-----------------------
Start of variable list:
-----------------------
Sample_ID:
E1-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 19:41:27 EDT 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790763
Current job name : Step_02_E1-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/8790763.1.linga

Loading required modules...


List files in scratch directory:

total 277M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 41 root   root      112K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 E1-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 135M Oct 12 19:41 SRR6575620_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 142M Oct 12 19:41 SRR6575620_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575620_1.fastq <==
@SRR6575620.1 1/1
CNTGATGAGGTATCCTAGGTAACATGTGGATAGACTGGAATTGGACTTCTCAGTGAGACAGGATGGAATGCAGATCACAGAATTTATACTGGGGATGCTG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF
@SRR6575620.2 2/1
GNAAATGACATAGCCTTGCTTAGCCTTGTATCCCAGTCTTCGAGCTTTATCAGGCCGGGTGGGGCGGGGAGCCCTGTGCAGNGCAGAGAGCTGGCGGTAT
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFFFF
@SRR6575620.3 3/1
GGCTCGGCTCCCGCCTGCCTCCACTGCTCGCCAGCCGCGCGCAGCTGCGCCTGATGCCCAGAGCAGCTCGGAGGTGGCCCCAGGACATCCCAGAGGGGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575620.4 4/1
TNCTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGGTNCGAAGACGATCAGATACC
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFFFF
@SRR6575620.5 5/1
ANATAATTCGGAGCACTCTTCATCTCTTACAGTATGGACTTTAAGAACTAAGGAATTCTCCAAGACATGGATTTGCTCCAGNAAAAGTCTAAAGTTGCCA
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFFFF

==> SRR6575620_2.fastq <==
@SRR6575620.1 1/2
NTACANGGGTGTGTCCATGCAGAAGAAGCTAGTTCTACGGGAAGGAAGTTTAATGTAGAAAAGATTAATGGGGAATGGCATACTATTATCCTGGCCTGTG
+
#F---#FFF8FF8FF-FFF88F-FF-FFF-FFFF-FFFFFFFFFFF--F-FF-F-F-FFFFFFFF-FFFFF-FFFFFFF8FFFFFFFFF---FF-FF--F
@SRR6575620.2 2/2
NTCCTNTCCTCTGNCGGCAGCCATCAGGTGAGCCAAGATGGGTGCATACAAGTACATCCAGGAGCTATGGAGGAAGAAGCAGTCCGACGTGATGCGCTTT
+
#FFFF#FFFFFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F
@SRR6575620.3 3/2
NGTTTATAGTGCAAGGTTCATCTGGATACCCATCAAAAGCAGACGGTGTGATAGTCTCTAGGCTCGCAGACACCACAAGACACAAGCTGAGGAGACCGAC
+
#FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575620.4 4/2
NACCANCACCCACGGAATCGAGAAAGAGCTATCAATCTGTCAATCCTGTCCGTGTCCGGGCCGGGTGAGGTTTCCCGTGTTGGGTCAAATTAAGCCGCAG
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFF-FFFFFFFFFFFF
@SRR6575620.5 5/2
NGTATNAACGCAGAGTACATGGGGGAGTGTAGCCACGATCACAAGAAAGACGTGGTCCTGACAGACAGACAATCCTTTTCCCTACCAAAATGAAGATGCT
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575620_1.fastq

Printing command:
fastqc --outdir SRR6575620_1.fastq

Analysis complete for SRR6575620_1.fastq

Processing SRR6575620_2.fastq

Printing command:
fastqc --outdir SRR6575620_2.fastq

Analysis complete for SRR6575620_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 1.6G
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 50 root   root      112K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:43 E1-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 817M Oct 12 19:41 SRR6575620_1.fastq
-rw-r--r--   1 kkarri waxmanlab 817M Oct 12 19:41 SRR6575620_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:24 EDT 2018
0 hours, 1 minutes and 57 seconds elapsed.
==========================================================