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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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== Error == exception caught: <class 'ValueError'> #441

Closed xiongqian123456789 closed 3 years ago

xiongqian123456789 commented 4 years ago

Command line: /home/u4244/anaconda3/envs/spades/bin/spades.py -k 21,33,55,77 --careful -1 /home/u4244/data/tb/0-ref/1-mapping/bwa_R1.fastq -2 /home/u4244/data/tb/0-ref/1-mapping/bwa_R2.fastq -o /home/u4244/data/tb/0-ref/2-assembly/spades

System information: SPAdes version: 3.14.0 Python version: 3.8.1 OS: Linux-4.4.0-166-generic-x86_64-with-glibc2.10

Output dir: /home/u4244/data/tb/0-ref/2-assembly/spades Mode: read error correction and assembling Debug mode is turned OFF

Dataset parameters: Standard mode For multi-cell/isolate data we recommend to use '--isolate' option; for single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq use '--rna'. Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/home/u4244/data/tb/0-ref/1-mapping/bwa_R1.fastq'] right reads: ['/home/u4244/data/tb/0-ref/1-mapping/bwa_R2.fastq'] interlaced reads: not specified single reads: not specified merged reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed Assembly parameters: k: [21, 33, 55, 77] Repeat resolution is enabled Mismatch careful mode is turned ON MismatchCorrector will be used Coverage cutoff is turned OFF Other parameters: Dir for temp files: /home/u4244/data/tb/0-ref/2-assembly/spades/tmp Threads: 16 Memory limit (in Gb): 94

======= SPAdes pipeline started. Log can be found here: /home/u4244/data/tb/0-ref/2-assembly/spades/spades.log

max() arg is an empty sequence Traceback (most recent call last): File "/home/u4244/anaconda3/envs/spades/bin/spades.py", line 589, in main build_pipeline(pipeline, cfg, output_files, tmp_configs_dir, dataset_data, log, File "/home/u4244/anaconda3/envs/spades/bin/spades.py", line 529, in build_pipeline spades_stage.add_to_pipeline(pipeline, get_stage, cfg, output_files, tmp_configs_dir, dataset_data, log, bin_home, File "/home/u4244/anaconda3/envs/spades/share/spades/spades_pipeline/stages/spades_stage.py", line 377, in add_to_pipeline pipeline.add(SpadesStage(cfg, get_stage, "as", output_files, tmp_configs_dir, File "/home/u4244/anaconda3/envs/spades/share/spades/spades_pipeline/stages/spades_stage.py", line 286, in init generateK(self.cfg, self.log, self.dataset_data) File "/home/u4244/anaconda3/envs/spades/share/spades/spades_pipeline/stages/spades_stage.py", line 121, in generateK RL = support.get_primary_max_reads_length(dataset_data, log, ["merged reads"], File "/home/u4244/anaconda3/envs/spades/share/spades/spades_pipeline/support.py", line 620, in get_primary_max_reads_length max_reads_lenghts = [get_max_reads_length(reads_file, log, num_checked) for reads_file in File "/home/u4244/anaconda3/envs/spades/share/spades/spades_pipeline/support.py", line 620, in max_reads_lenghts = [get_max_reads_length(reads_file, log, num_checked) for reads_file in File "/home/u4244/anaconda3/envs/spades/share/spades/spades_pipeline/support.py", line 651, in get_max_reads_length max_reads_length = max( ValueError: max() arg is an empty sequence

== Error == exception caught: <class 'ValueError'>

olga24912 commented 4 years ago

Hi @xiongqian123456789

Thank you for your bug report and for using spades! Please, can you check that both files bwa_R1.fastq and bwa_R2.fastq are not empty?

asl commented 3 years ago

Please reopen if this is still an issue