-----------------------
Start of variable list:
-----------------------
Sample_ID:
G7-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 19:46:08 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791209
Current job name : Step_02_G7-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/8791209.1.linga

Loading required modules...


List files in scratch directory:

total 111M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 101 root   root      180K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 G7-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  54M Oct 12 19:46 SRR6575684_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  57M Oct 12 19:46 SRR6575684_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575684_1.fastq <==
@SRR6575684.1 1/1
TAGTGATTCATCTTCTGAACAGCCAGCCTGTGCACGGAGCCTCACACTGAAAGGGCCAACTGTAAAGGACTTGGGAATTTGGCAATATCTTTGTTTAAGT
+
-FFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFF8FFFFFFFFFFFF-FFFF-FFFFFFFFFF-F--F---FFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6575684.2 2/1
GAATAATGGAATAGGACCGCGGTTCTATTTTGTTGGTTTTCGGAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGG
+
8FFFF8FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6575684.3 3/1
ACTTGAGACGATCGGTAAATCTAAAGTTGGCGTTCCGCCCCCAGCCAGACACGTAGCCCACACGGCCTGGTGCTATGTAGTCTTTGGAAGGCAGGCAGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6575684.4 4/1
GCCTAAAGGAAAGATCCAAAAAGATAAAAGGAACTCGGCAAACAAGAACCCCGCCTGTTTACCAAAAACATCACCTCTAGCATTACAAGTATTAGAGGCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575684.5 5/1
GGGTTAGGTCGCTCTGAGTGGTGGAGCAGTCCAGGAACTGCTTGATCTCATAGGAGCAGGGCCCCATCTGCAGGGGGTGAGAGGCAGGCCGGGCAGGGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575684_2.fastq <==
@SRR6575684.1 1/2
NTCTTCAGGTGGATAAAATGAATGGGATCTCGGTACCTATCATCTTATACCCAGACGGCTCTGAGAAAACAGCACAAAAACTTACAGATAAAACAGATAT
+
#FF--FFFF8FFFFFFFFFFFF-8FFFFFF-FFFFF-FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFF8-FFFF
@SRR6575684.2 2/2
NGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCTTTGCAACCATACTCCCCCCGGAACCCAAAGACTTTGGTTTCCCGGAAGCTGCCCGGCGGGTCA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF
@SRR6575684.3 3/2
GTGTGGGAAACCCAAGCACCCTGTGGACCAGGTGCAGCGCATCATCGGTGGCTCTATGGATGCCAAAGGCAGCTTTCCTTGGCAGGCCAAGATGATCTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FF8FFFFFFFF
@SRR6575684.4 4/2
CTTCACTGAAAGGTCAATTTCACTGATTAAAGATAAGAGACAGTTGGACCCTCGTTTAGCCGTTCATGCTAGTCCCTAATTAAGGAACAAGTGATTATGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF--
@SRR6575684.5 5/2
GCTGCCAGGCCGGTCAGCCGCCCAGCCCCGCCTCCTGCGCACCCACCACCCTCAGCGGCCGCCCCGGCACCTGCCGCTCCCGGCCAGCCGGGTCTTATGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFF-F-F-FFF

Starting FASTQC command


Processing SRR6575684_1.fastq

Printing command:
fastqc --outdir SRR6575684_1.fastq

Analysis complete for SRR6575684_1.fastq

Processing SRR6575684_2.fastq

Printing command:
fastqc --outdir SRR6575684_2.fastq

Analysis complete for SRR6575684_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 622M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 90 root   root      180K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:47 G7-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 311M Oct 12 19:46 SRR6575684_1.fastq
-rw-r--r--   1 kkarri waxmanlab 311M Oct 12 19:46 SRR6575684_2.fastq
==========================================================
Finished on : Fri Oct 12 19:47:01 EDT 2018
0 hours, 0 minutes and 53 seconds elapsed.
==========================================================