Versions Megahit after 1.1.4 do not contain megahit_toolkit?

[dutchscientist]

Megahit is one of the dependencies for Shovill (Torsten Seemann, https://github.com/tseemann/shovill/), and with the new version of Megahit there is no "megahit_toolkit" anymore. This is a dependency that Shovill looks for when installed via Conda, and hence stops running.

I can find version 1.1.1 on Conda, but that only runs in Python 2.7 to 3.6, while Conda3 is now already at Python 3.7.

Is this by design? Issue at Shovill can be seen at:
tseemann/shovill#112

Would be great if this can be resolved, thanks :)

[voutcn]

It is removed after 1.1.4. Some useful sub-commands (including contig2fastg, the one used by Shovill) have been moved to megahit_core. To solve this, I will create an alias of megahit_core as megahit_toolkit in the next release (in one or two days).

[dutchscientist]

Thank you, much appreciated! :)

[tseemann]

Thank you @voutcn and @dutchscientist for fixing this and maintaining backward compatibility!

[JHarrisonEcoEvo]

It seems like there is still some problems with legacy megahit_toolkit commands not working.

I just tried the following command to convert contigs to fastg:

megahit_core contig2fastq 99 ../intermediate_contigs/k99.contigs.fa > k99.contigs.fastg

I also tried the previous accepted command of:

megahit_toolkit contig2fastq 99 ../intermediate_contigs/k99.contigs.fa > k99.contigs.fastg

Both provide the usage help to stdout but do not throw any errors or write anything to the output file. There is nothing germane in the usage prompt ( I copied it below for reference). My input contigs look like this (just first two contigs):

k99_0 flag=1 multi=3.0000 len=526
ACCCTGCTTTCCGAAGCGGGCGACACGGCCGCCGCGATCTCGGCCTTCTCGTCGATCGGCAAGGACCGCTCCGTTCCGGAAGCGATCCGCGATGCGGCCAAGCTGCGCGCCGGCTGGCTGCTGGTCGATACCGGCACCTATGAGCAGGTTTCCGCCGAGGTCGAGGAACTGTCGAATGACGGCAATCCGTTCCGCTTCTCCGCCCGCGAAATACTCGGACTGTCGGCCTATCGGCTGAAGGATTACACCCGCGCCCAGCAATGGTTCGAGGCGATTGCCAACGACCCGGAAGCCCCGCGCAACGTGCTCAACCGCGCCCAGATCATGCTCGAGGTGATGACCGCCGACGGCAATGTCGCCGAAAGCGCGGCCGGCCGATCAAGCTGTTCGACACCGCCGGCATGCGCCGCAAGGCGCGGGTGGTCGAAAAGCTGGAAAAGCTCTCGGTTTCCGACGCTCTGCGTGCGATCCGGTTTGCCGAATGCGTGGTGATCGTCTTCGATGCGACGATCCCGTTTGAAAAACA
k99_4539 flag=1 multi=3.0000 len=798
CAGCGCCTCGCCATTGTCTCCCACCAGGTCGGGGGCGAGCGCGCGAATGTCATAGGTCAGATCGACATCCTCGGAGAACCGCCGGATGACGCCATAGGCCTTCGACAGCGAAGTGCCGCCCTTGAATACCAGATGTTCGCCGAGCAGCGAGCCGTAGAGCGTGGCCAGCGCCCACACCACCCACGCATCCTTCTCCAGCAGGTGCGCGGGTCGGCCCGAGCGGTCGGCGGCAACGCTCAATGCTTCAAGGCGATCCTCGGCCGGAAGGAGGAGGAAGGGGTCAGCCATGCGCGACCTTACCCACGCTGCGCGCGAGCCAGGTCGGAAGCTGAGGCGCCGCCGCCACCAGCTCGCTGAAAGCGGCAGGCGGAAGCTTGCGCTTCAGGGTCTGGAGCGCCGACTCAGCCCTCTCCGGTCCGAGCCAAGCAAGCGCCCGCACCGCCTGTCCCGCCGGCCGATGCGCCATGGCAAGTTGCCAGCGCGGAGCGTGACGAAGCTCGACGGTCTGCTTGCCTAGGCTCATCTTCCGGGTGCGTCCCGAGGTCAGATAGACCGACCGGACCGGCACCTGCGTCGTAAGGCCGAGGCTGTTGGCGGCCGCCGCACCGCTTGAGACGATGACCTCGCCGCGCTGGGCTGCAAGCGCCTCAACCGCCTGCTCCACCGATGGCGCCCGGGTGCCGAACCGGCTCGTGACCGGCAGCAGATAAACACCTCGCCCGGCCCGAAGCAGTTGGCCCCGCTCGGCCAGACGCGACAAGGCCTGGTCCACCGCGGCGCGATTGCCAAGGTGGAGCA

What is printed when I run the above referenced calls to megahit_core or toolkit

Usage: megahit_core <sub_program> [sub options]
sub-programs:
assemble assemble from SdBG
local local asssembly
iterate extract iterative edges
buildlib build read library
count kmer counting
read2sdbg build sdbg from reads
seq2sdbg build sdbg from megahit contigs + edges
contig2fastg convert MEGAHIT's k*.contigs.fa to fastg format
readstat calculate read stats (# of reads, bases, longest, shortest, average)
filterbylen filter contigs by length
checkcpu check whether the run-time CPU supports POPCNT and BMI2
checkpopcnt check whether the run-time CPU supports POPCNT
checkbmi2 check whether the run-time CPU supports BMI2
dumpversion dump version
kmax the largest k value supported

[dutchscientist]

I don't think this should be added here? Please open a new issue.