Meryl troubleshooting


I am experiencing a similar issue.

I am on Galaxy Australia. Input data is PacBio HiFi ccs.bam file

I am following the VGP genome assembly workflow (here), but when I run meryl to generate the histogram dataset it returns an empty file.

Dataset Information

Number 21
Name Meryl on data 5: read-db histogram
Created Wednesday Mar 15th 23:40:04 2023 UTC
Filesize -
Dbkey ?
Format tabular
File contents contents
History Content API ID a6e389a98c2d167856efc515cf917a62
History API ID b23256ed83e3b051
UUID 0c8512a2-0a71-4be3-8fcb-84d3690d4819
Full Path /mnt/user-data-7/012/980/dataset_12980484.dat
Originally Created From a File Named read-db.hist

Tool Parameters

Input Parameter Value
Operation type selector histogram-kmers
Input meryldb 5 : Merged meryl 1

Job Outputs

Tool Outputs Dataset
Meryl on : read-db histogram 21 : Meryl on data 5: read-db histogram

Job Information

Galaxy Tool ID:
Command Line export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && mkdir -p ./temp_db/ && tar -zxf /mnt/pulsar/files/staging/5846890/inputs/dataset_12980423.dat -C ./temp_db/ && mv ./temp_db/* tmp.meryl && meryl histogram tmp.meryl > read-db.hist
Tool Standard Output empty
Tool Standard Error Found 1 command tree.
Tool Exit Code: 0
Job API ID: 6fa87f23fa942a65

Dataset Storage

This dataset is stored in the default configured Galaxy object store .

Inheritance Chain

Meryl on data 5: read-db histogram

Job Metrics


Cores Allocated 2
Memory Allocated (MB) 7782
Job Start Time 2023-03-15 23:40:06
Job End Time 2023-03-15 23:40:08
Job Runtime (Wall Clock) 2 seconds


Processor Count 8


Total System Memory 30.6 GB
Total System Swap 90.7 MB

Hi @Lorenzo

Your job at the server used a tool version that includes the prior fix. Maybe something else is going wrong.

The tool is expecting reads as an input, not a BAM. Even if the BAM includes only-reads (not a mapping result), those reads should be extracted into fastq/fasta formatted datasets for this tool to understand the input. VGP assembly pipeline

Tools filter for appropriate inputs based on the datatype. Dragging and dropping inputs can avoid that check but it is not recommended, and expect errors if you try.

If this doesn’t address the problem, would you please generate and post back a shared history link Sharing your History? We can review in more detail that way. Or, you can post back more details just about the input 5 : Merged meryl 1 since that seems to be at least part of the problem.