-----------------------
Start of variable list:
-----------------------
Sample_ID:
G168_G169_M9
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/G168_TCPO_Env
OUTPUT_DIR:
/restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Mon Mar 11 20:25:56 EDT 2019
Running on node : scc-ka6
Current directory : /restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/02_FASTQC
Current job ID : 3516544
Current job name : Step_02_G168_G169_M9
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/3516544.1.linga

Loading required modules...


List files in scratch directory:

total 4.1G
drwx------   3 kkarri waxmanlab 4.0K Mar 11 20:26 .
drwxrwxrwt. 40 root   root       92K Mar 11 20:25 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 11 20:26 G168_G169_M9_FASTQC
-rw-r--r--   1 kkarri waxmanlab 2.0G Mar 11 20:26 G168_G169_M9_R1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 2.1G Mar 11 20:26 G168_G169_M9_R2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> G168_G169_M9_R1.fastq <==
@K00124:51:HT7MFBBXX:2:1101:5010:993 1:N:0:NATCAG
NTTACTACGGAGTCAGGAAGGACACACGTTGGTGGCGAGTCAAGTGAACCTAAAGAATGGTTGATCCTGATCCACATTGTATAGCCAGATAATAGAAAGATTGGCTGGAAAACACATTCATAAAAGCCGTCTCTCTGTAAGACGTAGTTT
+
#AAFFJFJFJJJJAJJJFJFJJJJJJJJJJJJJJJJJJJJJFJJFJFJFJJJJJJJJJJJFJJJJJJJJJJFJJJJJJJJJF<FJJJJJJJJJJJJJJJ<JJFJ-FJJFFJJFJJJ<-FJJJJJAJFJ<<<FJFJ-AF7FA--<-----7
@K00124:51:HT7MFBBXX:2:1101:7608:993 1:N:0:NATCAG
NCGGAAAGGGAGCATCACTTTCACAGGACTTAACAGACAGCTCTGAGGTCCTGGTGTCGTAGCAGGTGGGGTCAGCTCCCTCAGCACAGCACTCCTCAGTCAAGGAGACAACTTCCTTCACAAGCTGGTTGACCTGCTCAAATAGATCGG
+
#AAFFJJJJJJJJJJJFJJJJJJJJJJFJFJJJJJJJJJJJJJJAJJFJJJFJJFJJJFJJJJJFJJJJJJJJJJFFJJJJJJFJJJJJJJJFJJJJJFJJJJFJFFJJJJJJJJAFJJJJJJFJJJJJJFJJJJJA7FAJ7AA-AFFJJ
@K00124:51:HT7MFBBXX:2:1101:8623:993 1:N:0:NATCAG
NTCTTTCTTCAGCCACTTCTGCAGCTCCTGCAGGTTCTGCGGGGTGTAGTCAGTGACAATGATCTCCCGGAAGACCTCGCATGCTGAAAGCAGCTGGTAGATGGTAGGGCCAGAGCCAATGTCGATCAGGACGTCGCCCCCTACACCTCC
+
#AAFFJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJFJJJJJJJJJJJJJJFFJJJJJJJ<FJJJJJJJJFAJJJFJJJJFJJ-FJ
@K00124:51:HT7MFBBXX:2:1101:9922:993 1:N:0:NATCAG
NGCGACTTGATGTTGTAACTGCCCCGAGCAAGCATGCCTTTGGGAGCCTCCTCCATGGGTGTCAGGAACTCATACTCCTCGGCCCTCGGCCCATAGCTCCCGACCATGTAGTCAGTCTTGTCAATTTTGACCCCTTTCCTGTATGTGTGT
+
#AAAAFAJJJJJ<FJJAJJFJJJJJFFJJFFFJJFJJJJJJFJJJJJJJFJJJJAJAFAFF7FFJJJJJ<JFJJJ7FJJJJAJFJ<JFJJJFFJJFJFJFJF<F--7FFAJFJJJJJJJ<-AFJJFJJFAFFJJJJJF--AFAFAJJ<-F
@K00124:51:HT7MFBBXX:2:1101:17777:993 1:N:0:NATCAG
NTCTTTGTGTTGCAGGAAACATTCGTTTCTTTCGGGCTCTTGTTTTGTACAGCAGTCAGCCAGTTCACCATAGTTTTCACGGAGGTTTGGAATGGCACACAACTTATCTCCAAAAAGAGTGTGAAGGGATTTGTCACAGTTGGCGGCAGA
+
#AAFFJFJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJ<FJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJFJJJJJJJJJJFJJJJJJJFJF

==> G168_G169_M9_R2.fastq <==
@K00124:51:HT7MFBBXX:2:1101:5010:993 2:N:0:NATCAG
NTGTATTGTCCTGATAGTCCATCTATTCATCCTACGTCTGAGCCCAAAAACTGCGTCTTACAGAGAGACGGCTTTTATGAATGTGTTTTCCAGCCAATCTTTCTATTATCTGGCTATACAATTTGGATCAGGATCAACCATTCTTTAGGT
+
#AAAFJJJJJJJJJJJJJJJJFJJFJJJJJ7AJJJJJJJJFF7AJJJJJJJJJFA<FJJJJJJJJJJJJFJJJFFFAJJJJJFJFJJFJFA7JJJ77FJFJFAJ<JJ<JJF-FJJJJJFJ<F-AFJJFFJAFAJFFF-FAJJFF<A-77-
@K00124:51:HT7MFBBXX:2:1101:7608:993 2:N:0:NATCAG
NTTTGAGCAGGTCAACCAGCTTGTGAAGGAAGTTGTCTCCTTGACTGAGGAGTGCTGTGCTGAGGGAGCTGACCCCACCTGCTACGACACCAGGACCTCAGAGCTGTCTGTTAAGTCCTGTGAAAGTGATGCTCCCTTTCCGGAGATCGG
+
#AAAAJFJJJJJJJJJJJJJJJJJFJFJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJFFJJJJJJJJJJJ-FFJFJJJJJJJJFJJJJJFFFJFJFFJJJJJFJJFFAFJFJJJFJJJJFJ<AFAJJFFFFFJFJJFJJJ<A7-<F<FF
@K00124:51:HT7MFBBXX:2:1101:8623:993 2:N:0:NATCAG
NATGAAAAAGAGTTCACTCCCAAAGACTACCTGACCACCTACTACAGCTTCCACTCTGGCCCTGTGGCAGAGCAGGAAATCGTAAAGTTTAGCCTGCAGAACCTCTACCAGACCTTCTCTACAGGAGGTGTAGGGGGCGACGTCCTGATC
+
#AAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAFFJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ<JFJJJJJFJJAJJJJJJJJJJJJJJJJJJJJF
@K00124:51:HT7MFBBXX:2:1101:9922:993 2:N:0:NATCAG
NGACAGGTGATCTGGAGAGCTTCAAGAAACAGTCGTTTGTCTTGAAGGAAGGTGTGGAGTACCGGATAAAAATCTCTTTCCGGGTGAACAGAGAGATCGTGTCCGGCATGAAGTACATCCAACACACATACAGGAAAGGGGTCAAAATTG
+
#AAAA<A<JFJJJFJJJ<AAJFJF<AAJJJJJFFJJJJJJJ<FJAFJJJJFJJ7FJ7A7FFJJFFF7<JJJFJJ<7FAJFFJJJFJ<FFFJJJJA-7FJFFF7-7AFJF7AFJJJJJFFJJJJFJAFAJ<AAJA<JFF<A7<F<FFJJA<
@K00124:51:HT7MFBBXX:2:1101:17777:993 2:N:0:NATCAG
NGAGCATGCCAAATTAGTGCAGGAAGTAACAGACTTTGCAAAGACGTGTGTTGCCGATGAGTCTGCCGCCAACTGTGACAAATCCCTTCACACTCTTTTTGGAGATAAGTTGTGTGCCATTCCAAACCTCCGTGAAAACTATGGTGAACT
+
#AAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFFFJFJFJAJJAJJJJJJJJJJJJJJJJJFFAAJJJJJAFFJJFJJJJJ

Starting FASTQC command


Processing G168_G169_M9_R1.fastq

Printing command:
fastqc --outdir G168_G169_M9_R1.fastq

Analysis complete for G168_G169_M9_R1.fastq

Processing G168_G169_M9_R2.fastq

Printing command:
fastqc --outdir G168_G169_M9_R2.fastq

Analysis complete for G168_G169_M9_R2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 17G
drwx------   3 kkarri waxmanlab 4.0K Mar 11 20:35 .
drwxrwxrwt. 41 root   root       92K Mar 11 20:57 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 11 20:57 G168_G169_M9_FASTQC
-rw-r--r--   1 kkarri waxmanlab 8.3G Mar 11 20:26 G168_G169_M9_R1.fastq
-rw-r--r--   1 kkarri waxmanlab 8.3G Mar 11 20:26 G168_G169_M9_R2.fastq
==========================================================
Finished on : Mon Mar 11 20:57:22 EDT 2019
0 hours, 31 minutes and 26 seconds elapsed.
==========================================================