-----------------------
Start of variable list:
-----------------------
Sample_ID:
G168_G169_M5
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-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/02_FASTQC
Current job ID : 3516540
Current job name : Step_02_G168_G169_M5
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/3516540.1.linga

Loading required modules...


List files in scratch directory:

total 4.9G
drwx------   3 kkarri waxmanlab 4.0K Mar 11 20:27 .
drwxrwxrwt. 42 root   root      180K Mar 11 20:25 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 11 20:27 G168_G169_M5_FASTQC
-rw-r--r--   1 kkarri waxmanlab 2.4G Mar 11 20:26 G168_G169_M5_R1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 2.6G Mar 11 20:27 G168_G169_M5_R2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> G168_G169_M5_R1.fastq <==
@K00124:51:HT7MFBBXX:1:1101:3589:993 1:N:0:NAGATC
NGAGAAAGTGGGCAGCCTTGTCTAGTCCCTGATTTTAGTGGGATTGCTTCCAGCTTCTCTCCATTTACTTTGATGTTGGCTACTGGTTTGCTGTAGATTTCTTTCATCATGTTTTGGTATGGGTCTTTCATTCCTGATCTTTCCTGTACT
+
#AAAAAJFAAAJA7F7FFFAAA<<FJJJF<<-A<FJAJJJFF<FFFF<FFJJJ<FJJ7A<7AFF-AAAJJJ7FJ<FAFAJ-<AJ--FJAFAJ-F7AF7A-77FJ-A-7--7-AJ-7A-7AAA--7-7--7F7--AF7---AAAJ----7<
@K00124:51:HT7MFBBXX:1:1101:7466:993 1:N:0:NAGATC
NCGGCTCAGAAAGTGCTCCAGTGTGCTCAGGAATGTCCCGTCCTTGTCGAGAAGCTGGGCGGCCCGTGGCTGGTTGGTGAGCCAGTCCATGACTGAGTCTATCTGCTCCTCCTGGACCTGCAGATCGGAAGAGCACACGTCTGAACTCCA
+
#AAFFJFFJJJJJJJJFFJFJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAFJJJJJJJFJFJJJJFJJFJJJFFJAFJ-AAF<F-JAJJFFJAAFF-7A-7AJ-A--7AJJAJA7A-JF
@K00124:51:HT7MFBBXX:1:1101:7527:993 1:N:0:NAGATC
NGTTGGAGCCTCAGGAATCTCTGAAACCATGAATCGTACTTCAGCACCACCCACTCCAAAAGTATACTGTTTATCCTTATTCCAAAATATGAGAATGTCGTTAGAGTTCTTCTTGGTAGCATAAGAGTAGACACTGAGGCTGCGCACTGT
+
#-A7A-FJFAJJJJJFJAFFJJJJJJJJJJJJJJJJJJJJJJFJJFJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJ-FJJJJJJJJAJJJJFJJJJJJJJJ<-AJJJJJ<JJ7AA7-AAF<<F77-7<7---J<F-F7AJFJ))7)7A
@K00124:51:HT7MFBBXX:1:1101:11221:993 1:N:0:NAGATC
NCGGACACGAGACTAAGACAAAAAAGAAACCAGAAGAATCAGATGGCCTCTCCAAGGCCGGCCAATTGAGACCCTCTGCACGAGGTGGGACTCGAACCCACGATCCCGTGACCAGACGCGAGGTGGGACTCGAACCCTCGATCTCGCAAC
+
#A<A7FAJFJJJJJJFJJFJJJJJJJJJJJJJJFFJJJJJFJFJJJJJJJAJJJFJJJJJJJJJJJJJJJJJJJAFJJJJJJJJJJJJJJJFJJJJJJJ<FFJAJJJJFJJJJFFJJJJ<FF<FAFF7AA7<--7<J-AFAAJ<-AFAJJ
@K00124:51:HT7MFBBXX:1:1101:12540:993 1:N:0:NAGATC
NGATTCTTTCGATCTTCCATGATGGCCAGGCCCATGGACATCATGAGGAAGGGCCAGAGGCAAAGCTCATCCTAGGTGTTTACAATCTCTGCAGTCCTGTGGATTCTCACAATAGGCCAAGATGAAGCCCCAAGAAGCTAAGTTCACAGG
+
#AAAFJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFAJJFJJJJFJFJJJJJJJJJJJJJJJJJJFJJJJFFJJJJJJJAAJJFJFFJJAFJ<FAJJ<JJFFFJJ<<AF--7F<<-F<AJFJFJJJ7<

==> G168_G169_M5_R2.fastq <==
@K00124:51:HT7MFBBXX:1:1101:3589:993 2:N:0:NAGATC
NCCATTCTTGATAAAAGTTCTGGAAAGATCAGGAATTCAAGGACCATACCTAAACATGATAAAAGCAATCTACAGAAAACCAGTTGTCAACATCAAAGTAAATGTAGAGAAGATGGAAGCAATCACACTAAAATTAGGGATTAGACATGG
+
#<AAFJF-FA-<-FF<FFJFJJFJFFFJJ-<F<---<-FFFF---7<-<-<AJFAF<<A7---<F-<A7JJ-AF7-<AA--777-7--7-7F--7FFA-<<AJA-JJJF-7<-JAFAFF7--F<-A7AAFFA-A-<FF---7<-F-7--7
@K00124:51:HT7MFBBXX:1:1101:7466:993 2:N:0:NAGATC
NCAGGTCCAGGAGGAGCAGATAGACTCAGTCATGGACTGGCTCACCAACCAGCCACGGGCCGCCCAGCTTCTCGACAAGGACGGGACATTCCTGAGCACACTGGAGCACTTTCTGAGCCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGA
+
#AAAFJJ<FJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJFJJJJJJJJJJJJJJFFFJJJJFFFJFJJAFJJJ<FJJJJ-AFJFJFJFJFJFJFJJJJF<JFJJJJJFJJJFJAJJAJF<FFJJJJAFJJ<JFFJFAJ7FJJFJJ<JJ
@K00124:51:HT7MFBBXX:1:1101:7527:993 2:N:0:NAGATC
NTTCTGATCATGATCAGCTTCTCTCGGACTTTTGGTCATGAAGACATGTTTAAAAAGGCCTTTGTATTTCCCAAGGAGTCAGATAATTCCTATGTGTCTCTGGAAGCAGAGTCAAAGAAGCCACTGAACACCTTTACTGTGTGTCTCTAT
+
#AAAFJA-7FFFFJJAFFFFFJJJJFJJJJJJJ7JJJJJJJAF7A-FFFFJJJJJJJJFJFFJJJJJJJF-AAJJ<7FJJF<JJ--7FJFJJFFJ7J<-AJJJF-FJAF<JJFFFFJJJJJJFJJFFJ-A7FFJJJFJFJ<FJJA<A--<
@K00124:51:HT7MFBBXX:1:1101:11221:993 2:N:0:NAGATC
NACCTCGTGTTTTGTTGCGAGATCGTGGGTTCGAGTCCCACCTCGCGTCTGGTCACGGGATCGTGGGTTCGAGTCCCACCTCGTGCAGAGGGTCTCAATTGGCCGGCCTTGGAGAGGCCATCTGATTCTTCTGGTTTCTTTTTTGTCGTA
+
#AAAAJJJJFJJJJJJFJJJFFJJJAJJJJJJJJJJJFJFJJFJFJJA7AJJJJFJJJJ<JJFFJJJJJJJJJJAAJAJJJFJJJ-AF-FJJFJJJF<JJJJJJJJJJAJFJ-FJJFJJFJJJF-7-JJJFFFFFFJAFJJJJJAFJAF<
@K00124:51:HT7MFBBXX:1:1101:12540:993 2:N:0:NAGATC
NTCAGAACCAGTAAAGTTCAGGGGAAAGAGGCAGTAAAGTTCTGCCAAGGGGGAGTGATACAAAGGGGCTGGCAATATCCTGTGAACTTAGCTTCTTGGGGCTTCATCTTGGCCTATTGTGAGAATCCACAGGACTGCAGAGATTGTAAA
+
#AAFFJFJFJJJJJJJJJJJJJJJJ-FJAJJJJFJ<FFJJJJJJJJJJFAJJJ-A<F7FFJAJFJJJJ<AFJJFF<FJJJFFFFAJFFJAAJJJJJJFJJJJJJ<-FJFJFJJJFJJJFFJJJJJJJJJJJJJ7AFFFJJ-FAFFFJFA<

Starting FASTQC command


Processing G168_G169_M5_R1.fastq

Printing command:
fastqc --outdir G168_G169_M5_R1.fastq

Analysis complete for G168_G169_M5_R1.fastq

Processing G168_G169_M5_R2.fastq

Printing command:
fastqc --outdir G168_G169_M5_R2.fastq

Analysis complete for G168_G169_M5_R2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 20G
drwx------   3 kkarri waxmanlab 4.0K Mar 11 20:33 .
drwxrwxrwt. 39 root   root      180K Mar 11 20:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 11 20:49 G168_G169_M5_FASTQC
-rw-r--r--   1 kkarri waxmanlab 9.7G Mar 11 20:26 G168_G169_M5_R1.fastq
-rw-r--r--   1 kkarri waxmanlab 9.7G Mar 11 20:27 G168_G169_M5_R2.fastq
==========================================================
Finished on : Mon Mar 11 20:49:57 EDT 2019
0 hours, 24 minutes and 1 seconds elapsed.
==========================================================