ERROR: Process (DIAMOND?) failed

[LiZhihua1982]

lizhihua@lizhihua-T640:/mnt/FF/LZLJ/fastp_out/GJ$ singlem pipe --forward /mnt/FF/LZLJ/fastp_out/GJ/GJ01_R1.fastq.gz --reverse /mnt/FF/LZLJ/fastp_out/GJ/GJ01_R2.fastq.gz --otu-table /mnt/HH/lzlj_binchicken_out/coassemble/pipe/GJ01_read.otu_table.tsv --metapackage /media/lizhihua/software/singlem_database/S5.4.0.GTDB_r226.metapackage_20250331.smpkg.zb
2026/01/19 09:01:15 PM INFO: SingleM v0.18.1
2026/01/19 09:01:15 PM INFO: Acquiring SingleM metapackage from Zenodo backpack directory specified ..
2026/01/19 09:01:15 PM INFO: Retrieval successful. Location of backpack is: /media/lizhihua/software/singlem_database/S5.4.0.GTDB_r226.metapackage_20250331.smpkg.zb
2026/01/19 09:01:15 PM INFO: Loaded 59 SingleM packages
2026/01/19 09:01:15 PM INFO: Using as input 1 different pairs of sequence files e.g. /mnt/FF/LZLJ/fastp_out/GJ/GJ01_R1.fastq.gz & /mnt/FF/LZLJ/fastp_out/GJ/GJ01_R2.fastq.gz
2026/01/19 09:01:15 PM INFO: Filtering sequence files through DIAMOND blastx
2026/01/19 09:03:27 PM ERROR: Process (DIAMOND?) failed
Traceback (most recent call last):
File "/mnt/HH/binchicken/97436d6135154b96586228e621489c3c_/bin/singlem", line 709, in
singlem.pipe.SearchPipe().run(
File "/mnt/HH/binchicken/97436d6135154b96586228e621489c3c_/lib/python3.12/site-packages/singlem/pipe.py", line 69, in run
otu_table_object = self.run_to_otu_table(**kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/HH/binchicken/97436d6135154b96586228e621489c3c_/lib/python3.12/site-packages/singlem/pipe.py", line 380, in run_to_otu_table
raise e
File "/mnt/HH/binchicken/97436d6135154b96586228e621489c3c_/lib/python3.12/site-packages/singlem/pipe.py", line 373, in run_to_otu_table
self._num_threads, self.working_directory).run_diamond(
^^^^^^^^^^^^
File "/mnt/HH/binchicken/97436d6135154b96586228e621489c3c/lib/python3.12/site-packages/singlem/diamond_spkg_searcher.py", line 34, in run_diamond
fwds = self.prefilter(dmnd, forward_read_files, False, performance_parameters)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/HH/binchicken/97436d6135154b96586228e621489c3c/lib/python3.12/site-packages/singlem/diamond_spkg_searcher.py", line 95, in prefilter
qseqid_sseqid = extern.run(cmd)
^^^^^^^^^^^^^^^
File "/mnt/HH/binchicken/97436d6135154b96586228e621489c3c/lib/python3.12/site-packages/extern/init.py", line 41, in run
raise ExternCalledProcessError(process, command)
extern.ExternCalledProcessError: Command diamond blastx --outfmt 6 qseqid full_qseq sseqid --max-target-seqs 1 --evalue 0.01 --block-size 0.5 --target-indexed -c1 --min-orf 24 --query-gencode 4 --threads 1 --query /mnt/FF/LZLJ/fastp_out/GJ/GJ01_R1.fastq.gz --db /media/lizhihua/software/singlem_database/S5.4.0.GTDB_r226.metapackage_20250331.smpkg.zb/payload_directory/prefilter.fna.dmnd | tee >(sed 's/^/>/; s/\t/\n/; s/\t.*//' > /tmp/tmp0726_706/prefilter_forward/GJ01_R1.fna) | awk '{print $1,$3}' returned non-zero exit status 134.
STDERR was: b"diamond: malloc.c:2401: sysmalloc: Assertion `(old_top == initial_top (av) && old_size == 0) || ((unsigned long) (old_size) >= MINSIZE && prev_inuse (old_top) && ((unsigned long) old_end & (pagesize - 1)) == 0)' failed.\nbash: line 1: 30554 Aborted (core dumped) diamond blastx --outfmt 6 qseqid full_qseq sseqid --max-target-seqs 1 --evalue 0.01 --block-size 0.5 --target-indexed -c1 --min-orf 24 --query-gencode 4 --threads 1 --query /mnt/FF/LZLJ/fastp_out/GJ/GJ01_R1.fastq.gz --db /media/lizhihua/software/singlem_database/S5.4.0.GTDB_r226.metapackage_20250331.smpkg.zb/payload_directory/prefilter.fna.dmnd\n 30555 Done

[LiZhihua1982]

Is this a diamond version problem? Thank you

[wwood]

I believe this is a diamond version issue. I'm working on fixing the issue in bioconda. In the meantime you could try modifying the PATH so that it instead uses the newest diamond version (the singlem bioconda recipe currently pins 2.1.15 since I've had issues with diamond updates breaking singlem in the past - this is what I'm fixing in the above referenced commits).

[wwood]

this should hpefully be fixed now in bioconda, so I'm closing. Let me know if it still fails after the update. Thanks for the report, makes SingleM better.

[LiZhihua1982]

Hi, Professor, My diamond version is 2.1.19. You mean I change it to 2.1.15 or which version is better? Thanks Best regards Li Zhihua 获取Outlook for Android<https://aka.ms/AAb9ysg>

…

________________________________ From: Ben J Woodcroft ***@***.***> Sent: Wednesday, January 21, 2026 2:00:03 PM To: wwood/singlem ***@***.***> Cc: Li Zhihua ***@***.***>; Author ***@***.***> Subject: Re: [wwood/singlem] ERROR: Process (DIAMOND?) failed (Issue #282) [https://avatars.githubusercontent.com/u/15348?s=20&v=4]wwood left a comment (wwood/singlem#282)<#282 (comment)> this should hpefully be fixed now in bioconda, so I'm closing. Let me know if it still fails after the update. Thanks for the report, makes SingleM better. ― Reply to this email directly, view it on GitHub<#282 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AJI2BJK2MSSLOO7RBWI635D4H4IWHAVCNFSM6AAAAACSFCB34OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTONZWGM2DGNBUG4>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[wwood]

Oh, maybe not fixed by the update then. 2.1.19 is best I think.

Reading the error more closely it seems a malloc error, is it running out of ram?

[LiZhihua1982]

(binchicken) lizhihua@lizhihua-T640:/media/lizhihua/software/singlem_database$ diamond version
diamond version 2.1.10
(binchicken) lizhihua@lizhihua-T640:/media/lizhihua/software/singlem_database$ conda activate /mnt/HH/binchicken/97436d6135154b96586228e621489c3c_
(/mnt/HH/binchicken/97436d6135154b96586228e621489c3c_) lizhihua@lizhihua-T640:/media/lizhihua/software/singlem_database$ diamond version
diamond version 2.1.19

The version of diamond in binchicken is 2.1.10 while The version of diamond in singleM is 2.1.19, the result is still errors. My computer is 256G RAM.

[wwood]

Hi,

This is a bit strange. Can you please try running it with diamond outside of singlem i.e.

diamond --version

diamond blastx --outfmt 6 qseqid full_qseq sseqid --max-target-seqs 1 --evalue 0.01 --block-size 0.5 --target-indexed -c1 --min-orf 24 --query-gencode 4 --threads 1 --query /mnt/FF/LZLJ/fastp_out/GJ/GJ01_R1.fastq.gz --db /media/lizhihua/software/singlem_database/S5.4.0.GTDB_r226.metapackage_20250331.smpkg.zb/payload_directory/prefilter.fna.dmnd >diamond.out1.tsv

[LiZhihua1982]

(binchicken) lizhihua@lizhihua-T640:/mnt/FF/LZLJ/fastp_out/GJ$ diamond blastx --outfmt 6 qseqid full_qseq sseqid --max-target-seqs 1 --evalue 0.01 --block-size 0.5 --target-indexed -c1 --min-orf 24 --query-gencode 4 --threads 30 --query /mnt/FF/LZLJ/fastp_out/GJ/GJ01_R1.fastq.gz --db /media/lizhihua/software/singlem_database/S5.4.0.GTDB_r226.metapackage_20250331.smpkg.zb/payload_directory/prefilter.fna.dmnd >diamond.out1.tsv
It is OK. This command does not report error and obtained the results

[wwood]

Oh I meant the singlem environment.

But can I ask, why are you using such an old singlem version? Why not 0.20.3?