Meryl troubleshooting

[Lorenzo]

Hello,

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:	toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6
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

core

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

cpuinfo

Processor Count 8

meminfo

Total System Memory	30.6 GB
Total System Swap	90.7 MB

[jennaj]

Hi @Lorenzo

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

@Lorenzo

Input data is PacBio HiFi ccs.bam file

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.

@jennaj

if you are ever not sure what datatype(s) a tool accepts as input, any tool not just those that accept reads, try this:

1. Create a new empty history
2. Load up the tool form
3. Review the input datatypes listed in the tool form’s input area
4. Note: A tool could have more than one input area and this works for all user-supplied inputs from the history.

Example

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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.