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GoekeLab / m6anet

Detection of m6A from direct RNA-Seq data
https://m6anet.readthedocs.io/
MIT License
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m6anet-inference error #121

Open XichenZhao0223 opened 1 year ago

XichenZhao0223 commented 1 year ago

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:

{"22":{"204":{"GGAACCT":[[0.0073,9.829,116.3,0.00697,5.198,89.8,0.0035468749999999997,1.5630625,83.9,53.0],[0.005723235294117647,7.622029411764706,125.7,0.00531,4.123,95.1,0.00598,2.611,84.7,52.0],[0.014031408450704226,10.374661971830985,115.2,0.00564,1.425,88.2,0.006990952380952381,1.4848571428571429,83.8,49.0],[0.00266,8.427,126.9,0.010174230769230769,2.445653846153846,92.9,0.004182571428571429,1.4531142857142856,88.5,54.0],[0.00498,9.755,117.3,0.011040508474576272,3.035415254237288,97.4,0.01062,1.668,88.8,48.0],[0.0030266666666666667,8.472000000000001,114.8,0.013952815533980584,1.996368932038835,89.8,0.0083,2.014,87.5,44.0],[0.00465,12.101,115.2,0.00664,5.141,95.4,0.004088354430379746,1.8987215189873416,85.3,43.0],[0.00598,9.709,112.5,0.00664,2.568,91.3,0.004866206896551724,2.4143793103448274,83.8,61.0],[0.00996,10.354000000000001,121.3,0.004101176470588236,2.594705882352941,92.8,0.00232,1.709,86.9,51.0],[0.011241194029850746,7.123149253731343,116.9,0.0033529999999999996,3.70455,94.2,0.00282125,2.015,86.8,47.0],[0.0031327777777777777,9.215222222222222,115.0,0.00232,2.505,90.8,0.016325753424657537,2.7550000000000003,83.4,45.0],[0.01595206896551724,10.680103448275862,118.1,0.00432,8.327,100.1,0.007726315789473684,1.389,88.1,46.0],[0.0083,6.615999999999999,130.9,0.00398,3.1010000000000004,99.2,0.0025013333333333333,1.5821333333333334,87.7,60.0],[0.00564,3.923,127.6,0.00531,7.509,93.9,0.010365000000000001,1.5091666666666668,86.6,42.0],[0.005001999999999999,5.788333333333332,122.2,0.00398,3.336,93.2,0.0093,3.498,86.9,50.0],[0.00232,6.05,130.2,0.005605757575757576,3.56169696969697,94.1,0.00863,2.21,83.1,57.0],[0.00398,7.541,105.9,0.00398,2.959,92.0,0.00598,1.18,89.4,41.0],[0.01162,11.753,110.6,0.008012051282051283,2.636,94.3,0.00697,1.759,89.2,55.0],[0.00498,9.864,108.0,0.0156,3.479,90.2,0.00432,2.084,87.8,56.0],[0.01129,9.61,121.0,0.00465,3.064,87.6,0.00531,1.305,89.2,58.0]]}}}
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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.

chrishendra93 commented 1 year ago

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!

XichenZhao0223 commented 1 year ago

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.

AndreaYCT commented 7 months ago

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.

XichenZhao0223 commented 7 months ago

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

AndreaYCT commented 7 months ago

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

AndreaYCT commented 7 months ago

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

XichenZhao0223 commented 7 months ago

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