-----------------------
Start of variable list:
-----------------------
Sample_ID:
H8-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 19:46:09 EDT 2018
Running on node : scc-tk4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791254
Current job name : Step_02_H8-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/8791254.1.linga

Loading required modules...


List files in scratch directory:

total 42M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 38 root   root       52K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H8-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  21M Oct 12 19:46 SRR6575507_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  22M Oct 12 19:46 SRR6575507_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575507_1.fastq <==
@SRR6575507.1 1/1
CCCTATACGCGATGGATCGAGGTCATGACTGGACACTGCATCGGAAGACACTTCGTGCCGACACGAAGCAGCCTCAATATCTAACACGAGGATGTTCCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575507.2 2/1
CATATACCCTGTAGAACCCGACTTTTGGGTTTAGGGGCCTGCCGTCAGCTACAATTCATGCTTGAAGGTTTCACTAGATCGTGTTATGGACGATGACTAT
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575507.3 3/1
GTCCCCAAACACACAAACCCATATTATGATGAACTCAGGAGAGAATTTGTCTCTTTCATAAGAAACTTTTTCCTAGGTTAAAAATGTTCAGTATTTTAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575507.4 4/1
GCCATGTTGTGTCCAGTCGCTATCGGAGTAGCCGCGCTGGTGCCACACGACTACAACCCTCGTAATAGGGCTGCGTGCGTCCTAAATACACTCGCTGTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575507.5 5/1
GTGAGCATCCTGTGCTCGCATATACCGCTGCTGCACTGATATGAGCCAGTGCTGCTGCTCTCTACGGAGTGTGCTCGGCTATAACAGCGAGTGCTACGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575507_2.fastq <==
@SRR6575507.1 1/2
ATCTCAGCTAAACCGACGCAGTTTTGCTCCTTGGATTCTGAGCCCGGGCATCGCCCCTCGTTTATGAACTAGCCTATCGCAGACGGTATCAACAGGAACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575507.2 2/2
CTTCTACCCCGGCGCTCTTCCTAGTTGGTACAGAACTGAGTGTCATGTGTCCAAAGTTAAGCTCTGCACCTGTTACACTATAGTCATCGTCCATAACACG
+
FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF
@SRR6575507.3 3/2
GTATGAGAACACTAAAGAGAAACCTTCGAGATCATGATAGAGAAGCCTTAATACAGCTGGAGCTGTCCCTAACCGTGTGTCTGCCTCTCTCCCAGGAGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575507.4 4/2
CTCCTACATTTGCTATGCGTCTCAAGATAAGGATATTATCTCATATGGCGGAGTAGAACGTCTTTAGCGGCCTGTCATATTAACAACCGTTGCGACGGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-F-F8F
@SRR6575507.5 5/2
ATGTATCAGCCTATACGCTAATGTCAGAGTCTTATAGTAGATGCAGCGGCAGTCGAGTACATGCACCAGCTACAGTGCTAGACAGCCAGTTTAGGCGTAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575507_1.fastq

Printing command:
fastqc --outdir SRR6575507_1.fastq

Analysis complete for SRR6575507_1.fastq

Processing SRR6575507_2.fastq

Printing command:
fastqc --outdir SRR6575507_2.fastq

Analysis complete for SRR6575507_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 230M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 38 root   root       52K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H8-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 115M Oct 12 19:46 SRR6575507_1.fastq
-rw-r--r--   1 kkarri waxmanlab 115M Oct 12 19:46 SRR6575507_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:27 EDT 2018
0 hours, 0 minutes and 18 seconds elapsed.
==========================================================