ValueError: invalid literal for int() with base 10: '.'

[YanCheer]

When I run toga.py, it showed up such error info:

Is there anything wrong with my bed file or the python version?

Thanks a lot!

[kirilenkobm]

Hello,

seems like the bed file is corrupted.

Pls try something like:

with open("YOUR_BED_FILE", "r") as f:
    line_number = 1
    for line in f:
        fields = line.split("\t")
        if len(fields) >= 6:
            field_6 = fields[5]
            try:
                int(field_6)
            except ValueError:
                print(f"Line {line_number}: {line.strip()}")
        line_number += 1

to identify which line exactly is corrupted

[YanCheer]

Thank you very much for the reply at yesterday.
After generating the new bed and chain files, I got a new error that I cannot settle down today.

At the STEP 3: Merge step 2 output, the running log showed that the pipeline seemed to successfully read but failed to load
and combine all the results of transcript annotation, so then generated the empty merge_chains_output output results as follows:

STEP 3: Merge step 2 output

Reading /projects/yanchen/HiFi_tmp/01.HiFi_Assemble/Assemblies_hifiasm/02.Primary_Assembly_Annotation/TOGA/03.toga_outputs_Run2/TOGA_GRCg7b_Achr1/temp/toga_filt_ref_annot.bed
merge_chains_output: got data for 44858 transcripts
merge_chains_output: Loading the results...
merge_chains_output: There are 0 result files to combine
merge_chains_output: got 0 keys in chain_genes_data
merge_chains_output: got 0 keys in chain_raw_data
merge_chains_output: There were 0 transcript lines and 0 chain lines
merge_chains_output: chain_genes_data dict reverted, there are 0 keys now
merge_chains_output: Combining the data...
merge_chains_output: got combined dict with 0 keys
merge_chains_output: Writing output to /projects/yanchen/02.Primary_Assembly_Annotation/TOGA/03.toga_outputs_Run2/temp/chain_results_df.tsv
merge_chains_output: total runtime: 0:00:40.594500

Therefore, at the following step, it reported an ERROR info:

STEP 4: Classify chains using gradient boosting model

Classifying chains
classify_chains: loaded dataframe of size 0
classify_chains: total number of transcripts: 0
classify_chains: 0 rows with spanning chains
classify_chains: filtered dataset contains 0 records
classify_chains: omputing additional features...
classify_chains: WARNING! The final df for classification is empty
classify_chains: df for single-exon model contains 0 records
classify_chains: df for multi-exon model contains 0 records
classify_chains: loading models at /projects/yanchen/softwares/TOGA-1.1.7/models/se_model.dat (SE) and /projects/yanchen/softwares/TOGA-1.1.7/models/me_model.dat (ME)
classify_chains: applying models to SE and ME datasets...
classify_chains: applying -1.0 score to the spanning chains
classify_chains: applying -2.0 score to the processed pseudogene alignments
classify_chains: number of processed pseudogene alignments: 0
classify_chains: arranging the final output
classify_chains: classification result stats:

• orthologs: 0
• paralogs: 0
• spanning chains: 0
• processed pseudogenes: 0

classify_chains: using 0.5 as a threshold to separate orthologs from paralogs
classify_chains: combining results for 0 individual transcripts
classify_chains: saving the classification to /projects/yanchen/02.Primary_Assembly_Annotation/TOGA/03.toga_outputs_Run2/temp/trans_to_chain_classes.tsv
classify_chains: found no classifiable chains for 0 transcripts
classify_chains: saving these transcripts to: /projects/yanchen/02.Primary_Assembly_Annotation/TOGA/03.toga_outputs_Run2/temp/rejected/classify_chains_rejected.txt
Chain results file /projects/yanchen/02.Primary_Assembly_Annotation/TOGA/03.toga_outputs_Run2/temp/chain_results_df.tsv is empty! Abort.

From the last error info, it showed me the point was at the chain results file chain_results_df.tsv produced by the pipeline.
Do you have any idea where the error is hidden behind?

Thank you very much for provide such a tiny help for me!!!!!