search

cobilab / falcon

A tool to infer metagenomic sample composition
GNU General Public License v3.0
21 stars 7 forks source link

(core dump) in FALCON-filter-visual #9

Closed Xevkin closed 4 years ago

Xevkin commented 4 years ago

Hi,

I've been playing around with FALCON and have run into an issue following the FALCOM-meta.sh script. Specifically, I get a (core dump) messages:

7f6e980f8000-7f6e980f9000 r--p 00025000 fc:00 9306617 /lib/x86_64-linux-gnu/ld-2.23.so 7f6e980f9000-7f6e980fa000 rw-p 00026000 fc:00 9306617 /lib/x86_64-linux-gnu/ld-2.23.so 7f6e980fa000-7f6e980fb000 rw-p 00000000 00:00 0 7ffce87c9000-7ffce87ea000 rw-p 00000000 00:00 0 [stack] 7ffce87ec000-7ffce87ee000 r--p 00000000 00:00 0 [vvar] 7ffce87ee000-7ffce87f0000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] ../FALCON-meta.sh: line 4: 127006 Aborted (core dumped) /home/kdaly/programs/falcon/FALCON-filter-visual -v -F -o draw.map positions.pos

pratas commented 4 years ago

Hi, can you post here the positions.pos file? D

Xevkin commented 4 years ago

positions.pos.txt

pratas commented 4 years ago

Ok, this is not the positions.pos.txt... This is the Top without positions. So, we have to go back since I think maybe you misplaced the files. Which parameters did you used for FALCON ? And which files?

Xevkin commented 4 years ago

Hi,

The exact commands where as instructed on the manual page i.e. FALCON-meta.sh:

!/bin/bash

/home/kdaly/programs/falcon/FALCON -v -n 4 -t 200 -F -Z -l 47 -c 20 -y complexity.com $1 $2 /home/kdaly/programs/falcon/FALCON-filter -v -F -t 0.5 -o positions.pos complexity.com /home/kdaly/programs/falcon/FALCON-filter-visual -v -F -o draw.map positions.pos

Ran using:

~/programs/falcon/FALCON-meta.sh sample.fastq VDB.fa

The VDB.fa file is from the test folder included in the github installation.

On Thu, 28 Nov 2019 at 09:48, Diogo Pratas notifications@github.com wrote:

Ok, this is not the positions.pos.txt... This is the Top without positions. So, we have to go back since I think maybe you misplaced the files. Which parameters did you used for FALCON ? And which files?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/cobilab/falcon/issues/9?email_source=notifications&email_token=AB5YBT4YTCE3PXE4BXP5XFTQV6HWPA5CNFSM4JSRJ2K2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFMBPCI#issuecomment-559421321, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB5YBTZMNYHOMQ6EBEJLEHDQV6HWPANCNFSM4JSRJ2KQ .

-- Kevin Daly, PhD Postdoctoral Researcher Population Genetics Lab Smurfit Institute of Genetics Trinity College Dublin 2

pratas commented 4 years ago

can you show me positions.pos?

Xevkin commented 4 years ago

The file attached previously was the positions.pos file - I had to rename it to positions.pos.txt for github but is otherwise unchanged.

To be sure I have rerun falcon and attaching the positions.pos file.

On Thu, 28 Nov 2019 at 09:56, Diogo Pratas notifications@github.com wrote:

can you show me positions.pos?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/cobilab/falcon/issues/9?email_source=notifications&email_token=AB5YBTYVR7J4ZRPSEJYXPWTQV6ITDA5CNFSM4JSRJ2K2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFMCFTQ#issuecomment-559424206, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB5YBTYAU4D6JF2XXNB5SVLQV6ITDANCNFSM4JSRJ2KQ .

-- Kevin Daly, PhD Postdoctoral Researcher Population Genetics Lab Smurfit Institute of Genetics Trinity College Dublin 2

Xevkin commented 4 years ago

Again, renamed to make github happy.

positions.pos.round2.txt

pratas commented 4 years ago

It seems that is before. Can you show me: complexity.com ?

pratas commented 4 years ago

Of course that if you can share the reads it would be much easier...

Xevkin commented 4 years ago

complexity.com.txt

Xevkin commented 4 years ago

Accidentally closed the issue!

Attaching below the first 1000 reads of sequencing data (can't share it all). Core dump occurred at same time. Including the complexity.com and positions.pos files for that run.

Xevkin commented 4 years ago

positions.pos.round3.txt complexity.com.txt data.fastq.txt

pratas commented 4 years ago

For me it works fine. This is the output of complexity.com:

5.13193 3141 gi|124378202|ref|NC_008912.1|_Glypta_fumiferanae_ichnovirus_segment_C9,_complete_sequence

daCTGSIRddITHRIRccFTHRIRGRGRFQDOCNddIRHRIbHSHRETGRFRFnJQGSGJSmHHmcHHHmlRSllSmImcIHHGcbGmHHGGcTGmIRncbSlRmlJIlHHlldHHHcSclcSHmHIcIcHlmcIbllcI ScIHmbRImllbHScIlPJmmlHcmISIHHHHHmHGGmkclbdRmbSHllbcTlbISSImlcRmImlTlIcHmmmImlImHcGHlRRmIllkkklSRRdmcbRlbkaclImmmkHlIkHlIGTlSmllIlIlHHmllkIl IjljllIFFFdGccnImclHlIHHHlGmHHccHTmIcRlHlIlHbRlIJHHHmHnHlTcSmImIbIcSHmIHRRHSlImIHcSmcmIlbIIHHmImFdlHlHIHmIlHHcSmHIccScbcHmIHcSmmcISSRHRSHRIS RSbSSHSIRmbISbRmRIHcSHSHnRHRbRdcHRInmmlcHHlScSIlIlclcSlQclmbcIlmRcmlmSbHScHbHcbHHISSHIScHbRSSmHmllRHlbbRlYjdHmlRmRcHHbcmbIRlmlllISHHcRTSmmIm cmISlmSHIHmcccmccSbHcmHRlnlllljSdHHHIHmlcSHSlllRScHdmbSHImSHclbHlbmScGmQaHRIbcmRmJlHlRRllJGdcRlSlIIHSHHGcHlSTcIbHbHRlIRISbbIbGcIlImllIHGcnIH RSHlmRRlJlcSHbRHmIcmIHlbImmIRIllJllcmIlIcmllclIlIHSlcclRIRHmIHHHcTcbRcmcIlIRHHHSmHlHbIHlHHlclJHSTbkmIRlIlcSmbSHlHbcIHmIlllISmlHIIHlmlSlclSmb mblIcScHRIRIIIbHIcGImmkIHSHmlllHGTHmHGTRlRHIIHlHmHlkkTHJmmcclIclcIcHSmSlblSmmlIcclRmlQblbkbnmIcHlRmRSImcmmllclHlljjnkiTlHJFGmTHIImSlbllRmIHd mlmbSmHcISHmIlclTlIcmIlHSmHIHHHHFEnkdIHlbIlSIHSlISclRHdRmbmjEnlbZnccmbIHblcHIHmlRkIImIcdHcSHIHHHHGFEEnkdbknHSmkdIHGSHlllHIljmIHGFkmljdlTcHIR bHHQnJISHmllScmlIImcmRISlmHlmcbHJSlIImHllcHTcIlmmlIcScHcHmcHlRbmmImIHImIcScIlmIIHHlcHITmcHmRbmIlImIllIcllccIlmRHISSImmllmlkSdclblImbbHIHcSmm cllclIScHbSmlRcHImmmlllSdlIcmmcHlImcmmllRRcmRIHbmbIIHmcSSSHRbcHIRRSHIHcmmmRllcHIHSlJlcHHGGGcFHGHTGbmbHcGIHmcHmmbHIHGmIcmcIclISlRmlSJHHSSmlSH RImcHSIRcHbmImIISHllllmSHbcmlIHbHGTHmnllHHcmmmblIllIISHmHSHSmIlSIlllcRIHmImllbSRHlcHclkQcGJmIIHHHHScSlbmmRIIHmSJmbHlIIRcHIRmIlHmRlllJHlHlkkI TdmlRlRRllTImmlclISkRIbHSIbIlJIlmIHmcmRlbSRHJInHSHmcmIHbSIIRmRIIcSmRmIblIlSIlSlmIlllInIkSITSbcIHmlRIlIlmIIHGGbRTklIlHjnkTHSdHcIlmcImcmIIllmc SlSblmbHHIGHaTcIIISmIcIbISlIcmSHcHmIbHISHHHSSmllTISlIbHSHmRmIlmlIHSclmmllSHHmblmSSHmImRclRmIcmIIHmllSlIRlbJHmHllllSlmRmamSmbHFmmlclbmmSHlQln JllkdlIIcGGGHlITmmllIlkJRHkISbnlRIlblllRHHmbmblkSlSbnHknmSllImlIHHmllIlSHHSHccmISlHmSIHHbHIHlcFnbGHHmGGTlcRklmcHmImlRHblRmkRJmmSlbSSlSRHblcH cGIcbmmbblncImISclSmbmIHmHlRllllkRGlbJlllkIlIklccRHlInllllISlHlmlJmcImSIlmllccHSbRmRlJIHlmclbRIlHJIlScHlmllRlRlcHGPImnHQkkRlmJcISHImmbcSHHHl mcIlcIHHHmmlcSRHHRcmcmaJmbmbHlbHlJImmldlIllRFigdllTlllRdSIblmRbHmmbTIGnbIlbHcmccmSIlSlmcclcIllRcHbHlJmllbcImIIcSmcIlmcRIbIlJmSISSbSIlcRbHcII mcIcSmISbHcSmlIRcHISHIRlmcHcHIHHlmcbcISHcHHcFcJHcIkjJIbHmcbRIcSHImmRcHbRbHIbHIHZJcGkdSlbHmJclcbHIllIIcHHcHcPnbjXTIImmllccHSEdmSblIRSbbIcSISG nlHRccHaGlJIlmRlllRHmRcHSIlmblIcmRHmlSlllclbSRIllIlcHRIlmbHmHHmHHHcHFGTcaGmbTdIIRmmbmmcllcllmkkkiihhJjJjHbFdnllRTlbSllSmllTHSSHIQcHbmlJHGTmS lllISHHHHHmkHHGadGSmRJScIcRHmmllmIHlFhIllkSHJIHHHmcmmcmSIRbSHIHmRImmIHbSmmmlllkIHGGkccIIHmcHmSRHmRRmmbnSmlcHImHIlHSlmlbImIHHHHHnllHSGmSIInIc mlblIIllcSHScRIImmIbcIHSlRcHmIIHmlllIlkkSHSISHmlSGSGSHRGRFbHSHRbRIRbTJRbSIRHRIRHRGREPCNBNBMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMdSIRHRIRHRGRDOC NBNBMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMdcIRHRIbHSHREXCTHNCWBTmRHcHSIRHIISmSHbHSIRH bHSHPDWBnISIbHSHRHbHTHJIbHSHSHbHHGSmbHGGTHbGTHRHRGbHTHRGaFTHPDWCTHNCVBTHJIbHSHSHbHHGSmbHGGTHbGTHRHRGbHTHRGaFTHPDWCTHNCVBTHMCVBTHMBVBTHMBVBJH SHbHTHRHbHIGTGbGTHRHRGRFRFQDOCNBNBMAMAMAMAMAMAMAMAMAMdcIRHRIR

4.45403 1801 gi|9629210|ref|NC_001782.1|_Saccharomyces_cerevisiae_killer_virus_M1,_complete_genome

dGGGHHnGFFcGEEncGScHHcTSHHRTSHIcmImmHcllHdHlQTcmRIclImIllIlllklSHlRHRHkmHQkISHSSlJbmRblIbSaSkbIJScImclbcSRbblRSmbSHcIIHSHbSHRSHclcmRIllISlIS SlRcmbIHbScRSblcbnImcHRIIcHlPncbcHHbnIHIHdHmmcbRlIlmHSHbScmbSSHSIcIlcbRIHjlcccbSIHbmRcHlQIQRnaccbmlRHmmSclIcSbGdSbHmcSIbcmblHcmHIkSlklbcmHmR IIlblblbkIIdHHSlbSclbcbncHcRbmIHccImcHmIlSIblHPdcISmbRbbSIIbSIIHSHRllcSmllISmHclTHcSHlmllmclHbSIcllHRHlSRcbRSHmQHmQlmJlHlcdbclcclIHmIccSSbcl bmRbSIclRHcHmQTlJImcbSbSlISSbmmbRlRblRbmdJRInmmSlIRlblTbSIcIScccbHmImlRSHRlbbHTlmlIdmcScmmcHHRcHSHlIllIHHmcHISHmbcmIlmIclIlHSmSSSHcSlIHScSHm RHRHImHlclSHIIHbHmRJbISIRHbSRcIIRHRIScITIIcmlmlclHbmcJRSHHSIIRlHSISmmRmmlcSImIRSbHSRncImlRHlRHlcbmIImccHISHmHmHSSHScmlmISSHSHSRmSHRHmmSSIcSI blbcSSHIcRbllIldmllJlSRlJlcldScIbRImbbmIlRIIccRSmSHmIRlclHlZdSSSmlIImcHmbSRHlcdmbmRbbRmIIlcbmHISRmclIlbbHRlJcRIbHGHGbRmcmllIclcHccHlbHbccISH ImbccHbHRbHImmISlIlHHHmlclIlkdbHcmJRlbcSRIbmbbHmIIlclRcHmcHIcmlmIllcHbcHIIcmImmcImHHRcRSHImHHlcHSlllbIIbdSmblbHSJRHbcSRISmIbccSImSbmcmRlbHST mRmcHmbRcIlHHSmScHRSSmISIcHcSIRSccbRmIlHlHlIHmHlIclHccSIRHHHIlHGGGlGFDDEnkHHFFFFDDDDDDDDDDDDCCCCCCCCCCCCCCCCCCCBBBBBBBBBBBBBBBBBBBBBBBBBBBBB BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBdGDDCdFdFdHdHHdHHdGHdGHdFHFEDdEEDDCCSCCCCdDCCSCdEEDCCdDdFdHFTFdcHSGIRIIISdSIHRIHIHSHSHIISHRHIbTH SFMnRIRSmmbHcmRlIISmcclbbSHSbSIbSImIlRmRHRSSlcIbHSmIIRmccSccRIbcRbHSSbmcHbSHmIRIbSHmcRSRSISlRbHnmSbHbHTbScHmmRaSbSlQamJdcmHlRbHdRbcSmIRcmmcI cRmIlmHlccSHcmbIRImbScHlmRbSbSIRlbQPJIdHlQJbRmRIbRHHHbmnHHbGSRIcjJlScbHnIlcclIcISmIRmHRHImmScRISIbcmIlcHbIlmSlRIblSmIcmbmImbbHmbIbmIcmlcHbRS HHmcHHlRlIccblllHHHllISlIlcSHnlbHSHmIlHdRIbclISHIbRclIcHlIHlHSlmHSlIccSRRSIbSScclIRHSRSlclJllcIHlHIHmIScISmImmlccSSIbcmRmbdISccbbSHblScIImmI SlIccllaJbRISGOJRGRdidIImRHRHSHHSHmIHSIclblHccEJSHnHHlclbSSIllRclJcmRmcIcHScSSbSmIbRSlcblmlIHmcSHHSHbSHmIcHIcIIHSHRHSHmRH

pratas commented 4 years ago

(only the first two)

pratas commented 4 years ago

How did you installed FALCON?

pratas commented 4 years ago

Which operating system and distribution are you using? (If you can give me a phone number I can call you and see what is the problem)

Xevkin commented 4 years ago

Hi Diogo,

We're operating on Ubuntu 16.04.2 LTS. Falcon was installed using git clone, as instructed in the readme. I did not try the conda installation - I amy try that now and see if it's an installation issue.

On Thu, 28 Nov 2019 at 10:49, Diogo Pratas notifications@github.com wrote:

Which operating system and distribution are you using? (If you can give me a phone number I can call you and see what is the problem)

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/cobilab/falcon/issues/9?email_source=notifications&email_token=AB5YBTYVX6PJ4SNL6PAJAG3QV6O5HA5CNFSM4JSRJ2K2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFMG77Y#issuecomment-559443967, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB5YBTY74F2OK2X2DWKDNI3QV6O5HANCNFSM4JSRJ2KQ .

-- Kevin Daly, PhD Postdoctoral Researcher Population Genetics Lab Smurfit Institute of Genetics Trinity College Dublin 2

pratas commented 4 years ago

Hi, I rerun the compilation and it seems to be all ok. There may be something about the unicode or even in the compiler.

Xevkin commented 4 years ago

Hi, I tried the conda installation and had the exact same issue. I have no computer science background so can't comment on the source of the problem being the unicode/compiler. However I've installed falcon on my personal ubuntu machine and everything seems to be running fine. Thanks for spending so much time on this.

On Thu, 28 Nov 2019 at 11:16, Diogo Pratas notifications@github.com wrote:

Hi, I rerun the compilation and it seems to be all ok. There may be something about the unicode or even in the compiler.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/cobilab/falcon/issues/9?email_source=notifications&email_token=AB5YBT2TYBBLJFAFIBVHT63QV6SCRA5CNFSM4JSRJ2K2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFMJGEA#issuecomment-559452944, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB5YBT6GBLG3F3BJZ36ZHRTQV6SCRANCNFSM4JSRJ2KQ .

-- Kevin Daly, PhD Postdoctoral Researcher Population Genetics Lab Smurfit Institute of Genetics Trinity College Dublin 2

pratas commented 4 years ago

Unfortunately I won't know if it is something related to the installation or not. Thanks anyway! Best regards