Hi Fellow Bioinformaticians,
Hopefully you can help me with this problem regarding the EXCAVATOR CNV calling tool.
When I run EXCAVATOR the on screen log ends with this:
Working on sample DNA15-10927_p-BRC_R15-13004_H6_17185262.sorted.hfix.
Checking sample 'DNA15-10927_p-BRC_R15-13004_H6_17185262.sorted.hfix' folders...
...done!
Now working with SAMtools...
Removing temporary files...
...done!
Working on sample DNA15-10928_p-BRC_R15-13005_G3_17185326.sorted.hfix.
Checking sample 'DNA15-10928_p-BRC_R15-13005_G3_17185326.sorted.hfix' folders...
...done!
Now working with SAMtools...
Removing temporary files...
...done!
Working on sample DNA15-10928_p-BRC_R15-13005_G6_17185327.sorted.hfix.
Checking sample 'DNA15-10928_p-BRC_R15-13005_G6_17185327.sorted.hfix' folders...
...done!
Now working with SAMtools...
Removing temporary files...
...done!
Error in gzfile(file) : invalid 'description' argument
Calls: rbind -> loadRC -> load -> gzfile
Execution halted
Read 21 items
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
Calls: load -> readChar
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
cannot open compressed file '/home/koen/cnv_tool_comparison/EXCAVATOR/data/output_run_150710_omega_0dot3_theta_10emin3/Data/Control/RCNorm/Control.NRC.RData', probable reason 'No such fil
e or directory'
Execution halted
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file '/home/koen/cnv_tool_comparison/EXCAVATOR/data/output_run_150710_omega_0dot3_theta_10emin3/Results/DNA13-03669_p-BRC_R15-12944_F2_17180520.sorted.hfix/HSLMResults_DNA13-0
3669_p-BRC_R15-12944_F2_17180520.sorted.hfix.txt': No such file or directory
Execution halted
Analyzed samples:
DNA13-03669_p-BRC_R15-12944_F2_17180520.sorted.hfix DNA13-03669_p-BRC_R15-12944_F5_17180521.sorted.hfix DNA13-05589_p-BRC_R15-12943_D3_17180454.sorted.hfix DNA13-05589_p-BRC_R15-12943_D6_17
180455.sorted.hfix DNA13-12108_p-BRC_R15-12941_E2_17180375.sorted.hfix DNA13-12108_p-BRC_R15-12941_E5_17180376.sorted.hfix DNA13-13231_p-BRC_R15-12938_G2_17180167.sorted.hfix DNA13-13231_p-
BRC_R15-12938_G5_17180168.sorted.hfix DNA13-15939_p-BRC_R15-12939_C3_17180306.sorted.hfix DNA13-15939_p-BRC_R15-12939_C6_17180307.sorted.hfix DNA04-04209_BRCA1_R15-12598_B8_17151464.sorted.
hfix DNA04-04209_BRCA1_R15-12598_E7_17151463.sorted.hfix DNA14-27209_p-BRC_R15-13040_F3_17195406.sorted.hfix DNA14-27209_p-BRC_R15-13040_F6_17195407.sorted.hfix DNA14-32423_BRCA2_R15-12744_
A7_17174161.sorted.hfix DNA14-32423_BRCA2_R15-12744_C7_17174162.sorted.hfix DNA15-04076_BRCA1_R15-12739_C8_17162339.sorted.hfix DNA15-04076_BRCA1_R15-12739_F7_17162338.sorted.hfix DNA15-051
21_BRCA1_R15-12766_E8_17167116.sorted.hfix DNA15-05121_BRCA1_R15-12766_H7_17167115.sorted.hfix DNA15-10649_p-BRC_R15-12647_B1_17155097.sorted.hfix DNA15-10649_p-BRC_R15-12647_B4_17155098.so
rted.hfix DNA15-10650_p-BRC_R15-12648_D1_17155162.sorted.hfix DNA15-10650_p-BRC_R15-12648_D4_17155163.sorted.hfix DNA15-10695_BRCA1_R15-12739_D8_17162313.sorted.hfix DNA15-10695_BRCA1_R15-1
2739_G7_17162312.sorted.hfix DNA15-10718_BRCA2_R15-12744_B7_17162902.sorted.hfix DNA15-10718_BRCA2_R15-12744_D7_17162903.sorted.hfix DNA15-10722_p-BRC_R15-12747_E1_17163350.sorted.hfix DNA1
5-10722_p-BRC_R15-12747_E4_17163351.sorted.hfix DNA15-10752_BRCA1_R15-12766_A8_17167089.sorted.hfix DNA15-10752_BRCA1_R15-12766_F8_17167090.sorted.hfix DNA15-10797_p-BRC_R15-12780_F1_171682
32.sorted.hfix DNA15-10797_p-BRC_R15-12780_F4_17168233.sorted.hfix DNA15-10811_p-BRC_R15-12787_A2_17168553.sorted.hfix DNA15-10811_p-BRC_R15-12787_A5_17168554.sorted.hfix DNA15-10814_p-BRC_
R15-12788_B2_17168652.sorted.hfix DNA15-10814_p-BRC_R15-12788_B5_17168653.sorted.hfix DNA15-10815_p-BRC_R15-12789_C1_17168718.sorted.hfix DNA15-10815_p-BRC_R15-12789_C4_17168719.sorted.hfix
DNA15-10817_p-BRC_R15-12790_H1_17168781.sorted.hfix DNA15-10817_p-BRC_R15-12790_H4_17168782.sorted.hfix DNA15-10820_p-BRC_R15-12791_G1_17168852.sorted.hfix DNA15-10820_p-BRC_R15-12791_G4_1
7168853.sorted.hfix DNA15-10836_p-BRC_R15-12842_A1_17172258.sorted.hfix DNA15-10836_p-BRC_R15-12842_A4_17172259.sorted.hfix DNA15-10862_p-BRC_R15-12883_E3_17176195.sorted.hfix DNA15-10862_p
-BRC_R15-12883_E6_17176196.sorted.hfix DNA15-10877_p-BRC_R15-12918_D2_17178207.sorted.hfix DNA15-10877_p-BRC_R15-12918_D5_17178208.sorted.hfix DNA15-10879_p-BRC_R15-12922_C2_17178411.sorted
.hfix DNA15-10879_p-BRC_R15-12922_C5_17178412.sorted.hfix DNA15-10880_p-BRC_R15-12923_B3_17178473.sorted.hfix DNA15-10880_p-BRC_R15-12923_B6_17178474.sorted.hfix DNA15-10883_p-BRC_R15-12926
_A3_17178538.sorted.hfix DNA15-10883_p-BRC_R15-12926_A6_17178539.sorted.hfix DNA15-10888_p-BRC_R15-12928_H2_17178724.sorted.hfix DNA15-10888_p-BRC_R15-12928_H5_17178725.sorted.hfix DNA15-10
927_p-BRC_R15-13004_H3_17185261.sorted.hfix DNA15-10927_p-BRC_R15-13004_H6_17185262.sorted.hfix DNA15-10928_p-BRC_R15-13005_G3_17185326.sorted.hfix DNA15-10928_p-BRC_R15-13005_G6_17185327.s
orted.hfix
Is anyone familiar with EXCAVATOR giving errors regarding R?
I hope to hear from you soon!
Kind regards,
Koen
same problem here - did you find out what was causing it?
You have lot of error due to file not found. Examples.
Could you check the integrity of your input files? To pinpoint the errors, you may try to run EXcAvator separately for those files giving errors.
Also check in this folder
DNA15-10928_p-BRC_R15-13005_G6_17185327.sorted.hfix
It seems to me that EXCAVATOR is expecting a gzipped file there, while it is getting unzipped one, or may be the opposite.