-----------------------
Start of variable list:
-----------------------
Sample_ID:
H3-MAA000377-3_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 19:46:10 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791240
Current job name : Step_02_H3-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791240.1.linga

Loading required modules...


List files in scratch directory:

total 52M
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 H3-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  27M Oct 12 19:46 SRR6576247_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  26M Oct 12 19:46 SRR6576247_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576247_1.fastq <==
@SRR6576247.1 1/1
TGCCTGCATCCCGCTGCAACAGCAGCTCTGATGTTTTCTTTGCCTTCGTGCCAGTTTTCCTGGTCATCAACTCCAGCCGATCGCTTGCCAAGGCCGACCA
+
FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFF
@SRR6576247.2 2/1
TCCTTGAGGATGATGGTCACGTTGGGATCCAGGTCATGTTCAGGTATCTTCCCATTAGGTTTCTCTTCCTTTTTCTTGGTCTTTCCTTTCTTCTCCACGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFF
@SRR6576247.3 3/1
GTAACCATACCCTCTTCCACAACCCTCATGTGAACCCACTTCCGACCGGCTATGAAGATGAGTAAAGAGAACCTGGCCTCCCCCAGGCAACAAAGGGACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576247.4 4/1
GCTTATTCCTGAGGATCTGCATCGCCTCTACATTCAGACAATGCAGGAGAGAGTCCACCCTGAAGTTCAGAGGCACTTGGAGGATTTCCGACAGAAACGC
+
FF-FFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFF-FF-FFFFFFFFFFFFFFFFFF-FFFF
@SRR6576247.5 5/1
AGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCC
+
FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF

==> SRR6576247_2.fastq <==
@SRR6576247.1 1/2
GTCCCAGGGCCTTGTTTTAGGAATTTATGCCAAAGACAAAGATGATGACCTGCCACAATTTACAAGTGCGGGAGAGAGTTTTAATAAGTTGGTGTCTGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576247.2 2/2
CTACGACACTCAGACCTTGGGGGTTGTGGTCTTTGGCGGGTTTATGGTTGTTTCTGCCATCGGCATCTTCCTGGTGTCAACCTTCTCCATGAAGGAGACG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576247.3 3/2
TATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTAATTTATTTATTTAAGGCATCAACTCTTAAAAGCAGAAGGTATGGAATATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF---FFFFF-FFF-FFFFF-FF---F---------F-FF--F-FF---FF--FF-F--
@SRR6576247.4 4/2
CTCCACTCTGGCGCAACTTGGCAGGGTCCTGAGGCTCAGGACTCACAGACGAGGGAGTGGATAAGTGCTTCGGGTGGCGTGACTTCTGTATCTCCATGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FF88FFFF8FFFFFFF
@SRR6576247.5 5/2
CCAATTACAGGGCCTCGAAAGAGTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576247_1.fastq

Printing command:
fastqc --outdir SRR6576247_1.fastq

Analysis complete for SRR6576247_1.fastq

Processing SRR6576247_2.fastq

Printing command:
fastqc --outdir SRR6576247_2.fastq

Analysis complete for SRR6576247_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 263M
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 19:46 H3-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 132M Oct 12 19:46 SRR6576247_1.fastq
-rw-r--r--   1 kkarri waxmanlab 132M Oct 12 19:46 SRR6576247_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:42 EDT 2018
0 hours, 0 minutes and 32 seconds elapsed.
==========================================================