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bcgsc / abyss

:microscope: Assemble large genomes using short reads
http://www.bcgsc.ca/platform/bioinfo/software/abyss
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abyss-rresolver-short not assigning a value for -b (invalid option: `-b-j2') #368

Closed ericgarciaresearch closed 3 years ago

ericgarciaresearch commented 3 years ago

Hi There,

abyss-rresolver-short is terminating my runs, I believe, after failing to assign a value for "-b" as I interpreted from a similar post (https://www.gitmemory.com/issue/bcgsc/abyss/366/812285867) where Vladimir said he will "update it so that rresolver only runs in Bloom filter ABySS mode"

Yet, I can't find more info about this issue. What can I do? Thank you!

vlad0x00 commented 3 years ago

This has been fixed in the master branch and will be in the next release of ABySS. Until then, I can recommend either running the previous version or running current version with Bloom filter mode (by specifying the -B parameter). This parameter specifies the size of Bloom filter and depends on the number of reads / size of the genome you're assembling. Some of the common Bloom filter sizes we use are -B2G for C. elegans, -B40G for H. sapiens, and -B500G for large genomes like spruce.

desmodus1984 commented 3 years ago

Hi, I am running with the same problem. I couldn't install that thing of homebrew so I used the conda version. I used the following code for running which ran well until the rresolver; abyss-pe k=59 np=48 name=myse lib='BGI' BGI='/fs/scratch/PHS0338/appz/musket-1.1/BGI-Readz.0 /fs/scratch/PHS0338/appz/musket-1.1/BGI-Readz.1' \ long='ONT' ONT='/fs/scratch/PHS0338/appz/Ratatosk/bin/Rata-T3-Corr10K.fasta'

and the report is: 31: Assembled 49534054 k-mer in 453230 contigs. 41: Assembled 49326842 k-mer in 453550 contigs. 11: Assembled 49720430 k-mer in 467990 contigs. 37: Assembled 50094022 k-mer in 461638 contigs. 6: Assembled 49289166 k-mer in 457369 contigs. 5: Assembled 49614361 k-mer in 462785 contigs. 21: Assembled 49679695 k-mer in 462396 contigs. 40: Assembled 49841950 k-mer in 460174 contigs. 0: Assembled 49689297 k-mer in 463135 contigs. 44: Assembled 49643028 k-mer in 460170 contigs. 16: Assembled 49982515 k-mer in 465728 contigs. 32: Assembled 49536860 k-mer in 460534 contigs. 36: Assembled 49990791 k-mer in 467315 contigs. 24: Assembled 49868991 k-mer in 462242 contigs. 18: Assembled 49229501 k-mer in 453419 contigs. 30: Assembled 49240006 k-mer in 451837 contigs. 43: Assembled 49610542 k-mer in 463100 contigs. 42: Assembled 49705908 k-mer in 457602 contigs. 12: Assembled 49899551 k-mer in 462757 contigs. 22: Assembled 49477862 k-mer in 456036 contigs. 19: Assembled 49342631 k-mer in 456663 contigs. 4: Assembled 50175729 k-mer in 474550 contigs. 20: Assembled 50187262 k-mer in 467852 contigs. Assembled 2378322000 k-mer in 22003600 contigs. Concatenating fasta files to myse-1.fa Concatenating fasta files to myse-bubbles.fa Done. AdjList -k59 -m0 --dot myse-1.fa >myse-1.dot abyss-rresolver-short -b -j48 -k59 \ -h myse-1-rr --dot -c myse-1-rr.fa -g myse-1-rr.dot myse-1.fa myse-1.dot /fs/scratch/PHS0338/appz/musket-1.1/BGI-Readz.0 /fs/scratch/PHS0338/appz/musket-1.1/BGI-Readz.1 abyss-rresolver-short: invalid option: `-b-j48' make: *** [/users/PHS0338/jpac1984/.conda/envs/busco/bin/abyss-pe.Makefile:566: myse-1-rr.dot] Error 1

lcoombe commented 3 years ago

Hi @desmodus1984,

As @schutzekatze suggested, either try compiling ABySS from the current master branch, or run ABySS in the Bloom filter mode: https://github.com/bcgsc/abyss#assembling-using-a-bloom-filter-de-bruijn-graph

We will have a new release soon that has the fix currently in the master branch of the code.

vlad0x00 commented 3 years ago

I've released version 2.3.1 which fixes this.

desmodus1984 commented 3 years ago

Dear Lauren,

Sorry to bother you. Could you explain me how to and what to do. I tried with homebrew as stated and it started with an error "Error: Curl must be installed and in your PATH!" - and I do not have root permission to install Curl (which is extremely annoying), and with brew it stated: "==> Pouring abyss-2.2.5.x86_64_linux.bottle.tar.gz" So it was still downloading an old version, not the most updated version.

Thanks;

Juan Pablo Aguilar Cabezas

Ecology and Evolutionary Biology Ph.D. Candidate

Department of Biological Sciences

Ohio University, Athens OH

From: Lauren Coombe @.> Sent: Wednesday, April 21, 2021 10:48 AM To: bcgsc/abyss @.> Cc: Aguilar Cabezas, Juan Pablo @.>; Mention @.> Subject: Re: [bcgsc/abyss] abyss-rresolver-short not assigning a value for -b (invalid option: `-b-j2') (#368)

Hi @desmodus1984https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fdesmodus1984&data=04%7C01%7Cja569116%40ohio.edu%7C46ea0b919f1543e1d19b08d904dcf00e%7Cf3308007477c4a70888934611817c55a%7C0%7C0%7C637546169226929195%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=ncJPaSCiJH8MmnY5P7zMdNa6ka1pJP9e3DRAswkd7Rw%3D&reserved=0,

As @schutzekatzehttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fschutzekatze&data=04%7C01%7Cja569116%40ohio.edu%7C46ea0b919f1543e1d19b08d904dcf00e%7Cf3308007477c4a70888934611817c55a%7C0%7C0%7C637546169226929195%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=%2F%2FAIgKP8gDjXSWvuWLwTjx25RS781HYTByGzmFLuwVQ%3D&reserved=0 suggested, either try compiling ABySS from the current master branch, or run ABySS in the Bloom filter mode: https://github.com/bcgsc/abyss#assembling-using-a-bloom-filter-de-bruijn-graphhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbcgsc%2Fabyss%23assembling-using-a-bloom-filter-de-bruijn-graph&data=04%7C01%7Cja569116%40ohio.edu%7C46ea0b919f1543e1d19b08d904dcf00e%7Cf3308007477c4a70888934611817c55a%7C0%7C0%7C637546169226939188%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=vY6abu%2FLf0uCfVJOF3ZOOg0DVxmu5zSdSEAZTdksB10%3D&reserved=0

We will have a new release soon that has the fix currently in the master branch of the code.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbcgsc%2Fabyss%2Fissues%2F368%23issuecomment-824167746&data=04%7C01%7Cja569116%40ohio.edu%7C46ea0b919f1543e1d19b08d904dcf00e%7Cf3308007477c4a70888934611817c55a%7C0%7C0%7C637546169226939188%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=xhsRjoHBLX8CWE6oMfAHsCqMoOyewhHy65DmfjrSBls%3D&reserved=0, or unsubscribehttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAJWD2VL7YOMAROSCR4DVJBLTJ3XVTANCNFSM43AKCFSQ&data=04%7C01%7Cja569116%40ohio.edu%7C46ea0b919f1543e1d19b08d904dcf00e%7Cf3308007477c4a70888934611817c55a%7C0%7C0%7C637546169226949180%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=VNxPXIMAxce73Yj08D%2BjBFra8uOeULnIDZJ74Hgvipc%3D&reserved=0.

lcoombe commented 3 years ago

Hi @desmodus1984,

Thanks for the heads up - looks like we haven't updated ABySS in homebrew yet. We'll do that upstream and let you know when it's finished!

desmodus1984 commented 3 years ago

Hi Lauren,

It would be incredibly helpful and fantastic if you could first update it in conda. It is way much easier and simpler and straight forward to install.

lcoombe commented 3 years ago

Hi @desmodus1984,

Conda actually updates the packages automatically using a bot, so the update should be happening automatically in the next day or two -- but I'll keep an eye on it to make sure that PR gets opened!

desmodus1984 commented 3 years ago

Hi Lauren,

That's awesome. I will run the update during the weekend and test it then.

I wanted to ask you a question.

As I mentioned I have Nanopore data, error corrected, plus a library of PE-100 reads. I was confused how to parameterize the PE library. I used lib="" but I read that it is also mentioned using in= and pe=.

I want to make sure that I use the proper parameters and not waste CPU hours.

Thanks.

lcoombe commented 3 years ago

Hi @desmodus1984,

You can either use lib= as demonstrated here: https://github.com/bcgsc/abyss/#assembling-multiple-libraries Or using in is fine too: https://github.com/bcgsc/abyss/#assembling-a-paired-end-library

If you have multiple libraries, then using the lib approach is the way to go, but if you just have one paired-end library than either should work just fine.

ABySS is now updated in conda, btw!