m6anet
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Published
20 hours ago •
GoekeLab
GoekeLab
m6anet-inference error
Dear developers, Thank you for developing this tool. I have encountered two errors when running the inference step for two data.
The version I use is 2.0.2.
I have run the codes as follows for these two data:
find path/to/fastq/ -maxdepth 1 -name "*.fastq" | xargs cat > reads.fastq
seqtk seq -A reads.fastq > reads.fasta
nanopolish index -d /path/to/single/fast5 reads.fasta -s /path/to/sequencing_summary.txt
minimap2 -ax map-ont -t 6 hg19_UCSC_knownGene.fasta reads.fasta | samtools sort -T *.tmp -o reads.sorted.bam
samtools index reads.sorted.bam
nanopolish eventalign --reads reads.fasta --bam reads.sorted.bam --genome hg19_UCSC_knownGene.fasta --scale-events --signal-index --summary each_read_alignment_summary.txt --threads 10 > eventalign.txt
m6anet dataprep --eventalign eventalign.txt --out_dir ./dataprep --n_processes 4
m6anet inference --input_dir ./dataprep --out_dir ./prediction --n_processes 4 --num_iterations 1000
The data preparation fold has 4 files:
data.info data.json data.log eventalign.index
For the first error: Error message:
Traceback (most recent call last):
File "/home/Xichen.Zhao/.local/bin/m6anet", line 8, in <module>
sys.exit(main())
File "/home/Xichen.Zhao/.local/lib/python3.8/site-packages/m6anet/__init__.py", line 30, in main
args.func(args)
File "/home/Xichen.Zhao/.local/lib/python3.8/site-packages/m6anet/scripts/inference.py", line 86, in main
ds = NanopolishDS(input_dir[0], DEFAULT_MIN_READS, args.norm_path, mode='Inference')
File "/home/Xichen.Zhao/.local/lib/python3.8/site-packages/m6anet/utils/data_utils.py", line 100, in __init__
self.set_feature_indices()
File "/home/Xichen.Zhao/.local/lib/python3.8/site-packages/m6anet/utils/data_utils.py", line 109, in set_feature_indices
self.total_neighboring_features = self.get_total_neighboring_features()
File "/home/Xichen.Zhao/.local/lib/python3.8/site-packages/m6anet/utils/data_utils.py", line 149, in get_total_neighboring_features
kmer, _ = self._load_data(self.data_fpath, tx_id, tx_pos, start_pos, end_pos)
File "/home/Xichen.Zhao/.local/lib/python3.8/site-packages/m6anet/utils/data_utils.py", line 185, in _load_data
pos_info = json.loads(json_str)[tx_id][str(tx_pos)]
KeyError: 22
The preview of data.info:
transcript_id,transcript_position,start,end,n_reads
22,204,0,1909,20
22,221,1909,4208,21
22,249,4208,6381,20
22,357,6381,8315,21
22,648,8315,10576,20
22,699,10576,12580,20
22,1058,12580,14644,20
22,1134,14644,16964,20
22,1281,16964,19433,24
The preview of data.json:
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For the second error: Error message:
Traceback (most recent call last):
File "/home/Xichen.Zhao/.local/bin/m6anet", line 8, in <module>
sys.exit(main())
File "/home/Xichen.Zhao/.local/lib/python3.8/site-packages/m6anet/__init__.py", line 30, in main
args.func(args)
File "/home/Xichen.Zhao/.local/lib/python3.8/site-packages/m6anet/scripts/inference.py", line 86, in main
ds = NanopolishDS(input_dir[0], DEFAULT_MIN_READS, args.norm_path, mode='Inference')
File "/home/Xichen.Zhao/.local/lib/python3.8/site-packages/m6anet/utils/data_utils.py", line 100, in __init__
self.set_feature_indices()
File "/home/Xichen.Zhao/.local/lib/python3.8/site-packages/m6anet/utils/data_utils.py", line 109, in set_feature_indices
self.total_neighboring_features = self.get_total_neighboring_features()
File "/home/Xichen.Zhao/.local/lib/python3.8/site-packages/m6anet/utils/data_utils.py", line 149, in get_total_neighboring_features
kmer, _ = self._load_data(self.data_fpath, tx_id, tx_pos, start_pos, end_pos)
File "/home/Xichen.Zhao/.local/lib/python3.8/site-packages/m6anet/utils/data_utils.py", line 184, in _load_data
json_str = f.read(end_pos - start_pos)
TypeError: argument should be integer or None, not 'float'
The preview of data.info:
transcript_id,transcript_position,start,end,n_reads
74.0,382,0,2105,22
74.0,421,2105,4637,25
74.0,883,4637,6921,24
74.0,1044,6921,9612,26
74.0,1166,9612,11952,24
74.0,1223,11952,14384,24
74.0,1260,14384,17788,30
74.0,1405,17788,20300,28
74.0,1422,20300,23438,30
The preview of data.json:
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Could you please help me with these two issues? Thank you for your time, and I look forward to hearing from you.
hi @XichenZhao0223, at a glance, this seems to me that the error is caused by a mismatch of datatype between transcript_id in data.info and in data.json. I am suspecting that your transcript_id is not stored as string in data.info but is stored as string in data.json. An easy fix to this issue is to convert the transcript_id column in data.info manually to string. Alternatively, can you please send one of the data.info and data.json pair files for me to verify this? Thanks!
Dear developer,
Thank you for your patient reply. I have tried to convert the trans_id in data.info into characters in R language, but unfortunately, the error still exists. Below is the Dropbox link for the two files: https://www.dropbox.com/s/dpx6089nk3pu74c/Xichen0223.zip?dl=0 Although these are not the exact replicate data files mentioned above, it shows the same error in the inference step.
HI, @XichenZhao0223 @chrishendra93
I think I am having similar error. Is the problem solved?
Many thanks!
Andrea
Dear developer,
Thank you for your patient reply. I have tried to convert the trans_id in data.info into characters in R language, but unfortunately, the error still exists. Below is the Dropbox link for the two files: https://www.dropbox.com/s/dpx6089nk3pu74c/Xichen0223.zip?dl=0 Although these are not the exact replicate data files mentioned above, it shows the same error in the inference step.
HI, @XichenZhao0223 @chrishendra93
I think I am having similar error. Is the problem solved?
Many thanks!
Andrea
Dear developer, Thank you for your patient reply. I have tried to convert the trans_id in data.info into characters in R language, but unfortunately, the error still exists. Below is the Dropbox link for the two files: https://www.dropbox.com/s/dpx6089nk3pu74c/Xichen0223.zip?dl=0 Although these are not the exact replicate data files mentioned above, it shows the same error in the inference step.
Dear Andrea, Unfortunately, the issue has not been solved. May I ask about which version of the transcript reference file did you use in read alignment and nanopolish event alignment? I encountered this error when using UCSC transcript file (hg19_UCSC_knownGene.fasta). And the error message seemed to be the transcript id of UCSC transcripts. So I switched to the Ensemble transcript file (Homo_sapiens.GRCh38.cdna.all.fa) and the problem had been solved. Hope this information can help you with your problem.
Regards, Xichen
hi, @XichenZhao0223
thanks for quick reply. My reference is from gencode. I will switch to ESEMBEL and let you know the result.
your info is very appreciated!
Andrea
HI, @XichenZhao0223 @chrishendra93 I think I am having similar error. Is the problem solved? Many thanks! Andrea
Dear developer, Thank you for your patient reply. I have tried to convert the trans_id in data.info into characters in R language, but unfortunately, the error still exists. Below is the Dropbox link for the two files: https://www.dropbox.com/s/dpx6089nk3pu74c/Xichen0223.zip?dl=0 Although these are not the exact replicate data files mentioned above, it shows the same error in the inference step.
Dear Andrea, Unfortunately, the issue has not been solved. May I ask about which version of the transcript reference file did you use in read alignment and nanopolish event alignment? I encountered this error when using UCSC transcript file (hg19_UCSC_knownGene.fasta). And the error message seemed to be the transcript id of UCSC transcripts. So I switched to the Ensemble transcript file (Homo_sapiens.GRCh38.cdna.all.fa) and the problem had been solved. Hope this information can help you with your problem.
Regards, Xichen
Hi, @XichenZhao0223,
I got it done with ENSEMBL reference!
Thank you again for your suggestion and experience!!!!!!!
Andrea
HI, @XichenZhao0223 @chrishendra93 I think I am having similar error. Is the problem solved? Many thanks! Andrea
Dear developer, Thank you for your patient reply. I have tried to convert the trans_id in data.info into characters in R language, but unfortunately, the error still exists. Below is the Dropbox link for the two files: https://www.dropbox.com/s/dpx6089nk3pu74c/Xichen0223.zip?dl=0 Although these are not the exact replicate data files mentioned above, it shows the same error in the inference step.
Dear Andrea, Unfortunately, the issue has not been solved. May I ask about which version of the transcript reference file did you use in read alignment and nanopolish event alignment? I encountered this error when using UCSC transcript file (hg19_UCSC_knownGene.fasta). And the error message seemed to be the transcript id of UCSC transcripts. So I switched to the Ensemble transcript file (Homo_sapiens.GRCh38.cdna.all.fa) and the problem had been solved. Hope this information can help you with your problem.
Regards, Xichen
Hi, @XichenZhao0223,
I got it done with ENSEMBL reference!
Thank you again for your suggestion and experience!!!!!!!
Andrea
HI, @XichenZhao0223 @chrishendra93 I think I am having similar error. Is the problem solved? Many thanks! Andrea
Dear developer, Thank you for your patient reply. I have tried to convert the trans_id in data.info into characters in R language, but unfortunately, the error still exists. Below is the Dropbox link for the two files: https://www.dropbox.com/s/dpx6089nk3pu74c/Xichen0223.zip?dl=0 Although these are not the exact replicate data files mentioned above, it shows the same error in the inference step.
Dear Andrea, Unfortunately, the issue has not been solved. May I ask about which version of the transcript reference file did you use in read alignment and nanopolish event alignment? I encountered this error when using UCSC transcript file (hg19_UCSC_knownGene.fasta). And the error message seemed to be the transcript id of UCSC transcripts. So I switched to the Ensemble transcript file (Homo_sapiens.GRCh38.cdna.all.fa) and the problem had been solved. Hope this information can help you with your problem. Regards, Xichen
Hi Andrea,
You're welcome, and congratulations !! 😃
Regards, Xichen