Open luanxiao opened 5 years ago
ursky
commented
5 years ago Interesting. I have never seen this error from metaBAT... Could you open an issue on their page to see if they can provide some insight? The metaWRAP wrapper appears to be working correctly.
luanxiao
commented
5 years ago Thankyou for kind reply it. I have searched the problem they met about the “segmentation fault”, many of them due to the early version of metawrap and due to the samtools of server, but never of the issues occurred in the newest version 1.2.1 of metawrap. In fact, metabat and maxbin are working fine before we reinstall the server's linux system, except for concoct's openblas problem. So I suspect if there's some kind of access permission such as memory is missing. However, Our administrators also don't know how to solve it. The only tools we can ues is maxbin now. Really looking forward to the new version to see ifcan solve the problems we encountered before. Thanks again!
ursky
commented
5 years ago The openblas problem has been solved by me and the concoct developer previously. Have a look at https://github.com/BinPro/CONCOCT/issues/232.
luanxiao
commented
5 years ago Yes, concoct work normally. Thank for kind help!
RolandWirth
commented
4 years ago Hi all! I have the same problem like "luanxiao". Metawrap don't want to make done the binning process with metabat because of segmantation error. This problem occured after reinstallation of our server. Is there any solution for this? Thank you!
zzjl20
commented
3 years ago Hi dear friend. I got same mistake as luanxiao. But mine is metabat2 stop working.
The weird thing is I use same enviroument run concoct, maxbin, just replace by --concoct --maxbin, they successed.
According to the workflow chart, the metaBAT2 need depth.txt and .fasta as input. I checked both of them, no problem. I also checked BinPro/CONCOCT#232., not a help.
Any sugguestion is welcome.
command:
nohup metawrap binning -o /NGS/ACHQ/Binning/Initial/metabat2 -t 32 -a /NGS/ACHQ/Assemble/final_assembly.fasta --metaba2 /NGS/ACHQ/Read_QC/final_pure_reads_*.fastq &result:
[bam_sort_core] merging from 32 files and 32 in-memory blocks...
########################################################################################################################
##### RUNNING METABAT2 #####
########################################################################################################################
------------------------------------------------------------------------------------------------------------------------
----- making contig depth file... -----
------------------------------------------------------------------------------------------------------------------------
Output depth matrix to /NGS/ACHQ/Binning/work_files/metabat_depth.txt
Output matrix to /NGS/ACHQ/Binning/work_files/metabat_depth.txt
Opening 1 bams
Consolidating headers
Processing bam files
Thread 0 finished: ACHQ.bam with 90827001 reads and 26380778 readsWellMapped
Creating depth matrix file: /NGS/ACHQ/Binning/work_files/metabat_depth.txt
Closing most bam files
Closing last bam file
Finished
------------------------------------------------------------------------------------------------------------------------
----- Starting binning with metaBAT2... -----
------------------------------------------------------------------------------------------------------------------------
MetaBAT 2 (v2.12.1) using minContig 1500, minCV 1.0, minCVSum 1.0, maxP 95%, minS 60, and maxEdges 200.
/NGS/soft/metaWRAP/bin/metawrap-modules/binning.sh: line 296: 4655 Segmentation fault metabat2 -i ${out}/work_files/assembly.fa -a ${out}/work_files/metabat_depth.txt -o ${out}/metabat2_bins/bin -m $metabat_len -t $threads --unbinned
************************************************************************************************************************
***** Something went wrong with running MetaBAT2. Exiting *****
************************************************************************************************************************
real 90m58.218s
user 556m41.946s
sys 1m41.809s
famiji
commented
1 year ago i met the same question, if you have any way to solve it, please let me know
cberta11
commented
9 months ago Hello, if you were trying to run this on WSL and getting a sigfault from MetaBat2 both in metaWRAP and stand-alone, I think I might have a solution worth trying. WSL does not include zsyscall, a type of legacy system call memory (I am not a computer scientist. I study viruses so forgive me if this is explained poorly). You can check if this is true for your VM by running
$cat /proc/self/maps
You are looking for an address with a frankly excessive amount of "f"s and [vsyscall].
MetaBat2 calls on this memory, and this was causing a SIGSEGV error for me (according to GDB). I fixed this by editing the .wslconfig file (path C/users/<
"# Sets additional kernel parameters, in this case enabling older Linux base images such as Centos 6 kernelCommandLine = vsyscall=emulate"
This fixed the segfault issue for me in both metaWRAP and stand alone MetaBat2. Hope this is helpful, Joe
hello, handsome friend, When I run the binning module with “metawrap binning -o INITIAL_BINNING -t 24 -a ASSEMBLY/final_assembly.fasta --maxbin2 --metabat2 --run-checkm reads/*.fastq”,segmentation fault appeared. I try everything include re-install conda envs or check samtools, however it does not work. There was no problem with the previous days, but this happens after we reinstalling the debian system recently, but running maxbin is fine. I asked the server administrator, but they don't know how to fix it. So I hope to get some suggestions from you, The metawrap version is MetaWRAP v=1.2.1 and i think is the latest version. really thank you very much!
Here is the error list，