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
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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.
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:
Could you make just a sanity check of the file ID/CEstat/BWTaln/ID.mtp.err
just to make sure the problem is not in the Bowtie2 alignment step. If
thats ok I am guessing the sequence names in your assemblies are causing
troubles, could you simplify them? avoid using white spaces and characters
such as ":". You can parse the sam files directly, but if the alignments
are not so costly I would recommend just rerunning them with the new
sequence names in the fasta files of your assemblies.
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
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
Hi Katherine,
You should try compiling mummer in the 64-bit version as explained here:
https://sourceforge.net/p/mummer/mailman/message/22416185/
On Tue, Oct 10, 2017 at 1:56 PM, Katherine Dougan kdougan91@users.sf.net
wrote:
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:
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]
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]
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=
Could you make just a sanity check of the file ID/CEstat/BWTaln/ID.mtp.err
just to make sure the problem is not in the Bowtie2 alignment step. If
thats ok I am guessing the sequence names in your assemblies are causing
troubles, could you simplify them? avoid using white spaces and characters
such as ":". You can parse the sam files directly, but if the alignments
are not so costly I would recommend just rerunning them with the new
sequence names in the fasta files of your assemblies.
On Wed, Oct 11, 2017 at 10:58 AM, Katherine Dougan kdougan91@users.sf.net
wrote: