Fatal: Either a valid pairs file or sample names must be provided

[kelly-sovacool]

Error message from user

Hello,

I am trying to use the XAVIER pipeline to run WES on fastq files, but the pipeline keeps erroring when performing bamCheck and bam2fastq. I do not supply any .bam inputs, but it seems like these should be an output of the bwa_mem process (although this process says completed in the snamkemake log, but with missing output). I can’t figure out any parameters that would have to do with this, so is there something I should check with my fastq files to make sure they are compatible.

The error message I receive from bam_check is:

Config file config.json is extended by additional config specified via the command line.
NameError in file /data/LunaLab/acc_line/cellCUACC327_WES_20250521_LH00407_0137_A22YW73LT3/xavierOutput/workflow/Snakefile, line 148:

      Fatal: Either a valid pairs file or sample names must be provided.
            Pairs file path provided: None
            Sample names provided: set()
            
  File "/data/LunaLab/acc_line/cellCUACC327_WES_20250521_LH00407_0137_A22YW73LT3/xavierOutput/workflow/Snakefile", line 312, in <module>
  File "/data/LunaLab/acc_line/cellCUACC327_WES_20250521_LH00407_0137_A22YW73LT3/xavierOutput/workflow/Snakefile", line 148, in read_pairsfile

So it seems it is not is recognizing the paired reads files. However, I received outputs from fastq_screen and kraken, which confirm the human origin of the samples, so I believe the files were successfully read, but maybe are just not recognized as pairs?

I ran XAVIER with the following commands (I previously also tried using the absolute path for the input and output, but that did not have any impact)

xavier run --input *.R?*.fastq.gz  --output xavierOutputNew --genome hg38 --mode slurm --runmode init


xavier run --input *.R?*.fastq.gz  --output xavierOutputNew --genome hg38 --mode slurm --runmode run

And the contents of my directory are:

20250521_LH00407_0137_A22YW73LT3_L7_Kiseljak_demux.csv      xavierOutput
CUACC327_cells_WES_05072025_S86_L007_001.R1.fastq.gz        xavierOutputNew
CUACC327_cells_WES_05072025_S86_L007_001.R2.fastq.gz

Additionally, I’ve attached the log folder in case that would be useful. Please let me know if you have any suggestions or if I can provide any more information.

Thank you,
Cameron Wells

cameron-wells_logfiles.zip

[kelly-sovacool]

Cameron's config file: config.json

[kelly-sovacool]

samples is blank because name_symlinks is blank

[kelly-sovacool]

Also happens with the test data. The symlinks exist at input_files/fastq/ after the dryrun, but by the end of the full run they are gone.

./bin/xavier run \--input ./tests/data/*R?*.fastq.gz  \       
--output /data/$USER/xavier_hg38 \
--genome hg38 \
--mode slurm \
--runmode run

logfiles/slurmfiles/'9547835.9550758.bam_check.samples=WES_NC_T_1_sub.err'

Config file config.json is extended by additional config specified via the command line.
NameError in file /data/sovacoolkl/xavier_hg38/workflow/Snakefile, line 148:

	Fatal: Either a valid pairs file or sample names must be provided.
            Pairs file path provided: None
            Sample names provided: set()
            
  File "/data/sovacoolkl/xavier_hg38/workflow/Snakefile", line 313, in <module>
  File "/data/sovacoolkl/xavier_hg38/workflow/Snakefile", line 148, in read_pairsfile

logfiles/slurmfiles/'9547835.9550758.bam_check.samples=WES_NC_T_1_sub.out'

FQS_FOUND: WES_NC_T_1_sub.R1.fastq.gz, WES_NC_T_1_sub.R2.fastq.gz, WES_NC_N_1_sub.R2.fastq.gz, WES_NC_N_1_sub.R1.fastq.gz
NAME_SYMLINKS: 
SAMPLES: 

[kelly-sovacool]

Temporary workaround: use the bam files in input_files/bam as input instead of the fastq files.