EXCAVATOR Not working

Question

[koenhendriks89]

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

[lm687]

same problem here - did you find out what was causing it?

[Santosh Anand]

You have lot of error due to file not found. Examples.

'/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
'/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

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.

Answer 1

[QVINTVS_FABIVS_MAXIMVS]

Looks like something wrong with your file handles maybe?

Error in gzfile(file) : invalid 'description' argument
Calls: rbind -> loadRC -> load -> gzfile
Execution halted

Make sure the file variable is pointing to the correct file.

I've never heard of excavator. But there are more tried and true CNV callers for NGS like lumpy and metaSV.

Do you need to excavator for a specific experiment?

[koenhendriks89]

No, not really actually. I'm testing CNV calling tools to call CNV's in breast and colon cancer data, which was obtained by targeted sequencing by means of MIPs.

I've up to now tried EXCAVATOR, ExonDel, CoDeCZ and ExCopyDepth, but they're not able to correctly call all CNV's in my positive control samples. Therefore I'm looking into new tools.

[QVINTVS_FABIVS_MAXIMVS]

CNV callers use three main statistics to call CNVs: read depth, discordant paired ends, and split reads. For standard NGS this works because you'll have a constant read depth and insert size; deviations from the norm for either one of these statistics (plus chimeric mappings) will flag the region as "Structural variation probable"

In order to call discordant paired ends you need mate pairs. Does MIPS have mate pairs?

I'm not quite sure they do... I'm not familiar with MIPs all too much. Our lab made a pilot but the coverage was not consistent so it was crap.

Maybe it's a limitation of current CNV callers and you need one specifically for MIPs? But there are options that might work well for you:

• CNV callers that run on coverage (read depth):
  • ForestSV: extremely sensitive good for NAHR; not so good for complex events (like in cancer)
    • problems: needs R 2.15 also bioconductor packages from that time
• CNV callers that use split read:
  • Lumpy: very sensitive, not good for NAHR, but really good for translocations and complex SVs (like in cancer)
    • problems: might not accept your MIPs format; I'm not really sure about this. You do need mate pairs

However, make sure your coverage values are consistent. Wild variations in this will ruin any CNV caller.

How is it failing in the positive controls? Sorry I'm not able to help too much, your problem is very specific and novel .