Closed asdcid closed 5 years ago
Dear @asdcid , thank you for reporting this. We are planning to retire daijin assemble
soon, but I will try to fix the bugs you found as quickly as possible.
The problem most likely stems from the fact that I reorganised the configuration file recently (as it had become sprawling and with a lot of duplicated values). Hopefully it should not take too long to fix.
Dear @asdcid , I should have solved the small issues you reported. I will keep this report open until I have put a proper testing for daijin assemble
in place.
Many thanks for reporting this, we would have released with a bugged Snakefile otherwise.
Dear @asdcid , I have now implemented a proper test for daijin assemble
. While doing so, today I fixed a very large number of bugs in the pipeline.
Once the travis check completes successfully, I will merge back into the master
branch and close the issue.
Thank you again for reporting and prodding me to clean up the code in this section.
Thanks for your help.
However, I have another question. I tried to run mikado (with permissive mode) with trinity and scallop assembly results, but it seems that the BUSCO complete score in the final mikado result pick/mikado-permissive.loci.gff3
is pretty low (~30%, vs ~90% for original trinity or scallop assemblies). Do you have any idea about that?
Thank you.
I think I found the answer. I am using daijin mikado
, it seems that neither blastx nor diamond was run.
Also, it seems that the --use-diamond
always is true in the configure file even I set --use-blast
in mikado configure
.
The dag file for daijin mikado
is attached:
dag.pdf
Dear @asdcid, thank you again for your report. May I ask whether you specified one or more protein FASTA files during configuration? If they are missing, that would explain why mikado did not perform a blast run.
I will check and correct the bug regarding --use-blast
as soon as possible.
Dear @asdcid , unfortunately I cannot reproduce the bug regarding --use-blast
with the latest version of the code. I just trialled and daijin
correctly used BLAST+ instead of DIAMOND.
I am now testing it in Travis (see https://travis-ci.org/lucventurini/mikado/jobs/585974482), where I can confirm that the bug does not present itself.
Regarding your more concerning point:
However, I have another question. I tried to run mikado (with permissive mode) with trinity and scallop assembly results, but it seems that the BUSCO complete score in the final mikado result
pick/mikado-permissive.loci.gff3
is pretty low (~30%, vs ~90% for original trinity or scallop assemblies). Do you have any idea about that?
This is indeed not great. Please let me know if adding BLAST datasets solves the issue. If it does not, I will create another ticket to investigate the matter.
Closing as now daijin
performs as expected.
@asdcid , please let me know about BUSCO. If it is still not behaving properly, we will open another ticket.
Hi,
I tried to run the
daijin assemble
And then I got this error:
The configure file created by daijin configure is:
The version I used is
Mikado v2.0rc4
. Compared to the versionv1.2.4
on conda, it seems that thev2.0rc4
missed the intron_len, scoring_file and other information.Also, it seems that there are some bugs in
Mikado/daijin/tr.snakefile
, such as line 389@functools.lru_cahe(maxsize=4, typed=True)
(missing a c in cahe), line 709output: touch(os.path.join(ALIGN_DIR, "gmap", "index", NAME, "index.done") #os.path.join(ALIGN_DIR, "gmap", "index", NAME, NAME+".sachildguide1024")
, missing a ")" after "index.done)".In the
rule asm_map_trinitygg
, the variableSAMPLE_MAP[wildcards.sample]
andparams.strandedness
.Cheers, Raymond