Hello, I am running into an error running airrflow with

--translate

in version 4.3.1 and I wondered whether somebody here can help me. My command is:

#! usr/bin/bash
nextflow run nf-core/airrflow -r 4.3.1 \
-profile cfc \
--mode fastq \
--input samplesheet_tcr_14102025.tsv \
--library_generation_method sc_10x_genomics \
--reference_10x refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0 \
--clonal_threshold 0 \
--outdir results_tcr_14102025 \
--translate \
-resume

and the error I am getting

ERROR ~ Error executing process > 'NFCORE_AIRRFLOW:AIRRFLOW:TRANSLATE_EMBED:AMULETY_TRANSLATE (PatientX)'

Caused by:
 Process `NFCORE_AIRRFLOW:AIRRFLOW:TRANSLATE_EMBED:AMULETY_TRANSLATE (PatientX)` terminated with an error exit status (1)


Command executed:

 export IGDATA=igblast_base
 amulety translate-igblast PatientX__scqc-pass.tsv . igblast_base
  
 mv *_translated.tsv PatientX_translated.tsv
  
 cat <<-END_VERSIONS > versions.yml
 "NFCORE_AIRRFLOW:AIRRFLOW:TRANSLATE_EMBED:AMULETY_TRANSLATE":
   amulety: $( amulety --help 2>&1 | grep -o "version [0-9\.]\+" | grep -o "[0-9\.]\+" )
   igblastn: $( igblastn -version | grep -o "igblast[0-9\. ]\+" | grep -o "[0-9\. ]\+" )
 END_VERSIONS

Command exit status:
 1

Command output:
 (empty)

Command error:
 │ │          ...                          │ │
 │ │          5580 TTTGTCACAGATCTGT-1_contig_2-5 ...       │ │
 │ │          GNEYVYWYRQIHSQGPQ                   │ │
 │ │          5581 TTTGTCAGTCTAGGTT-1_contig_1-5 ...       │ │
 │ │          EDSAMYFCASKPGRAQKEDTQYFGPGT              │ │
 │ │          5582 TTTGTCAGTCTAGGTT-1_contig_2-5 ...       │ │
 │ │          IQPPTS                        │ │
 │ │          5583 TTTGTCATCTCGATGA-1_contig_1-5 ...       │ │
 │ │          EDSAMYFCASSEAQG                    │ │
 │ │          5584 TTTGTCATCTCGATGA-1_contig_2-5 ...       │ │
 │ │          WYRQDPGKGPEFLFTLYSAGEEKEKERLKATLTKKESFLHITAPKP...   │ │
 │ │                                     │ │
 │ │          [5585 rows x 3 columns]                │ │
 │ │ input_file_path = 'PatientX__scqc-pass.tsv'       │ │
 │ │    out_fasta = './PatientX__scqc-pass.fasta'     │ │
 │ │   out_igblast = './PatientX__scqc-pass_igblast.tsv'  │ │
 │ │  out_translated = './PatientX__scqc-pass_translated.tsv' │ │
 │ │    output_dir = '.'                          │ │
 │ │     overlap = []                          │ │
 │ │      pipes = <Popen: returncode: 0 args: ['igblastn',       │ │
 │ │          '-germline_db_V', 'igblast_base/dat...>        │ │
 │ │  reference_dir = 'igblast_base'                    │ │
 │ │       row = sequence_id                      │ │
 │ │          TTTGTCATCTCGATGA-1_contig_2-5             │ │
 │ │          sequence                       │ │
 │ │          ACAGAAGTGGCGCCTCTGAGAAAAGAAGGTTGGAATTATCGTAATT...   │ │
 │ │          rev_comp                       │ │
 │ │          F                           │ │
 │ │          productive                      │ │
 │ │          T                           │ │
 │ │          vj_in_frame                      │ │
 │ │          T                           │ │
 │ │          │  │  │  │  │  │  │  │  │  │  │   ...   │ │
 │ │          tissue                        │ │
 │ │          TCR                          │ │
 │ │          sex                          │ │
 │ │          NaN                          │ │
 │ │          age                          │ │
 │ │          NaN                          │ │
 │ │          biomaterial_provider                 │ │
 │ │          NaN                          │ │
 │ │          light_only_cell                    │ │
 │ │          False                         │ │
 │ │          Name: 5584, Length: 62, dtype: object         │ │
 │ │    start_time = 1760534657.7846708                  │ │
 │ │      stderr = b''                          │ │
 │ │      stdout = b''                          │ │
 │ ╰──────────────────────────────────────────────────────────────────────────╯ │
 ╰──────────────────────────────────────────────────────────────────────────────╯
 AttributeError: 'float' object has no attribute 'replace'

Work dir:
 ./work/8e/3befa8a2def5eb504844b9d690a995

Container:
 /nfsmounts/container/depot.galaxyproject.org-singularity-mulled-v2-92ebbfc09fc136b8e201cb187cd9567ba335d439-459e6ebe51fb2818cb6de807f2c5fa99599b1214-0.img

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

 -- Check '.nextflow.log' file for details

I am happy about any suggestions. Thanks a lot!

Hi @Melanie Kirch thanks for reporting. Inside the work directory: ./work/8e/3befa8a2def5eb504844b9d690a995, there should be the full error message in file called

.command.err

or

.command.out

or

.command.log

. Could you also share this one with us, as the error message here is truncated.

Hi @Gisela Gabernet thank you for your response. Yes sure, I am sending `.command.err`as well as

.command.log

attached.

.command.out

is empty. (To avoid confusion: These files are from a different run, then I posted before.) Thanks a lot for your help!

Thank you @Melanie Kirch. It seems like it doesn’t find a string in the sequence alignment column. Could you have a look inside the work directory, there should be a file called “airr_igblast.tsv” with a “sequence_alignment_aa” column. Is this file empty, or does any sequence inside have an empty value in this column? Does it also have an empty value for the “sequence” column? If you do not see this file in the work directory and you are running this on the cluster, you could resume the run with the following configuration, then the file will be copied inside the work directory:

process{
  scratch=False
}

Thank you @Gisela Gabernet. Unfortunately, I can't find the file

airr_igblast.tsv

in the work folder. As you suggested I resumed the run with scratch=false as process setting. Should I start a new run?

yes you can just resume the run that you previously started, and once it produces the same error the file should be visible in the work directory

Now I got it! The files are called $samplename__scqc-pass_igblast.tsv and both samples that failed have indeed each one empty position in the

sequence_alignment_aa

column! And yes I specified

-c <path to config>

and resuming was enough - it just took me a while to find the correct files 🙂

Could you share the row that threw this error together with the header of the $samplename__scqc-pass_igblast.tsv table? I’ll have a look whether there is a fix

Yes, sure (see attached file) - thanks a lot for your help!

Great, thank you. Yes I see it’s an unproductive sequence with a lot of stop codons. I’ll make the translation step filter these out so the error doesn’t occur

Hi @Gisela Gabernet! Thanks a lot for your help- that sounds great! Did you already manage to implement this?

This is an issue with

Amulety

rather than airrflow, we’ve fixed it in the Amulety python package, which is also part of Immcantation. We’ll try and make an Amulety release and add the fix to airrflow next week.

Nice, thanks a lot for the update and for taking care of the issue! That sounds great!