-----------------------
Start of variable list:
-----------------------
Sample_ID:
A5-MAA100140-3_57_F-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 19:42:19 EDT 2018
Running on node : scc-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790936
Current job name : Step_02_A5-MAA100140-3_57_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790936.1.linga

Loading required modules...


List files in scratch directory:

total 51M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 127 root   root      116K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 A5-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  26M Oct 12 19:42 SRR6575944_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  25M Oct 12 19:42 SRR6575944_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575944_1.fastq <==
@SRR6575944.1 1/1
GGATGGCACTGAAGGCTTGGTTAGAGGCCAGAAAGTACTGGATTCAGGGGCACCAATCAAAATTCCTGTTGGTCCTGAGACCTTGGGCAGAATCATGAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575944.2 2/1
AATCCCAACTATACCAAAGAATATCCCAATTATCCATAAAACTGTAACTAAGTGAGGCTCTCTCATTGGTTTATGCTTCAATATAAGCCTTGGTAGGGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575944.3 3/1
ATGCAGATCCCCTGAGACAGAGTCGCTATCGTTATTTCTCCTTCCCGCGGTCAAGGCGAAACCGCAGCAAACTTACTCAGACGCTGCCCTAACAGCGCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFF88F888F8F-F88FF-F-FF-F-F---F-F-F-FF-F----F-FFF-F-F-F--F------FF-FF------F-
@SRR6575944.4 4/1
GATGTGTGCTAGCCCGTCGAGACTGAAAAGCTATAACCCGCAGACCCGAGCGAAAGCGGCGGTCCTTACAAGTCCGCTCCTCGGGGAGCTTGATTGATAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-F-FFF-FF-FFF
@SRR6575944.5 5/1
CATCAGAGGAACCTTATGAGCACGACAGACGCCATTATAGCACGACATACCGCTGCATAACACGACACGTTCATACTACTCACGATGACTCGGTTATTCG
+
FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575944_2.fastq <==
@SRR6575944.1 1/2
CCTTTATCCCAGTCACCAGAATCTCCTGCTCAACACTCATCTCTATGAACTCAGGAGCCTCAGCATGAATAGGAGCAAATTGTTTGGTTTTGATAGGACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFF
@SRR6575944.2 2/2
TCTTAGCTGTCTTAGCAGTAGTTTATAAGGAATATATCCCATTTTTAGTTATAATGATGCCTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFF8FF8
@SRR6575944.3 3/2
CTTTCAGCCTTTTGGGTCCTGTATCCCAATTCTCAGAGGTCCCGCCGTACGCTGAGGACCACCTGAAACGGGCATCGTCGCTCTTCGTTGTTCGTCGACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6575944.4 4/2
AGTTAGGGCAGCGTCTGAGGAAGTTTGCTGCGGTTTCGCCTTGACCGCGGGAAGGAGACATAACGATAGCGACTCTGTCTCAGGGGATCTGCATATGTTT
+
FFFFFFFFFFFF88FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFF8FFF
@SRR6575944.5 5/2
GTAAATCGAGTGCTCCGTGCGAAATACGCGGTCATCGTGCGAATAACCGAGTCATCGTGAGTAGTATGAACGTGTCGTGTTATGCAGCGGTATGTCGTGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575944_1.fastq

Printing command:
fastqc --outdir SRR6575944_1.fastq

Analysis complete for SRR6575944_1.fastq

Processing SRR6575944_2.fastq

Printing command:
fastqc --outdir SRR6575944_2.fastq

Analysis complete for SRR6575944_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 280M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 127 root   root      116K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 A5-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 140M Oct 12 19:42 SRR6575944_1.fastq
-rw-r--r--    1 kkarri waxmanlab 140M Oct 12 19:42 SRR6575944_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:54 EDT 2018
0 hours, 0 minutes and 36 seconds elapsed.
==========================================================