-----------------------
Start of variable list:
-----------------------
Sample_ID:
PB_M2
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/home/waxmanlab/public_html/FASTQC/Water_Saline
OUTPUT_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Thu Jun 15 16:48:13 EDT 2017
Running on node : scc-ka5
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/02_FASTQC
Current job ID : 9342212
Current job name : Step_02_PB_M2
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9342212.1.linga

Loading required modules...


List files in scratch directory:

total 3.3G
drwxr-xr-x   3 kkarri montilab-p 4.0K Jun 15 16:48 .
drwxrwxrwt. 85 root   root        72K Jun 15 16:48 ..
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 15 16:48 PB_M2_FASTQC
-rw-r--r--   1 kkarri montilab-p 1.7G Jun 15 16:48 SRR1177962_R1.fastq.gz
-rw-r--r--   1 kkarri montilab-p 1.7G Jun 15 16:48 SRR1177962_R2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR1177962_R1.fastq <==
@SRR1177962.1 1 length=101
CAAAAATCAACCTGAAATCACAGCCTCTGGTACTGTCCCTGTTCATCTGTATCTTAAATGAAACATAGGTTATAAAAAGGAATGGCTCCCAAAACATAGTA
+SRR1177962.1 1 length=101
@@@DDD?AFFAFFCEEG,<CCH@3CC;<DGB@GEGFIIIEIIF99FECEGFEBFFGECFFGIBEFAF>)8==;CD=ECE=CE3.7?BB1=;>BB#######
@SRR1177962.2 2 length=101
CAAAAAAGCACAGATAAAAGGGAAGAGGGGAGCGAAGGGCAAACAGGCTGAAGTGGCTGACCAGCAAACTACAGATCTGCCTGCAGAAAATGGAGAGACGG
+SRR1177962.2 2 length=101
@@@DDDDDFHHHHIIIIIEHI@G;EFIIIIGIIGGH@AGGGEHC2?;?DECCCCCCBBBBCC@?B?<?BCAC@@CCC>@@C@A@<ACCCCACCCBCBBC@#
@SRR1177962.3 3 length=101
GAAACTGAAATTGAGACTGAAGAAACAGAAATGTTGACTCCTGATATGGACACAGAAAGAAAACGGATAAAGTCCTTATTACCTAAACTATCCTGTGGAGT
+SRR1177962.3 3 length=101
@@@FFBB>??FFF>HGGHE?HHHIIIIIIGEHGEFGGGIIIFGEGIIGI<DEHGGGDHHIIID@GGAEAEAH=;=CHDCD<DFEACEE@CCC>>(-;?>A@
@SRR1177962.4 4 length=101
AGAAGGTTGGTTGAGCCGATAAATATAATTAGGGATACAATTATTAGGGCTCAGGTTCGTCCTTGTGGTGTGTGGATTAACATTATTTGTTTGATGATAAG
+SRR1177962.4 4 length=101
?<=DDDDDF8DDD;:CF:CHIECEBAF?DHAGHGGHIGEDHHBGHH8BFGCDGIGHEGGHHBEE);>1.;=;(;@CCCCCCCCCCEEEA><CC34>34:@3
@SRR1177962.5 5 length=101
AAAAAATTAATAAAGACCTTGGAATTGTTTTTAGCCATGGAAATAGATGGAAAGAAATAAGACGCTTTACCCTCACGACTCTGCGGAATTTGGGCATGGGG
+SRR1177962.5 5 length=101
@@@FFFDDFFGHGIEGIJIJJCHIIIJDGIJIJGJJJJDHDHGGHIJIJJJIGHEEHIIIHGIGGIGHHECDFFFDDDDDDDDD?BBB2>CDDBBCDABD7

==> SRR1177962_R2.fastq <==
@SRR1177962.1 1 length=101
TACCTTTCCTTCTTCCATTCTTTCTTTCCTATCTNNNNNNNNNNNNTGATTATCTGTCTANNNNNNNNNTATGTTTTGGGAGCCATTCCTTTTTATAAACT
+SRR1177962.1 1 length=101
;;?:=D8D:BBFD+<CE?EHE@A<9C@HHHGC9?############)0)8BD?<B>FCBC#########--55@@@72/==13=?>CACCCCCC<:;>C@A
@SRR1177962.2 2 length=101
CTGGATTGTACAAGAAGGGAGGCAGGGACCACTGACAGACGTGATGGATGCTTAATCAGACTTNGCTTCTTTCTCTTCCTCAGAGGCTGGACTCTGGTTTC
+SRR1177962.2 2 length=101
@C@FDFDAFDHHHJJJJJJJJIIJJFGIHGIJHGGIIGHIH(;CF4=CDGCFH>EHCGHHHFF#,55;ACECEEDCAC@@CCCCD?BDBD<?CCAAC####
@SRR1177962.3 3 length=101
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTNNNTNNNNNNNNNNNNNNNN
+SRR1177962.3 3 length=101
#####################################################################################################
@SRR1177962.4 4 length=101
CAGAACGNNNNNNCNNNNNCNGACTACANNCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCCACACACNNNNNGGNCGNANN
+SRR1177962.4 4 length=101
@?@;DA?##############################################################################################
@SRR1177962.5 5 length=101
CCTCAATGTTCCTTTTCCCCATGCCCAAATTCCGNNNNNNNNNNNNNGTAAAGCGTCTTNNNNNNNNNNNTCTATTTCCATGGCTAAAAACAATTCCAAGG
+SRR1177962.5 5 length=101
BCCFFFDDHHHHHHIHHIIJJFHGICGHIIFHII#############0077CCFHFG@@###########,,5?BD;BDDFDDDDDCDDDDDB@C@CDDCD

Starting FASTQC command


Processing SRR1177962_R1.fastq

Printing command:
fastqc --outdir SRR1177962_R1.fastq

Analysis complete for SRR1177962_R1.fastq

Processing SRR1177962_R2.fastq

Printing command:
fastqc --outdir SRR1177962_R2.fastq

Analysis complete for SRR1177962_R2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 9.4G
drwxr-xr-x   3 kkarri montilab-p 4.0K Jun 15 16:50 .
drwxrwxrwt. 84 root   root        72K Jun 15 16:56 ..
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 15 16:57 PB_M2_FASTQC
-rw-r--r--   1 kkarri montilab-p 4.7G Jun 15 16:48 SRR1177962_R1.fastq
-rw-r--r--   1 kkarri montilab-p 4.7G Jun 15 16:48 SRR1177962_R2.fastq
==========================================================
Finished on : Thu Jun 15 16:57:06 EDT 2017
0 hours, 8 minutes and 53 seconds elapsed.
==========================================================