Quick start examples exit with error (-U missing) and give different numbers

[scogi]

Hi,

fantastic tool, promises to solve a lot of our problems!
I managed to install it (Ubuntu 18.04, conda installation as proposed in #36), but if I run the Quickstart examples for Nanopore data R9.4.1 and R10, i get an error message that the "-U" parameter is missing
-U is missing but required. Exiting.

I thus modified the commands to:

longread_umi nanopore_pipeline -d test_reads.fq -v 30 -o test_r941 -s 90 -e 90 -m 3500 -M 6000 -f CAAGCAGAAGACGGCATACGAGAT -F AGRGTTYGATYMTGGCTCAG -r AATGATACGGCGACCACCGAGATC -R CGACATCGAGGTGCCAAAC -c 3 -p 1 -q r941_min_high_g330 -t 1 -U r941_min_high_g360

and

longread_umi nanopore_pipeline -d ont_r10_zymo_rrna.fq -o test_r10 -v 25 -q r10_min_high_g340 -m 3500 -M 6000 -s 90 -e 90 -f CAAGCAGAAGACGGCATACGAGAT -F AGRGTTYGATYMTGGCTCAG -r AATGATACGGCGACCACCGAGATC -R CGACATCGAGGTGCCAAAC -c 2 -p 2 -t 1 -U r103_min_high_g360

which works.

However, the numbers in variants.fq and consensus_raconx3_medakax1.fa differ from what the Quick start section states

R9.4.1
variants.fq: 1 (should be 3, according to quick start section)
consensus_raconx3_medakax1.fa: 6 (should be 9)

R10
variants.fq: 12 sequences (should be 13)
consensus_raconx3_medakax1.fa 88 (should be 98)

My questions:

• Is it correctly to add -U as given above?
• If yes, what could be the reasons for the differing numbers? Or are they correct?

Thank you,
Stefan

[SorenKarst]

Hi Stefan,

Thank you for the thorough testing. I will have a look at what is going on here.

regards
Søren

[ziels]

Hey Stefan,
Would you mind sharing the output of longread_umi_version_dump.txt ? I am finding that different sub-package versions are leading to different numbers of outputted consensus sequences.

Thanks,
Ryan

[ziels]

Also, @scogi , do you mind letting me know how many sequences you have in test_r941/raconx3_medakax1/consensus_raconx3_medakax1.fa? (same for R10 set too).

Thanks,
Ryan

[scogi]

Hi Ryan,
sorry, took me a while to get back to this project. Thanks for your reply.

test_r941/raconx3_medakax1/consensus_raconx3_medakax1.fa: 6 sequences
test_r10 does not have this folder but only raconx2_medakax1 and ... medakax2
consensus_raconx3_medakax1.fa: 90 sequences
consensus_raconx3_medakax2.fa: 90 sequences

i have not been able to locate the file longread_umi_version_dump.txt. Where should it be saved?

Thanks,
Stefan

[scogi]

@ziels
Ok, i located longread_umi_version_dump.txt. The problem is that shortly after I had posted this issue, I had to delete and reinstall anaconda completely. So, unfortunately, I do not have the file of the original installation anymore.
I reinstalled longread_umi now, Updated values are:

test_r941/raconx3_medakax1/consensus_raconx3_medakax1.fa: 6 sequences
test_r941/variants/variants.fa: 1 sequence

test_r10/raconx2_medakax1/consensus_raconx3_medakax1.fa: 90 sequences
test_r10/raconx2_medakax2/consensus_raconx3_medakax2.fa: 90 sequences
test_r10/variants/variants.fa: 12 sequences

Content of longread_umi_version_dump.txt:
Script start: 2020-10-22-13:23:06
Software Version:
longread_umi -
seqtk - Version: 1.3-r106
Parallel - GNU parallel 20191122
Usearch - usearch v11.0.667_i86linux32
Racon - v1.4.10
Minimap2 - 2.17-r941
medaka - 1.0.1
medaka model -
Gawk - GNU Awk 4.1.3, API: 1.1
Cutadapt - 2.7
Porechop - 0.2.4 + modify porechop.py
Filtlong - Filtlong v0.2.0
BWA - Version: 0.7.17-r1188
Samtools - Version: 1.9 (using htslib 1.9)
Bcftools - bcftools 1.9