HISAT2 Error message

Hello -

I keep getting an error reading as the following.

Error executing tool with id ‘toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy0’: ‘HistoryDatasetAssociation’ object has no attribute ‘forward’
The server could not complete this request. Please verify your parameter settings, retry submission and contact the Galaxy Team if this error persists. A transcript of the submitted data is shown below.
“history_id”: “23a225085c9279cd”,
“tool_id”: “toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy0”,
“tool_version”: “2.2.1+galaxy0”,
“inputs”: {
“reference_genome|source”: “indexed”,
“reference_genome|index”: “hg38canon”,
“library|type”: “paired_interleaved”,
“library|input_1”: {
“values”: [
“id”: “f9cad7b01a472135251a6d4487ba53a9”,
“hid”: 19,
“name”: “FASTQ interlacer singles from data 2 and data 1”,
“tags”: ,
“src”: “hda”,
“keep”: false
“batch”: false
“library|rna_strandness”: “”,
“library|paired_options|paired_options_selector”: “defaults”,
“sum|new_summary”: “false”,
“sum|summary_file”: true,
“adv|input_options|input_options_selector”: “defaults”,
“adv|alignment_options|alignment_options_selector”: “defaults”,
“adv|scoring_options|scoring_options_selector”: “defaults”,
“adv|spliced_options|spliced_options_selector”: “defaults”,
“adv|reporting_options|reporting_options_selector”: “defaults”,
“adv|output_options|output_options_selector”: “advanced”,
“adv|output_options|unaligned_file”: true,
“adv|output_options|aligned_file”: “false”,
“adv|sam_options|sam_options_selector”: “defaults”,
“adv|other_options|other_options_selector”: “defaults”,
“__job_resource|__job_resource__select”: “no”

Can you please help me? I’m not quite sure what the issue is here and I’m still new to this line of analysis. Thanks!

Hello @jmn97

We replied to your email directly. This was the advice last Friday:

  1. HISAT2 tends to work best with non-interleaved fastq inputs
  2. When you rerun, use distinct forward and reverse read datasets
  3. Run QA/QC on the read data before mapping if you have not already (FastQC then quality filtering/trimming tools if needed).