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Exit code -6 #68
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Hi Maria, Could you send me the log file, and the sdbg_info file tmp/k77/77.sdbg_info to me? |
Hello Dinghua, I rerun the analysis from scratch (only raising the numbers of threads) and MEGAHIT v1.0.3-29-g707d683 --- [Thu Jan 21 09:22:42 2016] Extracting iterative edges from k = 27 to 37--- [Thu Jan 21 09:38:04 2016] Building graph for k = 37 --- I am attaching the log file and the temp/k37/37.sdbg_info of this current I really appreciate your help! Best, On 21 January 2016 at 01:22, Dinghua Li notifications@github.com wrote:
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Hi Maria, Could you send the log & sdbg_info file to my email voutcn at gmail dot com? |
just experienced the same problem on multiple runs with separate input files. hope you can help? maybe just a memory issue, but its got 480gb to play with? MEGAHIT v1.0.2 |
I dropped the ball on this because I was too busy the last week. I got the error when I was running it in the institution's cluster, where I have 1T of RAM and 1T of disk space. Dinghua suggested me to try the dataset in "https://github.com/voutcn/megahit/wiki/An-example-of-real-assembly?" but meanwhile I installed megahit on an Ubuntu virtual box in the lab's desktop (64G RAM; 100G of disk space) and it worked fine with the same datasets that were creating the error in the cluster. |
@mpachiad I guess it is a platform related problem, related to hardward atomic operations. @rjsorr The error you came across is different from that of @mpachiad . You are putting long sequences into MEGAHIT, which makes the graph construction halt. I will fix this issue in one week. |
cheers @voutcn. great if you can come with a solution. Actually this is pacbio reads assembled using canu, so 1mb+ contigs. This best would be if I could submit pacbio raw (filtered) reads with the -r option, but Megahit does not seem to deal with this so well, hence the assembly of pacbio before assembling it with the PE reads. regards |
@voutcn Hi, I just started compiling and testing my first sample using MegaHit. However, something seems wrong when I start the program. Here's what's in the log file. MEGAHIT v1.1.0-pre |
@wanghanchenwhc Could you please show your command to run Megahit here? It seems that you are using incorrect paired-end files. |
@rjsorr Sorry I am a bit busy this week, I will push a new commit ASAP |
@voutcn I'm running them on UNIX server: /global/software/megahit/megahit-1.1.0-pre/megahit --presets meta -1 $R1file -2 $R2file -o $megahit_dir --out-prefix $megahit_out; I'm suspecting that could it be problematic when I try to run FASTQ-converted FASTA files instead of using the original FASTQ files? |
I recently encountered this eror code as well. I am not using any long reads and Megahit used to work perfectly before on this exact server. I am using MEGAHIT v1.0.1. I gave it 390 Gb of RAM of which it used only a little fraction (peak RAM usage monitored by our SGE queuing system).
I restarted the assembly (using "--continue") in the vague hope that this error just does not happen again but do not have much hope in that. |
@jvollme -6 was returned by an assertion failure, the log file should have recorded that failure. So even though this thread is talking about "-6", the problems here are not the same. Would you open a new issue and paste the full contents of log file there? |
I encountered this eror code as well. I am using MEGAHIT v1.2.1-beta. hope you can help? The log file is following: |
Hello,
I am using MEGAHIT v1.0.3-29-g707d683 and I got an error. Here is the part of the log that will be useful. Let me know if you need the entire file. (I got the error one and then I executed the same command with the --continue so it skipped the assembly of the previous k)
--- [Wed Jan 20 08:52:07 2016] Start assembly. Number of CPU threads 12 ---
--- [Wed Jan 20 08:52:07 2016] Available memory: 1084374925312, used: 975937432780
--- [Wed Jan 20 08:52:07 2016] k list: 27,37,47,57,67,77,87 ---
--- [Wed Jan 20 08:52:07 2016] Assembling contigs from SdBG for k = 77 ---
cmd: /home/vedgcomb/megahit/megahit_asm_core assemble -s /home/vedgcomb/MEGAhit_test/20160119_Megahit_large_D2b237B/tmp/k77/77 -o /home/vedgcomb/MEGAhit_test/20160119_Megahit_large_D2b237B/intermediate_contigs/k77 -t 12 --min_standalone 260 --prune_level 2 --merge_len 20 --merge_similar 0.98 --low_local_ratio 0.2 --min_depth 2 --max_tip_len -1 --careful_bubble
[assembler.cpp : 148] Loading succinct de Bruijn graph: /home/vedgcomb/MEGAhit_test/20160119_Megahit_large_D2b237B/tmp/k77/77 megahit_asm_core: succinct_dbg.cpp:672: void SuccinctDBG::LoadFromMultiFile(const char*, bool): Assertion `tip_label_offset == num_tip_nodes_ * sdbg_reader.words_per_tip_label()' failed.
Error occurs when assembling contigs for k = 77, please refer to /home/vedgcomb/MEGAhit_test/20160119_Megahit_large_D2b237B/log for detail
[Exit code -6]
I really appreciate your insights.
Best,
Maria
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