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GoekeLab / xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing
https://xpore.readthedocs.io/
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Empty diffmod.table file, only header generated when running xpore diffmod after preprocessing my runs #209

Closed nickst85 closed 7 months ago

nickst85 commented 8 months ago

Hi, I followed your guide and I successfully preprocessed my eventalign files of my two conditions. I have one repeat per condition. Then I run the command xpore diffmod --config $CONFIGFILE/my_config.yml --n_processes 32

the config file was:

data: Patient: rep1: /scratch/xPore/data/patient-rep1/dataprep CONTROL: rep1: /scratch/xPore/data/CONTROL-rep1/dataprep

out: ./out_condition1_FdR

method: prefiltering: method: t-test threshold: 0.1

The diffmod.log starts with --- DIFFMOD --- has 91800 lines like the following ENST00000000442.11|ENSG00000173153.17|OTTHUMG00000150641.9|OTTHUMT00000319303.3|ESRRA-201|ESRRA|2274|protein_coding| --- SUCCESSFULLY FINISHED ---

Can you understand what's going on?

Thanks,

N

yuukiiwa commented 8 months ago

Hi @nickst85,

The first column of your eventalign.txt file has to be just the ENSTxxxxx. You will have to modify the eventalign.txt from currently:

ENST00000000442.11|ENSG00000173153.17|OTTHUMG00000150641.9|OTTHUMT00000319303.3|ESRRA-201|ESRRA|2274|protein_coding|

to the following:

ENST00000000442.11

Do you mind also providing the fasta and gtf files used for the processing, please?

Thanks!

Best wishes, Yuk Kei

nickst85 commented 8 months ago

Hi Yuk,

I will modify the eventalign.txt (I guess I need to re-run the nanopolish with a gtf that has only transcript IDs and coordinates, right?)

Please see part of the annotation file that is downloaded from genecode:

gff-version 3

description: evidence-based annotation of the human genome (GRCh38), version 44 (Ensembl 110)

provider: GENCODE

contact: @.***

format: gff3

date: 2023-03-01

sequence-region chr1 1 248956422

chr1 HAVANA gene 11869 14409 . + . ID=ENSG00000290825.1;gene_id=ENSG00000290825.1;gene_type=lncRNA;gene_name=DDX11L2;level=2;tag=overlaps_pseudogene chr1 HAVANA transcript 11869 14409 . + . ID=ENST00000456328.2;Parent=ENSG00000290825.1;gene_id=ENSG00000290825.1;transcript_id=ENST00000456328.2;gene_type=lncRNA;gene_name=DDX11L2;transcript_type=lncRNA;transcript_name=DDX11L2-202;level=2;transcript_support_level=1;tag=basic,Ensembl_canonical;havana_transcript=OTTHUMT00000362751.1 chr1 HAVANA exon 11869 12227 . + . ID=exon:ENST00000456328.2:1;Parent=ENST00000456328.2;gene_id=ENSG00000290825.1;transcript_id=ENST00000456328.2;gene_type=lncRNA;gene_name=DDX11L2;transcript_type=lncRNA;transcript_name=DDX11L2-202;exon_number=1;exon_id=ENSE00002234944.1;level=2;transcript_support_level=1;tag=basic,Ensembl_canonical;havana_transcript=OTTHUMT00000362751.1 chr1 HAVANA exon 12613 12721 . + . ID=exon:ENST00000456328.2:2;Parent=ENST00000456328.2;gene_id=ENSG00000290825.1;transcript_id=ENST00000456328.2;gene_type=lncRNA;gene_name=DDX11L2;transcript_type=lncRNA;transcript_name=DDX11L2-202;exon_number=2;exon_id=ENSE00003582793.1;level=2;transcript_support_level=1;tag=basic,Ensembl_canonical;havana_transcript=OTTHUMT00000362751.1 chr1 HAVANA exon 13221 14409 . + . ID=exon:ENST00000456328.2:3;Parent=ENST00000456328.2;gene_id=ENSG00000290825.1;transcript_id=ENST00000456328.2;gene_type=lncRNA;gene_name=DDX11L2;transcript_type=lncRNA;transcript_name=DDX11L2-202;exon_number=3;exon_id=ENSE00002312635.1;level=2;transcript_support_level=1;tag=basic,Ensembl_canonical;havana_transcript=OTTHUMT00000362751.1 chr1 HAVANA gene 12010 13670 . + . ID=ENSG00000223972.6;gene_id=ENSG00000223972.6;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;level=2;hgnc_id=HGNC:37102;havana_gene=OTTHUMG00000000961.2 chr1 HAVANA transcript 12010 13670 . + . ID=ENST00000450305.2;Parent=ENSG00000223972.6;gene_id=ENSG00000223972.6;transcript_id=ENST00000450305.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=DDX11L1-201;level=2;transcript_support_level=NA;hgnc_id=HGNC:37102;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000002844.2 chr1 HAVANA exon 12010 12057 . + . ID=exon:ENST00000450305.2:1;Parent=ENST00000450305.2;gene_id=ENSG00000223972.6;transcript_id=ENST00000450305.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=DDX11L1-201;exon_number=1;exon_id=ENSE00001948541.1;level=2;transcript_support_level=NA;hgnc_id=HGNC:37102;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000002844.2 chr1 HAVANA exon 12179 12227 . + . ID=exon:ENST00000450305.2:2;Parent=ENST00000450305.2;gene_id=ENSG00000223972.6;transcript_id=ENST00000450305.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=DDX11L1-201;exon_number=2;exon_id=ENSE00001671638.2;level=2;transcript_support_level=NA;hgnc_id=HGNC:37102;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000002844.2 chr1 HAVANA exon 12613 12697 . + . ID=exon:ENST00000450305.2:3;Parent=ENST00000450305.2;gene_id=ENSG00000223972.6;transcript_id=ENST00000450305.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=DDX11L1-201;exon_number=3;exon_id=ENSE00001758273.2;level=2;transcript_support_level=NA;hgnc_id=HGNC:37102;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000002844.2 chr1 HAVANA exon 12975 13052 . + . ID=exon:ENST00000450305.2:4;Parent=ENST00000450305.2;gene_id=ENSG00000223972.6;transcript_id=ENST00000450305.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=DDX11L1-201;exon_number=4;exon_id=ENSE00001799933.2;level=2;transcript_support_level=NA;hgnc_id=HGNC:37102;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000002844.2 chr1 HAVANA exon 13221 13374 . + . ID=exon:ENST00000450305.2:5;Parent=ENST00000450305.2;gene_id=ENSG00000223972.6;transcript_id=ENST00000450305.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=DDX11L1-201;exon_number=5;exon_id=ENSE00001746346.2;level=2;transcript_support_level=NA;hgnc_id=HGNC:37102;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000002844.2 chr1 HAVANA exon 13453 13670 . + . ID=exon:ENST00000450305.2:6;Parent=ENST00000450305.2;gene_id=ENSG00000223972.6;transcript_id=ENST00000450305.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=DDX11L1-201;exon_number=6;exon_id=ENSE00001863096.1;level=2;transcript_support_level=NA;hgnc_id=HGNC:37102;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000002844.2 chr1 HAVANA gene 14404 29570 . - . ID=ENSG00000227232.5;gene_id=ENSG00000227232.5;gene_type=unprocessed_pseudogene;gene_name=WASH7P;level=2;hgnc_id=HGNC:38034;havana_gene=OTTHUMG00000000958.1 chr1 HAVANA transcript 14404 29570 . - . ID=ENST00000488147.1;Parent=ENSG00000227232.5;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;level=2;transcript_support_level=NA;hgnc_id=HGNC:38034;ont=PGO:0000005;tag=basic,Ensembl_canonical;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 chr1 HAVANA exon 29534 29570 . - . ID=exon:ENST00000488147.1:1;Parent=ENST00000488147.1;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;exon_number=1;exon_id=ENSE00001890219.1;level=2;transcript_support_level=NA;hgnc_id=HGNC:38034;ont=PGO:0000005;tag=basic,Ensembl_canonical;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 chr1 HAVANA exon 24738 24891 . - . ID=exon:ENST00000488147.1:2;Parent=ENST00000488147.1;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;exon_number=2;exon_id=ENSE00003507205.1;level=2;transcript_support_level=NA;hgnc_id=HGNC:38034;ont=PGO:0000005;tag=basic,Ensembl_canonical;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 chr1 HAVANA exon 18268 18366 . - . ID=exon:ENST00000488147.1:3;Parent=ENST00000488147.1;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;exon_number=3;exon_id=ENSE00003477500.1;level=2;transcript_support_level=NA;hgnc_id=HGNC:38034;ont=PGO:0000005;tag=basic,Ensembl_canonical;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 chr1 HAVANA exon 17915 18061 . - . ID=exon:ENST00000488147.1:4;Parent=ENST00000488147.1;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;exon_number=4;exon_id=ENSE00003565697.1;level=2;transcript_support_level=NA;hgnc_id=HGNC:38034;ont=PGO:0000005;tag=basic,Ensembl_canonical;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 chr1 HAVANA exon 17606 17742 . - . ID=exon:ENST00000488147.1:5;Parent=ENST00000488147.1;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;exon_number=5;exon_id=ENSE00003475637.1;level=2;transcript_support_level=NA;hgnc_id=HGNC:38034;ont=PGO:0000005;tag=basic,Ensembl_canonical;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 chr1 HAVANA exon 17233 17368 . - . ID=exon:ENST00000488147.1:6;Parent=ENST00000488147.1;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;exon_number=6;exon_id=ENSE00003502542.1;level=2;transcript_support_level=NA;hgnc_id=HGNC:38034;ont=PGO:0000005;tag=basic,Ensembl_canonical;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 chr1 HAVANA exon 16858 17055 . - . ID=exon:ENST00000488147.1:7;Parent=ENST00000488147.1;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;exon_number=7;exon_id=ENSE00003553898.1;level=2;transcript_support_level=NA;hgnc_id=HGNC:38034;ont=PGO:0000005;tag=basic,Ensembl_canonical;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 chr1 HAVANA exon 16607 16765 . - . ID=exon:ENST00000488147.1:8;Parent=ENST00000488147.1;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;exon_number=8;exon_id=ENSE00003621279.1;level=2;transcript_support_level=NA;hgnc_id=HGNC:38034;ont=PGO:0000005;tag=basic,Ensembl_canonical;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 chr1 HAVANA exon 15796 15947 . - . ID=exon:ENST00000488147.1:9;Parent=ENST00000488147.1;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;exon_number=9;exon_id=ENSE00002030414.1;level=2;transcript_support_level=NA;hgnc_id=HGNC:38034;ont=PGO:0000005;tag=basic,Ensembl_canonical;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 chr1 HAVANA exon 15005 15038 . - . ID=exon:ENST00000488147.1:10;Parent=ENST00000488147.1;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;exon_number=10;exon_id=ENSE00001935574.1;level=2;transcript_support_level=NA;hgnc_id=HGNC:38034;ont=PGO:0000005;tag=basic,Ensembl_canonical;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 chr1 HAVANA exon 14404 14501 . - . ID=exon:ENST00000488147.1:11;Parent=ENST00000488147.1;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;exon_number=11;exon_id=ENSE00001843071.1;level=2;transcript_support_level=NA;hgnc_id=HGNC:38034;ont=PGO:0000005;tag=basic,Ensembl_canonical;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 chr1 ENSEMBL gene 17369 17436 . - . ID=ENSG00000278267.1;gene_id=ENSG00000278267.1;gene_type=miRNA;gene_name=MIR6859-1;level=3;hgnc_id=HGNC:50039 chr1 ENSEMBL transcript 17369 17436 . - . ID=ENST00000619216.1;Parent=ENSG00000278267.1;gene_id=ENSG00000278267.1;transcript_id=ENST00000619216.1;gene_type=miRNA;gene_name=MIR6859-1;transcript_type=miRNA;transcript_name=MIR6859-1-201;level=3;transcript_support_level=NA;hgnc_id=HGNC:50039;tag=basic,Ensembl_canonical chr1 ENSEMBL exon 17369 17436 . - . ID=exon:ENST00000619216.1:1;Parent=ENST00000619216.1;gene_id=ENSG00000278267.1;transcript_id=ENST00000619216.1;gene_type=miRNA;gene_name=MIR6859-1;transcript_type=miRNA;transcript_name=MIR6859-1-201;exon_number=1;exon_id=ENSE00003746039.1;level=3;transcript_support_level=NA;hgnc_id=HGNC:50039;tag=basic,Ensembl_canonical

My fasta is downloaded from ensembl, it corresponds to human transcriptome p14 and it looks like

ENST00000456328.2|ENSG00000290825.1|-|OTTHUMT00000362751.1|DDX11L2-202|DDX11L2|1657|lncRNA| GTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTC TCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGA TGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTG……

Best,

Nick From: Yuk Kei Wan @.> Date: Tuesday, January 9, 2024 at 3:09 AM To: GoekeLab/xpore @.> Cc: Settas, Nikolaos @.>, Mention @.> Subject: [EXT] Re: [GoekeLab/xpore] Empty diffmod.table file, only header generated when running xpore diffmod after preprocessing my runs (Issue #209) ATTENTION: External Email! Do not click attachments/links unless sender is known.

Hi @nickst85 [github. com], The first column of your eventalign. txt file has to be just the ENSTxxxxx. You will have to modify the eventalign. txt from currently: ENST00000000442. 11|ENSG00000173153. 17|OTTHUMG00000150641. 9|OTTHUMT00000319303. 3|ESRRA-201|ESRRA|2274|protein_coding|

Hi @nickst85 [github.com]https://urldefense.com/v3/__https:/github.com/nickst85__;!!FMDslA!YESVEDTMH3AgnY_759QtZ8dL5IpCeep0XMbU0oe8bg_AM1yEleeNaRSbXNpJc7JGsEi6AggfiHFAEOcxXytFYghN2lRvpn4$,

The first column of your eventalign.txt file has to be just the ENSTxxxxx. You will have to modify the eventalign.txt from currently:

ENST00000000442.11|ENSG00000173153.17|OTTHUMG00000150641.9|OTTHUMT00000319303.3|ESRRA-201|ESRRA|2274|protein_coding|

to the following:

ENST00000000442.11

Do you mind also providing the fasta and gtf files used for the processing, please?

Thanks!

Best wishes, Yuk Kei

— Reply to this email directly, view it on GitHub [github.com]https://urldefense.com/v3/__https:/github.com/GoekeLab/xpore/issues/209*issuecomment-1882181970__;Iw!!FMDslA!YESVEDTMH3AgnY_759QtZ8dL5IpCeep0XMbU0oe8bg_AM1yEleeNaRSbXNpJc7JGsEi6AggfiHFAEOcxXytFYghNOalsIiI$, or unsubscribe [github.com]https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/A5QGITWXAPTDCCIRLZL5H6LYNSRFLAVCNFSM6AAAAABBRMQEQGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBSGE4DCOJXGA__;!!FMDslA!YESVEDTMH3AgnY_759QtZ8dL5IpCeep0XMbU0oe8bg_AM1yEleeNaRSbXNpJc7JGsEi6AggfiHFAEOcxXytFYghNiR0hakc$. You are receiving this because you were mentioned.Message ID: @.***>

Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

yuukiiwa commented 8 months ago

Hi Nick (tagging you here @nickst85),

You can use the following script (not tested) to change the first column of the eventalign.txt file (please change the paths to make sure you have enough storage space for the new modified_eventalign.txt file):

outfile=open('modified_eventalign.txt','w')
file=open('eventalign.txt','r')
outfile.write(file.readline())
for ln in file:
    ln=ln.split('\t')
    outln=[ln.split('|')[0]]+ln[1:]
    outfile.write('\t'.join(outln))
outfile.close()
file.close()

If you prefer to run nanopolish eventalign instead, we would suggest you using the ENSEMBL reference fasta and gtf files (we are trying to fix the problem with gencode reference on our end).

Thanks!

Best wishes, Yuk Kei

nickst85 commented 8 months ago

Hi Yuk Kei,

Thank you for your reply. I’ll try to modify the file with the code you sent me.

I have one more question. I used the m6Anet tool from your lab but I got an output file with no probability estimation per kmer postion and I am afraid that something went wrong. Can you connect me with someone that can assist me with this issue?

Best,

Nick

From: Yuk Kei Wan @.> Date: Thursday, January 18, 2024 at 3:26 AM To: GoekeLab/xpore @.> Cc: Settas, Nikolaos @.>, Mention @.> Subject: [EXT] Re: [GoekeLab/xpore] Empty diffmod.table file, only header generated when running xpore diffmod after preprocessing my runs (Issue #209) ATTENTION: External Email! Do not click attachments/links unless sender is known.

Hi Nick (tagging you here @nickst85 [github. com]), You can use the following script (not tested) to change the first column of the eventalign. txt file (please change the paths to make sure you have enough storage space for the new modified_eventalign. txt

Hi Nick (tagging you here @nickst85 [github.com]https://urldefense.com/v3/__https:/github.com/nickst85__;!!FMDslA!fuN3rhKDXkgZneiJlZI1ckbugySLu1BNRjzwKbFN4ZZppoeDuDL9X1Z22rpnSEfLQ82LBU21czsTSEUpViRH0GuinUhjf-g$),

You can use the following script (not tested) to change the first column of the eventalign.txt file (please change the paths to make sure you have enough storage space for the new modified_eventalign.txt file):

outfile=open('modified_eventalign.txt','w')

file=open('eventalign.txt','r')

outfile.write(file.readline())

for ln in file:

ln=ln.split('\t')

outln=[ln.split('|')[0]]+ln[1:]

outfile.write('\t'.join(outln))

outfile.close()

file.close()

If you prefer to run nanopolish eventalign instead, we would suggest you using the ENSEMBL reference fasta and gtf files (we are trying to fix the problem with gencode reference on our end).

Thanks!

Best wishes, Yuk Kei

— Reply to this email directly, view it on GitHub [github.com]https://urldefense.com/v3/__https:/github.com/GoekeLab/xpore/issues/209*issuecomment-1898011251__;Iw!!FMDslA!fuN3rhKDXkgZneiJlZI1ckbugySLu1BNRjzwKbFN4ZZppoeDuDL9X1Z22rpnSEfLQ82LBU21czsTSEUpViRH0GuiKzQ-Gts$, or unsubscribe [github.com]https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/A5QGITQWFIJO5IUN6ATNZVTYPDMDBAVCNFSM6AAAAABBRMQEQGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJYGAYTCMRVGE__;!!FMDslA!fuN3rhKDXkgZneiJlZI1ckbugySLu1BNRjzwKbFN4ZZppoeDuDL9X1Z22rpnSEfLQ82LBU21czsTSEUpViRH0Gui_MwlIy0$. You are receiving this because you were mentioned.Message ID: @.***>

Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

yuukiiwa commented 8 months ago

Hi @nickst85,

I maintain that too. Will follow on this issue: https://github.com/GoekeLab/m6anet/issues/147

Thanks!

Best wishes, Yuk Kei