-----------------------
Start of variable list:
-----------------------
Sample_ID:
H2-MAA000907-3_11_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 19:47:49 EDT 2018
Running on node : scc-pc3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791331
Current job name : Step_02_H2-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791331.1.p

Loading required modules...


List files in scratch directory:

total 23M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:47 .
drwxrwxrwt. 20 root   root       16K Oct 12 19:47 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:47 H2-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  11M Oct 12 19:47 SRR6576393_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  12M Oct 12 19:47 SRR6576393_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576393_1.fastq <==
@SRR6576393.1 1/1
CCCTATTAGTGGGTGAACAATCCAACGCTTGGTGAATTCTGCTTCACAATGATAGGAAGAGCCGACATCGAAGGATCAAAAAGCGACGTCGCTATGAACG
+
FFFFFF-FFFFFFFFFFFFFFF8FF8FFFF8FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFF-FFF-FFFFFFFFFF-F
@SRR6576393.2 2/1
GACCAGGATGCCGCGCAGCAGAGCTCTGATTCTGGGGGTCCTCGCCCTGACCACCATGCTCAGCCTCTGTGGAGGTGAAGACGACATTGAGGCCGACCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFFFFFFFFFFF
@SRR6576393.3 3/1
GAATAATGGAATAGGACCGCGGTTCTATTTTGTTGGTTTTCGGAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGG
+
FFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF
@SRR6576393.4 4/1
GCTCATCTGCATAGGTCTTCACACGAATCCTAGAGTTGAACCGCAGAGACAGCAGGTTGTAGACAATCTCAAAACGGTTCTGCCGAGTTGGGACATCCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576393.5 5/1
GTCGTGTATTATAAATGACTAGAATTACTTTCGTTATTGAGTTTAGGTCCTAACAATGAATTTTCACATATAAGTTGGATTTTAATTCTATTTATTTATT
+
FFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576393_2.fastq <==
@SRR6576393.1 1/2
NGTGGGGAGTTTGACTGGGGCGGTACACCTGTCAAACGGTAACGCAGGTGTCCTAAGGCGAGCTCAGGGAGGACAGAAACCTCCCGTGGAGCAGAAGGGC
+
#8FFF-FFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576393.2 2/2
GCACACCACTTCTTCCCTGAAGAGGGACACACGCCTTCCTTTCCAGGGTGTGACTCATAAAGGCCCTGGGTGTCTGGAGGTGCCACCTGATCGCAGGCCT
+
FFFFFFFFFFFFFFFF8FF8FFFFFFFFF-FF---FFFFFFFF-FFF-FFFFF-FF--FF-FFF-FFFFFFFFFFF-FFFFFFF--FFFFFFFF-FF8F-
@SRR6576393.3 3/2
CCCAAAGACTTTGGTTTCCCGGAAGCTGCCCGGCGGGTCATGGGAATAACGCCGCCGCATCGCCAGTCGGCATCGTTTATGGTCGGAACTACGACGGTAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576393.4 4/2
TTTGGAGAGTATGTGGCTGAAATCTTACCCAAGTATGTCCAACAAGTTCAGGTGTCCTGCCTTGATGAGTTAGAAATCTGTATCCATCCCGATGGAGTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF
@SRR6576393.5 5/2
CCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACA
+
FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576393_1.fastq

Printing command:
fastqc --outdir SRR6576393_1.fastq

Analysis complete for SRR6576393_1.fastq

Processing SRR6576393_2.fastq

Printing command:
fastqc --outdir SRR6576393_2.fastq

Analysis complete for SRR6576393_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 124M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:47 .
drwxrwxrwt. 20 root   root       16K Oct 12 19:47 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:48 H2-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  62M Oct 12 19:47 SRR6576393_1.fastq
-rw-r--r--   1 kkarri waxmanlab  62M Oct 12 19:47 SRR6576393_2.fastq
==========================================================
Finished on : Fri Oct 12 19:48:03 EDT 2018
0 hours, 0 minutes and 14 seconds elapsed.
==========================================================