-----------------------
Start of variable list:
-----------------------
Sample_ID:
H6-MAA100042-3_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 19:41:29 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790804
Current job name : Step_02_H6-MAA100042-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790804.1.linga

Loading required modules...


List files in scratch directory:

total 198M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 84 root   root       92K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 H6-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  96M Oct 12 19:41 SRR6575707_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 102M Oct 12 19:41 SRR6575707_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575707_1.fastq <==
@SRR6575707.1 1/1
TNTATGAGAAGCGCATGGCCACGGAAGTAGCCGCTGATGCTCTTGGTGAAGAGTGGAAGGGTTATGTGGTCCGGATCAGCGGTGGGAATGACAAGCAAGG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF
@SRR6575707.2 2/1
TCTGTTTATAGCATGCACTTTTAAAACCCAACTATTCAGTCCCTTTTAAACAGAGACAGGATGATAGAAACCCACCACCATGACTTCCGGAAGGGGCTAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575707.3 3/1
GGTATCAACGCAGAGTACATGGGAACCTGTTACCTAAATATCTTTTTATTATATTGTTAATATGTAATTCTACTGTAGACCAAAAATATAAAAACAAATT
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFF
@SRR6575707.4 4/1
GGCGTGCGATCGGCCCGAGGTTATCTAGAGTCACCAAAGCCGCCGGCGCCCGACCCCCGGCCGGAGCCGGGAGGGAGCTCACCGGGTTGGTTTTGATCTG
+
FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575707.5 5/1
GGATAATAGTATGCCATTCCCCATTAATCTTTTCTACATTAAAGTTCCTTCCCGTAGAACTAGCTTCTTCTGCATGGACACACACTAGGGTCAGCCCCAA
+
FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575707_2.fastq <==
@SRR6575707.1 1/2
NCTTTNTTTACCATGACCAAGTTGAGAACACTGAGATTAGCGTCCACAATGCATCCACGAACAGACTTGCGCTTCCTCTCTCCAGTTCTCCTTGGCCTGT
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFF-F-FF
@SRR6575707.2 2/2
NGATTATGTATATTTAGTTGGATATTGGACATCTTGGCAACACAATCTTACAAAGGCAGATTCAGCTGCCCCCATACCACTGTGTTCCTTCTGTAACGCC
+
#FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6575707.3 3/2
NTATAATAAAATCAGGCATTACCAAAAGAAAAAAACAATAGCATCATTGTGCAACCTCGAACACATCAAAGGAAACAGACAGACAAGGCTTGCAGAACGT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575707.4 4/2
NTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFFFFFF-FFFF8FF
@SRR6575707.5 5/2
NTACCAAAATGAAGATGCTGCTGCTGCTGTGTTTGGGGCTGACCCTAGTGTGTGTCCATGCAGAAGAAGCTAGTTCTACGGGAAGGAACTTTAATGTAGA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575707_1.fastq

Printing command:
fastqc --outdir SRR6575707_1.fastq

Analysis complete for SRR6575707_1.fastq

Processing SRR6575707_2.fastq

Printing command:
fastqc --outdir SRR6575707_2.fastq

Analysis complete for SRR6575707_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 1.1G
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 95 root   root       92K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 H6-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 556M Oct 12 19:41 SRR6575707_1.fastq
-rw-r--r--   1 kkarri waxmanlab 556M Oct 12 19:41 SRR6575707_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:50 EDT 2018
0 hours, 1 minutes and 21 seconds elapsed.
==========================================================