TypeError: 'bool' object is not iterable

[bioluria]

I tested make _lastz _chains with the mouse genome mm10 and the human genome hg19, running the script as follows: python3 /home/luria/make_lastz_chains-2.0.8/make_chains.py hg19 mm10 /home/luria/hg19_chrom.fa /home/luria/mm10_chrom.fa --project_dir /home/luria/mm10_vs_hg19

But I got the following error： fatal: Not a git repository (or any parent up to mount point /work) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).

Make Lastz Chains

Version 2.0.8 Commit: unknown Branch: unknown

• found run_lastz.py at /home/luria/make_lastz_chains-2.0.8/standalone_scripts/run_lastz.py
• found run_lastz_intermediate_layer.py at /home/luria/make_lastz_chains-2.0.8/standalone_scripts/run_lastz_intermediate_layer.py
• found chain_gap_filler.py at /home/luria/make_lastz_chains-2.0.8/standalone_scripts/chain_gap_filler.py
• found faToTwoBit at /home/luria/software/UCSCTOOLS/faToTwoBit
• found twoBitToFa at /home/luria/software/UCSCTOOLS/twoBitToFa
• found pslSortAcc at /home/luria/make_lastz_chains-2.0.8/HL_kent_binaries/pslSortAcc
• found axtChain at /home/luria/software/UCSCTOOLS/axtChain
• found axtToPsl at /home/luria/software/UCSCTOOLS/axtToPsl
• found chainAntiRepeat at /home/luria/software/UCSCTOOLS/chainAntiRepeat
• found chainMergeSort at /home/luria/software/UCSCTOOLS/chainMergeSort
• found chainCleaner at /home/luria/make_lastz_chains-2.0.8/HL_kent_binaries/chainCleaner
• found chainSort at /home/luria/software/UCSCTOOLS/chainSort
• found chainScore at /home/luria/software/UCSCTOOLS/chainScore
• found chainNet at /home/luria/software/UCSCTOOLS/chainNet
• found chainFilter at /home/luria/software/UCSCTOOLS/chainFilter
• found lastz at /home/luria/software/lastz/lastz-1.04.22/src/lastz
• found nextflow at /home/luria/software/nextflow/nextflow All necessary executables found. Making chains for /home/luria/hg19_chrom.fa and /home/luria/mm10_chrom.fa files, saving results to /home/luria/mm10_vs_hg19 Pipeline started at 2024-06-14 10:42:39.138852
• Setting up genome sequences for target genomeID: hg19 input sequence file: /home/luria/hg19_chrom.fa is 2bit: False planned genome dir location: /home/luria/mm10_vs_hg19/target.2bit Initial fasta file /home/luria/hg19_chrom.fa saved to /home/luria/mm10_vs_hg19/target.2bit For hg19 (target) sequence file: /home/luria/mm10_vs_hg19/target.2bit; chrom sizes saved to: /home/luria/mm10_vs_hg19/target.chrom.sizes
• Setting up genome sequences for query genomeID: mm10 input sequence file: /home/luria/mm10_chrom.fa is 2bit: False planned genome dir location: /home/luria/mm10_vs_hg19/query.2bit Initial fasta file /home/luria/mm10_chrom.fa saved to /home/luria/mm10_vs_hg19/query.2bit For mm10 (query) sequence file: /home/luria/mm10_vs_hg19/query.2bit; chrom sizes saved to: /home/luria/mm10_vs_hg19/query.chrom.sizes

Partition Step

Partitioning for target

Saving partitions and creating 26 buckets for lastz output In particular, 23 partitions for bigger chromosomes And 3 buckets for smaller scaffolds Saving target partitions to: /home/luria/mm10_vs_hg19/target_partitions.txt

Partitioning for query

An error occurred while executing partition: 'bool' object is not iterable Traceback (most recent call last): File "/home/luria/make_lastz_chains-2.0.8/modules/step_manager.py", line 70, in execute_steps step_result = step_to_function[step](params, project_paths, step_executables) File "/home/luria/make_lastz_chains-2.0.8/modules/pipeline_steps.py", line 43, in partition_step executables) File "/home/luria/make_lastz_chains-2.0.8/steps_implementations/partition.py", line 80, in do_partition_for_genome bulk_num_to_chroms = create_buckets_for_little_scaffolds(little_scaffolds_to_bulk, chunk_size) File "/home/luria/make_lastz_chains-2.0.8/steps_implementations/partition.py", line 41, in create_buckets_for_little_scaffolds for chrom, size in little_scaffolds_to_bulk or chrom_count_in_bulk >= Constants.MAX_CHROM_IN_BULK: TypeError: 'bool' object is not iterable

[jurin0811]

Hello, I have the same problem, did you solve it? Maybe using this should also want to use TOGA to do gene conversion, do you have any good software recommendation？Thank you ！

[MichaelHiller]

Hi,

this is a weird error, which should in principle occur everytime. @kirilenkobm Do you have an idea how to fix that?

@jurin0811 Did you run the quick test sample successfully? If so, there is a quirk in your data. Otherwise, if the same bool error occurs, something is not right with your system.

Thx