BUSCO fails with exit error 1, cannot parse null string

[masalgar]

Description of the bug

I'm trying to run the pipeline, but BUSCO always fails. It seems to manage to run successfully on some bins and I can check the statistics inside the job's folder, but at some point it throws an error, and the job fails. I've been trying to troubleshoot this to no avail, could you perhaps point me in the right direction? My parms and custom resources are as follows.

Custom resources (this is just to avoid errors with CATPACK and to give metaspades enough resources to finish on the first attempt):

process {
    resourceLimits = [
    	cpus: 48,
    	memory: 799.GB
  ]
    withName: METASPADES {
        cpus	= { params.spades_fix_cpus != -1 ? params.spades_fix_cpus : (20 * task.attempt) }
        memory	= { 128.GB * (2 ** (task.attempt - 1)) }
    }
    withName: 'NFCORE_MAG:MAG:CATPACK:CATPACK_BINS' {
        cpus	= {12 * task.attempt}
        time 	= {24.h * task.attempt}
    }
    withName: 'NFCORE_MAG:MAG:CATPACK:CATPACK_SUMMARISE_BINS' {
        ext.when = false
    }
}
params {
    skip_cat_summarise = true
}

Params json:

{
    "input": "\/home\/masalgar\/DeiC-KU-L59\/users\/masalgar\/CF_metagenome\/mag_samples.csv",
    "outdir": "\/home\/masalgar\/DeiC-KU-L59\/users\/masalgar\/CF_metagenome\/mag\/",
    "multiqc_title": "CF_Metagenome mag assembly",
    "skip_clipping": true,
    "skip_shortread_qc": true,
    "cat_db": "\/home\/masalgar\/DeiC-KU-L59\/databases\/CAT\/nr\/",
    "run_checkm2": true,
    "checkm2_db": "\/home\/masalgar\/DeiC-KU-L59\/databases\/CheckM2\/CheckM2_database\/uniref100.KO.1.dmnd",
    "gtdb_db": "\/home\/masalgar\/DeiC-KU-L59\/databases\/GTDB\/gtdbtk_data.tar.gz",
    "skip_prokka": true,
    "exclude_unbins_from_postbinning": true,
    "run_busco": true,
    "busco_clean": true,
    "busco_db": "\/home\/masalgar\/DeiC-KU-L59\/databases\/BUSCO\/",
    "refine_bins_dastool": true,
    "gtdbtk_pplacer_useram": true,
    "postbinning_input": "refined_bins_only",
    "run_gunc": true,
    "gunc_db": "\/home\/masalgar\/DeiC-KU-L59\/databases\/GUNC\/gunc_db_progenomes2.1.dmnd",
    "generate_bigmag_file": true
}

Command used and terminal output

nextflow run nf-core/mag -r 5.4.0 -profile apptainer -resume \
-name CF_m_mag_trimmed-and-dedup_final5 \
-c /home/masalgar/DeiC-KU-L59/users/masalgar/CF_metagenome/mag_custom_resources.config \
-work-dir /home/masalgar/DeiC-KU-L59/users/masalgar/tmp \
-params-file /home/masalgar/DeiC-KU-L59/users/masalgar/CF_metagenome/mag_CF_metagenome_parms.json

Relevant files

I've attached nextflow.json and the log files of one of the failed of one of the failed BUSCO jobs.

.nextflow.log

.command.log

.command.err.txt

.command.out.txt

The error from the .err file is as follows:

Exception in thread "main" java.lang.NumberFormatException: Cannot parse null string
	at java.base/java.lang.Integer.parseInt(Integer.java:550)
	at java.base/java.lang.Integer.<init>(Integer.java:1065)
	at phylolab.taxonamic.PPlacerJSONMerger.relabelJson(PPlacerJSONMerger.java:172)
	at phylolab.taxonamic.PPlacerJSONMerger.main(PPlacerJSONMerger.java:288)

Traceback (most recent call last):
  File "/opt/conda/bin/run_sepp.py", line 26, in <module>
    ExhaustiveAlgorithm().run()
  File "/opt/conda/lib/python3.12/site-packages/sepp/algorithm.py", line 205, in run
    self.merge_results()
  File "/opt/conda/lib/python3.12/site-packages/sepp/exhaustive.py", line 292, in merge_results
    mergeJsonJob.run()
  File "/opt/conda/lib/python3.12/site-packages/sepp/jobs.py", line 150, in run
    raise JobError("\n".join([
sepp.scheduler.JobError: The following execution failed:
java -jar /opt/conda/bin/seppJsonMerger.jar - - /faststorage/project/DeiC-KU-L59/users/masalgar/tmp/1a/8ab5b582aba99b1387baa123069741/CF_metagenome_dedup-auto-busco/MEGAHIT-MaxBin2Refined-CF_metagenome_dedup.003.fa/auto_lineage/run_bacteria_odb12/placement_files/output_placement.json
json locations: [/faststorage/project/DeiC-KU-L59/users/masalgar/tmp/1a/8ab5b582aba99b1387baa123069741/CF_metagenome_dedup-auto-busco/MEGAHIT-MaxBin2Refined-CF_metagenome_dedup.003.fa/auto_lineage/run_bacteria_odb12/sepp_tmp_files/output._tenenrn/root/P_0/pplacer.extended.0.38dx0iyf.jplace, /faststorage/project/DeiC-KU-L59/users/masalgar/tmp/1a/8ab5b582aba99b1387baa123069741/CF_metagenome_dedup-auto-busco/MEGAHIT-MaxBin2Refined-CF_metagenome_dedup.003.fa/auto_lineage/run_bacteria_odb12/sepp_tmp_files/output._tenenrn/root/P_0/pplacer.extended.1.ec1om_7a.jplace, /faststorage/project/DeiC-KU-L59/users/masalgar/tmp/1a/8ab5b582aba99b1387baa123069741/CF_metagenome_dedup-auto-busco/MEGAHIT-MaxBin2Refined-CF_metagenome_dedup.003.fa/auto_lineage/run_bacteria_odb12/sepp_tmp_files/output._tenenrn/root/P_0/pplacer.extended.2.x_nnddst.jplace, /faststorage/project/DeiC-KU-L59/users/masalgar/tmp/1a/8ab5b582aba99b1387baa123069741/CF_metagenome_dedup-auto-busco/MEGAHIT-MaxBin2Refined-CF_metagenome_dedup.003.fa/auto_lineage/run_bacteria_odb12/sepp_tmp_files/output._tenenrn/root/P_1/pplacer.extended.0.i0uwb1ad.jplace, /faststorage/project/DeiC-KU-L59/users/masalgar/tmp/1a/8ab5b582aba99b1387baa123069741/CF_metagenome_dedup-auto-busco/MEGAHIT-MaxBin2Refined-CF_metagenome_dedup.003.fa/auto_lineage/run_bacteria_odb12/sepp_tmp_files/output._tenenrn/root/P_1/pplacer.extended.1.jmtuj2t6.jplace, /faststorage/project/DeiC-KU-L59/users/masalgar/tmp/1a/8ab5b582aba99b1387baa123069741/CF_metagenome_dedup-auto-busco/MEGAHIT-MaxBin2Refined-CF_metagenome_dedup.003.fa/auto_lineage/run_bacteria_odb12/sepp_tmp_files/output._tenenrn/root/P_1/pplacer.extended.2.xx22nr8m.jplace, /faststorage/project/DeiC-KU-L59/users/masalgar/tmp/1a/8ab5b582aba99b1387baa123069741/CF_metagenome_dedup-auto-busco/MEGAHIT-MaxBin2Refined-CF_metagenome_dedup.003.fa/auto_lineage/run_bacteria_odb12/sepp_tmp_files/output._tenenrn/root/P_2/pplacer.extended.0.69nlt327.jplace, /faststorage/project/DeiC-KU-L59/users/masalgar/tmp/1a/8ab5b582aba99b1387baa123069741/CF_metagenome_dedup-auto-busco/MEGAHIT-MaxBin2Refined-CF_metagenome_dedup.003.fa/auto_lineage/run_bacteria_odb12/sepp_tmp_files/output._tenenrn/root/P_2/pplacer.extended.1.zxe6bwxa.jplace, /faststorage/project/DeiC-KU-L59/users/masalgar/tmp/1a/8ab5b582aba99b1387baa123069741/CF_metagenome_dedup-auto-busco/MEGAHIT-MaxBin2Refined-CF_metagenome_dedup.003.fa/auto_lineage/run_bacteria_odb12/sepp_tmp_files/output._tenenrn/root/P_4/pplacer.extended.0.bsqyufq8.jplace, /faststorage/project/DeiC-KU-L59/users/masalgar/tmp/1a/8ab5b582aba99b1387baa123069741/CF_metagenome_dedup-auto-busco/MEGAHIT-MaxBin2Refined-CF_metagenome_dedup.003.fa/auto_lineage/run_bacteria_odb12/sepp_tmp_files/output._tenenrn/root/P_7/pplacer.extended.0.nhkmd5t2.jplace, /faststorage/project/DeiC-KU-L59/users/masalgar/tmp/1a/8ab5b582aba99b1387baa123069741/CF_metagenome_dedup-auto-busco/MEGAHIT-MaxBin2Refined-CF_metagenome_dedup.003.fa/auto_lineage/run_bacteria_odb12/sepp_tmp_files/output._tenenrn/root/P_7/pplacer.extended.1._ymc4c_0.jplace, /faststorage/project/DeiC-KU-L59/users/masalgar/tmp/1a/8ab5b582aba99b1387baa123069741/CF_metagenome_dedup-auto-busco/MEGAHIT-MaxBin2Refined-CF_metagenome_dedup.003.fa/auto_lineage/run_bacteria_odb12/sepp_tmp_files/output._tenenrn/root/P_7/pplacer.extended.2.q7g73_u9.jplace, /faststorage/project/DeiC-KU-L59/users/masalgar/tmp/1a/8ab5b582aba99b1387baa123069741/CF_metagenome_dedup-auto-busco/MEGAHIT-MaxBin2Refined-CF_metagenome_dedup.003.fa/auto_lineage/run_bacteria_odb12/sepp_tmp_files/output._tenenrn/root/P_8/pplacer.extended.0.og_13lua.jplace, /faststorage/project/DeiC-KU-L59/users/masalgar/tmp/1a/8ab5b582aba99b1387baa123069741/CF_metagenome_dedup-auto-busco/MEGAHIT-MaxBin2Refined-CF_metagenome_dedup.003.fa/auto_lineage/run_bacteria_odb12/sepp_tmp_files/output._tenenrn/root/P_8/pplacer.extended.1.87wbxge5.jplace, /faststorage/project/DeiC-KU-L59/users/masalgar/tmp/1a/8ab5b582aba99b1387baa123069741/CF_metagenome_dedup-auto-busco/MEGAHIT-MaxBin2Refined-CF_metagenome_dedup.003.fa/auto_lineage/run_bacteria_odb12/sepp_tmp_files/output._tenenrn/root/P_8/pplacer.extended.2.onn18c8q.jplace, /faststorage/project/DeiC-KU-L59/users/masalgar/tmp/1a/8ab5b582aba99b1387baa123069741/CF_metagenome_dedup-auto-busco/MEGAHIT-MaxBin2Refined-CF_metagenome_dedup.003.fa/auto_lineage/run_bacteria_odb12/sepp_tmp_files/output._tenenrn/root/P_12/pplacer.extended.0.1p2kflh0.jplace, /faststorage/project/DeiC-KU-L59/users/masalgar/tmp/1a/8ab5b582aba99b1387baa123069741/CF_metagenome_dedup-auto-busco/MEGAHIT-MaxBin2Refined-CF_metagenome_dedup.003.fa/auto_lineage/run_bacteria_odb12/sepp_tmp_files/output._tenenrn/root/P_14/pplacer.extended.0.f2l4_sot.jplace, /faststorage/project/DeiC-KU-L59/users/masalgar/tmp/1a/8ab5b582aba99b1387baa123069741/CF_metagenome_dedup-auto-busco/MEGAHIT-MaxBin2Refined-CF_metagenome_dedup.003.fa/auto_lineage/run_bacteria_odb12/sepp_tmp_files/output._tenenrn/root/P_14/pplacer.extended.1.ubgw_ugq.jplace]
Exception in thread "main" java.lang.NumberFormatException: Cannot parse null string
	at java.base/java.lang.Integer.parseInt(Integer.java:550)
	at java.base/java.lang.Integer.<init>(Integer.java:1065)
	at phylolab.taxonamic.PPlacerJSONMerger.relabelJson(PPlacerJSONMerger.java:172)
	at phylolab.taxonamic.PPlacerJSONMerger.main(PPlacerJSONMerger.java:288)

System information

No response

[dialvarezs]

Hi @masalgar!

This issue seems to be a BUSCO specific issue... tbh I'm not sure what could be happening there, but, for the meantime, you could try these things:

1. Update your BUSCO local db on /home/masalgar/DeiC-KU-L59/databases/BUSCO/
2. Try running BUSCO with 1 CPU, to discard issues related to parallelism + network fs
3. Try running BUSCO independently, i.e. copy on the failing fasta files, and run BUSCO manually on another directory (you can install BUSCO with conda for that matter before trying to use the singularity container).

[dialvarezs]

Hi @masalgar
I’m going to close this issue for now due to inactivity.

Based on the information so far, it doesn’t seem to be an issue with mag itself. If you’re still experiencing the problem or have additional details to share, feel free to reopen the issue anytime.