-----------------------
Start of variable list:
-----------------------
Sample_ID:
H10-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 19:46:08 EDT 2018
Running on node : scc-kb6
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791216
Current job name : Step_02_H10-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/8791216.1.linga

Loading required modules...


List files in scratch directory:

total 86M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 97 root   root       84K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H10-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  41M Oct 12 19:46 SRR6575511_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  45M Oct 12 19:46 SRR6575511_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575511_1.fastq <==
@SRR6575511.1 1/1
ATCCTGTCCGTGTCCGGGCCGGGTGAGGTTTCCCGTGTTGGGTCTAATTAAGCCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTGTATGTT
+
FFFFFFFF--FFFFFFFFFFFFFFFFFF8FFFFFFF8FFFF-8F--F-FFFFF-FFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFF-FF-FFF
@SRR6575511.2 2/1
ATTCCATGCTTCTCACATAGTTGTGCAAACCTTTCCTTGATGTCTGAACTCAAATCTGGTTCTCGGCCATAGAGCCCCATCAGCTGGAAGGTTTCCCCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF
@SRR6575511.3 3/1
GTCCTTTCCTTGCTTGGAGCCCGCTGTGCCTTCATGGGCTCTTTGGCCCCTGGCCACGTTGCCGACTTCCTGGTGGCTGACTTCAGGCAGAGGGGCGTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575511.4 4/1
CATGAGTACAGCCGAGTGATAACAGTAGATGGGAACATATGCTCTGGGAAAAACAAGCTCGCAAAGGAGATCGCACAGCAACTAGGCATGAAGCACTACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575511.5 5/1
GCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTCAAGGGTAAAAAATTTTTTAAAAGTAAAATTAAAAAATTAAATAAAAATTTTAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-F---F-FFF-F-F---F-FFF-FFF---F-----F-FFF--FF--FFFFF-F-FFF

==> SRR6575511_2.fastq <==
@SRR6575511.1 1/2
NAACAATACAGGACTCTTTCGAGGCCCTGAAATTGGAATGAGTCCACTTTAAATCCTTTAACGAGGATCCAGTGTAGGGCAAGTCTGGTGCCAGCAGCCG
+
#FFF-FFFFFFFFFFFFFFFFFF8FF-FF-FFFFF-FFFFF-FF-FFF-FF--FFFFF--FF--F-FFFFF-FF-FF-F8-FFFFFFFFFFFFFF-F-FF
@SRR6575511.2 2/2
NATTAATGGGGAATGGCATACTATTATCCTGGCCTCTGACAAGAGAGAAAAGATAGAAGATAATGGCAACTTTAGACTTTTTCTGGAGCAAATCCATGTC
+
#FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575511.3 3/2
NTGTGGATCCACTTGAACCGGGTCAGATCGACCTTCTCAAAGTCCTTAGCAGACACATCTGGCAGGTTCGTGTCGTAGAGTATAATGGTACGGGAGCCAT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575511.4 4/2
GCTCTGTACCTCCGGCACGGGCACATCGATATAGATGACTGCGTGTGGTGGCAGGTACTCCGGGAGAGTGAGCCGCTTAATTTCATTATAGTGGTCCACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF
@SRR6575511.5 5/2
ATCCAATGCCAATCGCTGCCTCCAGGCCCGAGAATGAAGAATGGCCTGAGCCTCCAGTGTTGAGTGGAGACTTCTCACCAGGACTCCACCATCATCCCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575511_1.fastq

Printing command:
fastqc --outdir SRR6575511_1.fastq

Analysis complete for SRR6575511_1.fastq

Processing SRR6575511_2.fastq

Printing command:
fastqc --outdir SRR6575511_2.fastq

Analysis complete for SRR6575511_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 469M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 89 root   root       84K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H10-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 235M Oct 12 19:46 SRR6575511_1.fastq
-rw-r--r--   1 kkarri waxmanlab 235M Oct 12 19:46 SRR6575511_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:55 EDT 2018
0 hours, 0 minutes and 47 seconds elapsed.
==========================================================