-----------------------
Start of variable list:
-----------------------
Sample_ID:
G168_G169_M4
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 : 3516539
Current job name : Step_02_G168_G169_M4
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/3516539.1.linga

Loading required modules...


List files in scratch directory:

total 5.2G
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_M4_FASTQC
-rw-r--r--   1 kkarri waxmanlab 2.5G Mar 11 20:26 G168_G169_M4_R1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 2.7G Mar 11 20:27 G168_G169_M4_R2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> G168_G169_M4_R1.fastq <==
@K00124:51:HT7MFBBXX:1:1101:3792:993 1:N:0:NCCAAT
NGGCTCCCACCTCCCGAACAAAACCGCGCAGTGTGGTGTCCAACAGGCTCTGTTCTGGTCCACTATCGGGGACTAGGTACTCGATGATCCGTTCCTTTGGGTCGAAGGGTGCCAGCGAATCCAGGTCCAGACGGTTCACCACCAGACGTA
+
#AAA--A7FAJFAFF<FJJFFF<FAJJAFFFJJ-<AF<7JJJJJJFFFAJJ<JJJJF<7AFJJFJFJ<<AJFJJFJJJJJFFFF<-F7AJJFFJ-A7AA7J-F77J7A-7A77AA---A--7F-7---7------7----77AF)-<A<7
@K00124:51:HT7MFBBXX:1:1101:3975:993 1:N:0:NCCAAT
NGCTGAATTATCAAGAGATGGTCAGGTAGAGCGGGGTTTATCGAGTATAGAACAGGCTCCTCTAGATGCATAGCAAGTACCTCCAAGTCCTGTGAAATTTAAGCTATGGCTAGTAGCTCGCTGGCAAACAGTTTTGTTAACTCGAAGTAT
+
#AA77AFJFFAFFFJA--<-<<-7AF-<<F<-7<7-7A--<F7F-<FAJ<FJJJA<A-7<7AAJ-<F77--<--<7--7<F-<7---7<AA-<7---777<A-<77A<7F-<7A77-7-7777-A7-A-7-AF<F--7-7-7--7--7-7
@K00124:51:HT7MFBBXX:1:1101:7425:993 1:N:0:NCCAAT
NGTGGTATTGCGCTTGATGAGGACAGTCATGACTCCGCCAGCAGTTTCAATACCAAGGGAAAGAGGAGTGACATCCAAGAGCAGCAAATCCTGAACGTTCTCAGACTTGTCTCCAGATAGAATGGCTGCCTGGCCAGATGCACCATAGGC
+
#A--7FJFAJJJJJJJJJFAJJJJJJJJJJJFJFJJJJJJJJJFFJFJJJJJJJFJFJJ<JJJJJJJJFJJJFJJJJJJJJJFJJJFFFJJFFJFJJF<<A-<--FJFJJJJJJFFFJJFFAAJJFA-A7FJJ--7--7AJAJJF---AA
@K00124:51:HT7MFBBXX:1:1101:7669:993 1:N:0:NCCAAT
NCAGAGAGCATCTTCAGTGTTCCTAGATAGGAAGCCCAGACCCCACCCTCAGGACCCCAACACAGCCTTCTGAACTAATAGGAGGACTCTCAGTATTTGGCAGGCAGTCCAGGAGGTCTGTAGTAATTGGGGAGATCGGAAGAGCACACG
+
#<AFAJJJ<JJJFJJFJFJFFFJJJJJJJJJJFFJJJF<FJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAFJ<AJJFFJ<JJJFJAJ<JAFJAAJ-7--7--FJ77JA-<F<-7AAFF7<JA<FJJJJ<FFJFJFFJJJJJFJF
@K00124:51:HT7MFBBXX:1:1101:8927:993 1:N:0:NCCAAT
NAACTTCTCATCTGTGGTGAGCCCGTGCAGCTCTCCAGACTCCGCGGTCTTCCCAGAGGCAAAGGGCTCCCAGGATCCCTCAGAGGTCTTTTTGAACACTTTTACAGCCACGTCTACAGCAGGGCTGACTCGGACAGCATCCAGGACTTT
+
#AAAFFFJAJJJJJJ<JJFAJJJJJFJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJFJJJJJAJJJFFJJJ<JJJJJJJJ<7JJ<J-FJFJJFJJJJFJJJJJF-FJFFJFFJJ---JFJJF)FFAA

==> G168_G169_M4_R2.fastq <==
@K00124:51:HT7MFBBXX:1:1101:3792:993 2:N:0:NCCAAT
NCCGCAGCCTTCTACTGTGACAAGGAGATGCTGTTTGTTCTGGAGGAGGAGCATCGGATACGGCTGGTGGTGAACCGGCTGGGCCTGGATTCGCTGGCACCCTTTGAACTAAAGGAACGGATCATCGAGTACTTAGTCTCTGATCGTGGA
+
#AA7AFA-A<FJFJJJFF7A7FJJ<-<J-<-<FAFFJJJFJJJJJJJJAJFFJJJFJA7FFAFA-7AFAJ7FJJFAFJJFJJ7--7A77AF7FFFFF-<AJ--7-77-<---7-F-AJFFJJAFJJAA7A<A-------7-7<<--7-)<
@K00124:51:HT7MFBBXX:1:1101:3975:993 2:N:0:NCCAAT
NGCTTCGCCATAAACCTAAATAATTAAATTTAACAAAACTATTTGCCAGAGAACTACTAGCCATATCCTCAAACTCCAAGCACTTGACGGTACTTTCTATCCATCTAGAGGATCCGGTTCTATAATCCAAAAACCCCGCTCTACCACACC
+
#AAAF--7AFFJFFJFF7--<JF<<-FJA-<7F-<FF-FA<<-<-F-F77<FJJA-FAFAA7JA--7--77A7--7-777-7<77--7-7AAAAFJ--FFJJ7A777----7-7F---77FJ-7A-7-----7AJA)--)7)AF77-7<<
@K00124:51:HT7MFBBXX:1:1101:7425:993 2:N:0:NCCAAT
NTCTTGGTGGGTGGTTCTACCAGAATCACCAAGATTCAGAAACTTCTGCAAGACTTCTTCAATGGAAAAGAGCTGAACAAGAGCATTAACCCCGATGAAGCTGTTGCATATGGTGCAGCTGTCCAGGCAGCCTTTCTATCTGGAGACAAG
+
#AAAFFJAFJJ7JJFFJFJFF7FFFAF-FFFJJJFJF7<JJJJ<<<FJJFFJFJ<JFJFFJ-7FJ-7<AJAFFAJAFJJJFAFFJFJFJJFFJ7-AJJJ<FFJAF7J-A<FFFFFJFFFJ7<-AFJFJ<A)A)7-7FA-<<F<<FJF---
@K00124:51:HT7MFBBXX:1:1101:7669:993 2:N:0:NCCAAT
NCCCAATTACTACAGACCTCCTGGACTGCCTGCCAAATACTGAGAGTCCTCCTATTAGTTCAGAAGGCTGTGTTGGGGTCCTGAGGGTGGGGTCTGGGCTTCCTATCTAGGAACACTGAAGATGCTCTCTGGAGATCGGAAGAGCGTCGT
+
#AAAFJJF-JJFJFJFJJJFJJJJFAFJFJJJJJJFJJJJJJJJJJJJ<F<JFJJFFJJJJAFJFJJJ7JJFFFJAAJ<FJJJJAFJAJFJJ-AA<JJJJJJJJFJJJJFF-FFFJJFFJJJJF-<FFJFAAFFJJJJJJJJJJJJJ<<A
@K00124:51:HT7MFBBXX:1:1101:8927:993 2:N:0:NCCAAT
NTGGAGAATCCAAATGTCCTCTGATGGTCAAAGTCCTGGATGCTGTCCGAGGCAGCCCTGCTGTAGACGTGGCTGTAAAAGTGTTCAAAAAGACCTCTGAGGGATCCTGGGAGCCCTTTGCCTCTGGGAAGACCGCGGAGTCTGGAGCGC
+
#AAAAFFAFJJJJJJJJJJJ<JJJJFJJJJJJJJJJJJJFJJJJJJ<JJJJJJJJJJAJJJJJJJJFFJFAAFAJJFJJFJJJFFFJFJFJJJJ-FFJJJJJJFJJJAJJJ7<-<JJFFJFJJA<FFJJAFJFJJJJJ)<<AFJFJJ<<F

Starting FASTQC command


Processing G168_G169_M4_R1.fastq

Printing command:
fastqc --outdir G168_G169_M4_R1.fastq

Analysis complete for G168_G169_M4_R1.fastq

Processing G168_G169_M4_R2.fastq

Printing command:
fastqc --outdir G168_G169_M4_R2.fastq

Analysis complete for G168_G169_M4_R2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 21G
drwx------   3 kkarri waxmanlab 4.0K Mar 11 20:33 .
drwxrwxrwt. 37 root   root      180K Mar 11 20:50 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 11 20:51 G168_G169_M4_FASTQC
-rw-r--r--   1 kkarri waxmanlab  11G Mar 11 20:26 G168_G169_M4_R1.fastq
-rw-r--r--   1 kkarri waxmanlab  11G Mar 11 20:27 G168_G169_M4_R2.fastq
==========================================================
Finished on : Mon Mar 11 20:51:17 EDT 2019
0 hours, 25 minutes and 21 seconds elapsed.
==========================================================