ERROR: Signal 6 occurred. VG has crashed.

[mariarecuerda6]

ERROR: Signal 6 occurred. VG has crashed.

[jeizenga]

Can you also share the commands you used to make the graph, map reads, and make the pack file? Often these errors result from some mismatch between the graphs used at different stages in the analysis.

[mariarecuerda6]

Hello, The weird thing is that I've been running in the same machine with the same graphs using the same commands for all of them and now they are giving me this error. To generate the graph I used cactus minigraph Then I run: vg gbwt -o spp-pg.d2.gbwt -Z spp-pg.d2.gbz ##Then I mapped the reads with vg giraffe vg giraffe -Z spp-pg.d2.gbz -m spp-pg.d2.min -d spp-pg.d2.dist -f /min_O5.pair1.fa -f min_O5.pair2.fa > min_O5.gam vg convert -Hx spp-pg.d2.gbz > spp-pg.d2.xg vg convert -Hp spp-pg.d2.gbz > spp-pg.d2.vg ##Then make the pack file vg pack -x spp-pg.xg -g min_O5_p12.gam -Q 5 -o min_O5.pack ##Then vg call vg call spp-pg.d2.xg -k min_O5.pack -a > min_O5.vcf I've been running these commands in 3 different machines and they work (some of them are running right now) but I don't know why it is not working anymore. Thank you for your help, Maria El mar, 5 mar 2024 a las 15:05, Jordan Eizenga ***@***.***>) escribió:

…

Can you also share the commands you used to make the graph, map reads, and make the pack file? Often these errors result from some mismatch between the graphs used at different stages in the analysis. — Reply to this email directly, view it on GitHub <#4238 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A7AU2SYD6CSC2V23Z5JBQP3YWYQQ3AVCNFSM6AAAAABEHXR6TGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNZZGUZTSOBQGA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- María Recuerda, PhD Postdoctoral Research Associate Department of Ecology and Evolutionary Biology Fuller Evolutionary Biology Program Cornell Lab of Ornithology Cornell University ***@***.*** *https://mariarecuerda.weebly.com/ <https://mariarecuerda.weebly.com/>*

[jeizenga]

Presumably this is new sequencing data, despite using the same graphs, correct?

In any case, nothing jumps out to me as incorrect in the pipeline, although you don't seem to be actually using all of the indexes/graphs that you create. Are you able to share the data?

[mariarecuerda6]

I manage to run the pipeline previously with all the samples, but I have to repeat it because I mapped the wrong files and I lost a lot of information.. I thought that the vg graph was used when you call in the command the xg index, but you don't have to specify the graph directly. What files do you need? the graph (vg), the index (xg) and a pack file? the graph and the index are 6.1 and 8.7 GB El mar, 5 mar 2024 a las 15:25, Jordan Eizenga ***@***.***>) escribió:

…

Presumably this is new sequencing data, despite using the same graphs, correct? In any case, nothing jumps out to me as incorrect in the pipeline, although you don't seem to be actually using all of the indexes/graphs that you create. Are you able to share the data? — Reply to this email directly, view it on GitHub <#4238 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A7AU2S7SZN5GZ2UNHMP5ZVLYWYS3JAVCNFSM6AAAAABEHXR6TGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNZZGU3TSMBXGQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- María Recuerda, PhD Postdoctoral Research Associate Department of Ecology and Evolutionary Biology Fuller Evolutionary Biology Program Cornell Lab of Ornithology Cornell University ***@***.*** *https://mariarecuerda.weebly.com/ <https://mariarecuerda.weebly.com/>*

[jeizenga]

Ideally, the d2 GBZ file, the full GBZ, and the sequences you're mapping.

Before that though, can you check what happens if you use spp-pg.xg instead of spp-pg.d2.xg in vg call?

[mariarecuerda6]

I have tried with the spp-pg.xg file and I got the same error (ERROR: Signal 6 occurred. VG has crashed. ) El mar, 5 mar 2024 a las 17:21, Jordan Eizenga ***@***.***>) escribió:

…

Ideally, the d2 GBZ file, the full GBZ, and the sequences you're mapping. Before that though, can you check what happens if you use spp-pg.xg instead of spp-pg.d2.xg in vg call? — Reply to this email directly, view it on GitHub <#4238 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A7AU2SZN532EIV5N6LVHXY3YWZAP3AVCNFSM6AAAAABEHXR6TGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNZZG4ZTMMBTGM> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- María Recuerda, PhD Postdoctoral Research Associate Department of Ecology and Evolutionary Biology Fuller Evolutionary Biology Program Cornell Lab of Ornithology Cornell University ***@***.*** *https://mariarecuerda.weebly.com/ <https://mariarecuerda.weebly.com/>*

[mariarecuerda6]

Hi Jordan, I have solved the problem, It seems that the pack files were somehow corrupted. I just repeated the pack step and now vg call it's working fine. Thank you for your time and suggestions. Best, Maria El mié, 6 mar 2024 a las 0:08, Maria Recuerda Carrasco (< ***@***.***>) escribió:

…

I have tried with the spp-pg.xg file and I got the same error (ERROR: Signal 6 occurred. VG has crashed. ) El mar, 5 mar 2024 a las 17:21, Jordan Eizenga ***@***.***>) escribió: > Ideally, the d2 GBZ file, the full GBZ, and the sequences you're mapping. > > Before that though, can you check what happens if you use spp-pg.xg > instead of spp-pg.d2.xg in vg call? > > — > Reply to this email directly, view it on GitHub > <#4238 (comment)>, or > unsubscribe > <https://github.com/notifications/unsubscribe-auth/A7AU2SZN532EIV5N6LVHXY3YWZAP3AVCNFSM6AAAAABEHXR6TGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNZZG4ZTMMBTGM> > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> > -- María Recuerda, PhD Postdoctoral Research Associate Department of Ecology and Evolutionary Biology Fuller Evolutionary Biology Program Cornell Lab of Ornithology Cornell University ***@***.*** *https://mariarecuerda.weebly.com/ <https://mariarecuerda.weebly.com/>*

-- María Recuerda, PhD Postdoctoral Research Associate Department of Ecology and Evolutionary Biology Fuller Evolutionary Biology Program Cornell Lab of Ornithology Cornell University ***@***.*** *https://mariarecuerda.weebly.com/ <https://mariarecuerda.weebly.com/>*

[jeizenga]

Glad it worked out!