error at canoes_call_CNV.sh

[kokyriakidis]

I get the following error when I run canoes_call_CNV.sh

kokyriakidis@Konstantinos:~/Desktop/CNLearn/CN_Learn$ 
kokyriakidis@Konstantinos:~/Desktop/CNLearn/CN_Learn$ cd scripts/
kokyriakidis@Konstantinos:~/Desktop/CNLearn/CN_Learn/scripts$ sudo bash canoes_extract.sh
Job started on Konstantinos at Σαβ 28 Σεπ 2019 03:40:17 πμ EEST
Job ended on Konstantinos at Σαβ 28 Σεπ 2019 03:51:00 πμ EEST
kokyriakidis@Konstantinos:~/Desktop/CNLearn/CN_Learn/scripts$ 
kokyriakidis@Konstantinos:~/Desktop/CNLearn/CN_Learn/scripts$ sudo bash canoes_call_CNVs.sh
Job started on Konstantinos at Σαβ 28 Σεπ 2019 03:51:16 πμ EEST
INFO  00:51:18,542 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  00:51:18,544 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56 
INFO  00:51:18,544 HelpFormatter - Copyright (c) 2010 The Broad Institute 
INFO  00:51:18,544 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO  00:51:18,547 HelpFormatter - Program Args: -T GCContentByInterval -L /home/kokyriakidis/Desktop/CNLearn/CN_Learn/source/targets_auto_no_chr.bed -R /home/kokyriakidis/Desktop/CNLearn/CN_Learn/source/human_g1k_v37_decoy.fasta -o /home/kokyriakidis/Desktop/CNLearn/CN_Learn/data/canoes/gc.txt 
INFO  00:51:18,551 HelpFormatter - Executing as root@76b7203b903b on Linux 5.0.0-29-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_201-b09. 
INFO  00:51:18,551 HelpFormatter - Date/Time: 2019/09/28 00:51:18 
INFO  00:51:18,551 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  00:51:18,551 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  00:51:18,683 GenomeAnalysisEngine - Strictness is SILENT 
INFO  00:51:18,761 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 
INFO  00:51:19,132 IntervalUtils - Processing 44584105 bp from intervals 
INFO  00:51:19,179 GenomeAnalysisEngine - Preparing for traversal 
INFO  00:51:19,212 GenomeAnalysisEngine - Done preparing for traversal 
INFO  00:51:19,212 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  00:51:19,212 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining 
INFO  00:51:19,213 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime 
INFO  00:51:36,176 ProgressMeter -            done   4.4584105E7    16.0 s       0.0 s      100.0%    16.0 s       0.0 s 
INFO  00:51:36,176 ProgressMeter - Total runtime 16.96 secs, 0.28 min, 0.00 hours 
INFO  00:51:37,244 GATKRunReport - Uploaded run statistics report to AWS S3 
Error in apply(counts[, sample.names], 2, mean) : 
  dim(X) must have a positive length
Calls: CallCNVs -> mean -> apply
Execution halted
cp: cannot stat '/home/kokyriakidis/Desktop/CNLearn/CN_Learn/data/canoes/canoes_calls.csv': No such file or directory
Job ended on Konstantinos at Σαβ 28 Σεπ 2019 03:51:40 πμ EEST

@vijaymp38 @girirajanlab Any thoughts?

[girirajanlab]

Hello,
Obviously, line #179 in the following script is resulting in this exception.
https://github.com/girirajanlab/CN_Learn/blob/master/scripts/rscripts/CANOES.R

I would ensure that the file that corresponds to the variable CONS_READS, i.e., 'cons_canoes_reads', is available and valid. This file is generated within the same script.

Vijay