Inconsistent insert lengths in sample

Bob Harris — Thu, 03 Oct 2019 16:50:07 -0000

The sample in v1.5 appears to limit insert lengths to [1000,3000] for bowtie but to [1300,2300] for mateAn.

Is this is mistake, or is there a reason why I should use different limits for the same sequencing run?

For example, in my data I estimate most of the inserts are in [100,1100] with a mode around 500. Is there some reason I should tighten up that interval for mateAn?

FYI, the MANUAL doesn't describe all the columns in the .metassem file

Michael Schatz — Thu, 25 Jul 2019 19:26:50 -0000

Hi Bob,

Thanks for the note. Columns 1-8 are the only ones that are needed to assemble the final contigs using meta2fasta.pl. The additional columns are debugging codes and coordinates of the original assemblies encoding the status of the CE statistic over the breakpoints of the alignments. Since they are not used in the downstream analysis, you can safely ignore them.

Good luck

Mike

Metassembler error in the very last step

Carlos Farkas — Mon, 28 May 2018 16:59:00 -0000

Hi All

I'm trying to merge contigs from a mini-metagenome built with SPAdes and Metaspades asemblers using the step_by_step script. CE statisticts looks fine and metassemble MergePipeline worked outputting a fasta file. When the pipeline tried to retrieve sequences in the last step of Metassembler, the following error appear:

---------- Loading Fastas ----------
---Loading A.fa
---Loading B.fa

---------- Retrieving sequences ----------

Error:
B.A_0 300901 447 0 NODE_3_length_300922_cov_62.4173 300901 447 + X X X X R.NODE_3_length_300922_cov_62.4173 212 447 Q.NODE_195_length_36249_cov_101.886 36249 36014
could not be retrieved

The test worked fine but I do not know what causes this error.

**Note: For simplicity I replaced the files "A" and "B" provided in the test with the contigs obtained from the assemblies.

Thanks in advance

Carlos

Resume a run after fixing error?

Katherine Dougan — Mon, 05 Feb 2018 20:11:10 -0000

Thanks for the feedback! That's kind of what I gathered (but I was hoping there was an easier way) so I have already started running the individual steps.

Resume a run after fixing error?

Katherine Dougan — Mon, 05 Feb 2018 15:17:44 -0000

Hello,

I tried looking through the manual to figure out if it was possible to resume a run rather than starting all the way at the beginning. It seems to have ~1 week run time on the species I am working on and I would rather not re-start after fixing an error that resulted from an incorrect path to a file. Is it possible to resume after correcting the error in the config file? Thanks!

Katherine

prenuc error

HoYong LEE — Sat, 09 Dec 2017 06:07:24 -0000

Thanks for your help. I have another problems.
I tried to use long read fasta with metassembler results.
It works well till nucmer.

when running nucmer, error happen like

prenuc: tigrinc.cc:337: int ReadString(FILE, char&, long int&, char, int): Assertion 'Len > 0 && Line [Len - 1] == '\n'' failed.
Aborted (core dumped)
ERROR: prenuc returned non-zero
ERROR: Could not parse delta file, MergePipeline/B.A.delta
error no: 400
ERROR: Could not parse delta file, MergePipeline/B.A.1delta
error no: 402

I searched and guessed.

Is it related with fasta file format? if does, how can i change file format?

my fasta file (Long lead have some info like)

1 edges=1591107,7141363,1069246 left=2162353 right=2077639 ver=1.7 style=3
ATATGTTT......
...
3 edges=3323521 left=2162354 right=2061244 ver=1.7 style=3
....

Thanks.

Error textlen larger than maximal textlen

Katherine Dougan — Wed, 11 Oct 2017 15:58:25 -0000

Ah, thank you! I fixed that. I made it farther but the process once again failed and I got this error:

4: FINISHING DATA
ERROR: cannot open /scratch/kdoug023/genome_reads/metassembler_output//frac65/CEstat/frac65.ce/frac65.mateAn.

I went back to see if I could find this file but couldn't find it. I also have an error within that folder, the ID.ce folder in CEstat:
Error:
Your sam file contains no headers and you didn't provide any file with contig sizes.

I think I'm doing something wrong in my configuration file in the mateAn section. My config file is below:

Metassemble configuration file suggested template

[global]

Mate-pair mapping parameters:

bowtie2_threads=10
bowtie2_read1=/scratch/kdoug023/genome_reads/trenchii_forward_seqtk_trimmed.fastq
bowtie2_read2=/scratch/kdoug023/genome_reads/trenchii_reverse_seqtk_trimmed.fastq
bowtie2_maxins=1100
bowtie2_minins=300

CE-stat computation parameters:

mateAn_A=300
mateAn_B=800

Or:

mateAn_s=<float>

mateAn_m=<float>

Whole Genome Alignment parametesr:

nucmer_l=50
nucmer_c=300

nucmer=/home/kdoug023/programs/MUMmer3.23/nucmer
delta-filter=/home/kdoug023/programs/MUMmer3.23/delta-filter
show-coords=/home/kdoug023/programs/MUMmer3.23/show-coords
mateAn=/home/kdoug023/programs/Metassembler/bin/mateAn
asseMerge=/home/kdoug023/programs/Metassembler/bin/asseMerge
meta2fasta=/home/kdoug023/programs/Metassembler/bin/meta2fasta
gage=/home/kdoug023/programs/Metassembler/bin/gage

[1]

Metassemble configuration file suggested template

[global]

Mate-pair mapping parameters:

CE-stat computation parameters:

mateAn_A=300
mateAn_B=800

Or:

mateAn_s=<float>

mateAn_m=<float>

Whole Genome Alignment parametesr:

nucmer_l=50
nucmer_c=300

[1]

mateAn_m=<float>

Whole Genome Alignment parametesr:

nucmer_l=50
nucmer_c=300

[1]

fasta=/scratch/kdoug023/genome_reads/Supernova_Trenchii_600m_pseudohap.fasta
ID=600m

mateAn_file=

[2]

fasta=/scratch/kdoug023/genome_reads/Supernova_Trenchii_frac065_pseudohap.fasta
ID=frac65

mateAn_file=

Error textlen larger than maximal textlen

Katherine Dougan — Tue, 10 Oct 2017 18:56:55 -0000

Hello everyone,

I am attempting to merge two draft genome assemblies of a dinoflagellate species. Upon running metassembler, I am receiving this following error:

/home/kdoug023/programs/MUMmer3.23/mummer: suffix tree construction failed: textlen=920760240 larger than maximal textlen=536870908
ERROR: mummer and/or mgaps returned non-zero
ERROR: Could not parse delta file, /scratch/kdoug023/genome_reads/metassembler_output//Metassembly/Qfrac65.600m/Qfrac65.600m.delta
error no: 400
ERROR: Could not parse delta file, /scratch/kdoug023/genome_reads/metassembler_output//Metassembly/Qfrac65.600m/Qfrac65.600m.1delta
error no: 402
ERROR: cannot open /scratch/kdoug023/genome_reads/metassembler_output//frac65/CEstat/frac65.ce/frac65.mateAn.

Does anyone know how to fix this?

Cheers,
Katherine

config file - I want to merge two assemblies

Kenny Tsang — Wed, 04 Oct 2017 23:37:14 -0000

Dear all,

I have one illumina TruSeq long read assembly and three MiSeq 2x75 short reads assemblies. I want to merge the long read assembly to each of the short reads assemblies so that at the end I will have three total assmblies:

1) Long read scaffold + Velvet scaffolds
2) Long read scaffold + AbySS scaffolds
3) Long read scaffold + SOAP scaffolds

However, I do not know how to denife the parameters in the config file, it looks like this:

[global]

mateAn_A=200
mateAn_B=300
bowtie2_read1=/lustre/projects/holfordlab/ktsang/TSSLR-BDA11_LongRead.fastq
bowtie2_read2=/lustre/projects/holfordlab/ktsang/oenopla-reads1.fastq
bowtie2_maxins=500
bowtie2_minins=50
bowtie2_threads=1
meta2fasta_keepUnaligned=0
meta2fasta_sizeUnaligned=500 500
nucmer_l=50
nucmer_c=300

nucmer=/home/ktsang/.conda/envs/MyVirtualEnv/bin/nucmer
delta-filter=/home/ktsang/.conda/envs/MyVirtualEnv/bin/delta-filter
show-coords=/home/ktsang/.conda/envs/MyVirtualEnv/bin/show-coords
bowtie2=/home/ktsang/.conda/envs/MyVirtualEnv/bin/bowtie2
bowtie2-build=/home/ktsang/.conda/envs/MyVirtualEnv/bin/bowtie2-build
samtools=/home/ktsang/.conda/envs/MyVirtualEnv/bin/samtools

[1]
fasta=/lustre/projects/holfordlab/ktsang/oenopla_VOscaffolds011216.fasta
ID=LongRead

[2]
fasta=/lustre/projects/holfordlab/ktsang/scaffolds/SOAPdenovo.final.scaffolds.fasta
ID=SOAP

I have read the manual but I still do not understand. What number I should put at mateAn_A, mateAn_B, bowtie2_maxins, bowtie2_minins, meta2fasta?

I do not know the insert size of the short reads, can someone help me with deciding he numbers in bold?

Thank you!

Kenny

running time

HoYong LEE — Wed, 30 Aug 2017 04:59:00 -0000

Hi. I'm Lee.
I'm now running Metassembler using Pig-tailed rhesus data(154G).
it works well(bowtie2, mateAn, etc) but have problem in MUMmer : [TIME].
I searched and changed MUMmer because my reference sequence is larger than is supported by default.
After changing, It makes another file (B.A.ntref - 3G , B.A.mgaps - 140G).
I think it is used when making B.A.delta. but it take too much time ( 17 days now and still working - 43G).
Is there any method to reduce time like parallel processing?

And I want to know how much time it take when using human sequence data.

Thanks you.

Recent posts to General Discussion

Inconsistent insert lengths in sample

FYI, the MANUAL doesn't describe all the columns in the .metassem file

Metassembler error in the very last step

Resume a run after fixing error?

Resume a run after fixing error?

prenuc error

Error textlen larger than maximal textlen

Metassemble configuration file suggested template

Mate-pair mapping parameters:

CE-stat computation parameters:

Or:

mateAn_s=<float>

mateAn_m=<float>

Whole Genome Alignment parametesr:

Metassemble configuration file suggested template

Mate-pair mapping parameters:

CE-stat computation parameters:

Or:

mateAn_s=<float>

mateAn_m=<float>

Whole Genome Alignment parametesr:

mateAn_m=<float>

Whole Genome Alignment parametesr:

mateAn_file=

mateAn_file=

Error textlen larger than maximal textlen

config file - I want to merge two assemblies

running time