empty dataprep data.json and data.log

[nickst85]

Hi,

I am using the new RNA flowcells to call for m6a modification. I used the f5c eventalign command to get the eventalign.tsv and used this file to run the dataprep.

The run finished without error, but the data.log and data.json are empty.

the eventalign.index looks like this:

transcript_id,read_index,pos_start,pos_end ENST00000655252.1,213,172,183853 ENST00000655252.1,216,183853,274146 ENST00000655252.1,217,274146,381035 ENST00000655252.1,218,381035,461603 ENST00000655252.1,219,461603,493651 ENST00000424587.7,11125,493651,839165 ENST00000424587.7,11127,839165,987809 ENST00000424587.7,11129,987809,1249168 . . .

the data.info file has only the header : transcript_id,transcript_position,start,end,n_reads

Can you please help me?

Thank you in advance,

Nick

[yuukiiwa]

Hi Nick (tagging you here @nickst85),

Sorry for the delayed reply (was out of town and will be on vacation)!

Do you mind showing my the first ten lines of your eventalign file head eventalign.txt please?

Thanks!

Best wishes, Yuk Kei

[nickst85]

Hi Yuk Kei,

Thank you for your response. See below:

contig position reference_kmer read_index strand event_index event_level_mean event_stdv event_length model_kmer model_mean model_stdv standardized_level start_idx end_idx

ENST00000655252.1 1 AGTCCTACT 213 t 598 63.95 2.483 0.00425 AGTCCTACT 63.14 2.48 0.28 36697 36714

ENST00000655252.1 2 GTCCTACTG 213 t 599 74.20 2.184 0.00625 GTCCTACTG 72.22 2.15 0.78 36672 36697

ENST00000655252.1 3 TCCTACTGA 213 t 600 77.92 1.399 0.00300 TCCTACTGA 76.24 2.02 0.71 36660 36672

ENST00000655252.1 4 CCTACTGAG 213 t 601 83.85 1.511 0.00550 CCTACTGAG 81.28 2.35 0.94 36638 36660

ENST00000655252.1 5 CTACTGAGT 213 t 602 87.34 1.400 0.00225 CTACTGAGT 86.39 2.91 0.28 36629 36638

ENST00000655252.1 5 CTACTGAGT 213 t 603 85.17 1.468 0.00150 CTACTGAGT 86.39 2.91 -0.36 36623 36629

ENST00000655252.1 5 CTACTGAGT 213 t 604 83.17 1.083 0.00250 CTACTGAGT 86.39 2.91 -0.94 36613 36623

ENST00000655252.1 5 CTACTGAGT 213 t 605 85.09 2.107 0.00900 CTACTGAGT 86.39 2.91 -0.38 36577 36613

ENST00000655252.1 5 CTACTGAGT 213 t 606 89.80 2.735 0.00250 CTACTGAGT 86.39 2.91 1.00 36567 36577

I also sorted by the read_index the eventalign file of the f5c and after sorting it looks like this:

contig position reference_kmer read_index strand event_index event_level_mean event_stdv event_length model_kmer model_mean model_stdv standardized_level start_idx end_idx

ENST00000655252.1 1000 GAGACCAGC 213 t 2066 94.98 18.284 0.00300 GAGACCAGC 77.43 6.23 2.41 10045 10057

ENST00000655252.1 1000 GAGACCAGC 213 t 2067 72.12 1.807 0.00525 GAGACCAGC 77.43 6.23 -0.73 10024 10045

ENST00000655252.1 1001 AGACCAGCC 213 t 2068 66.75 1.313 0.00675 AGACCAGCC 66.06 2.98 0.20 9997 10024

ENST00000655252.1 1002 GACCAGCCT 213 t 2069 83.66 2.203 0.00425 GACCAGCCT 84.29 3.65 -0.15 9980 9997

ENST00000655252.1 1002 GACCAGCCT 213 t 2070 87.12 1.869 0.00350 GACCAGCCT 84.29 3.65 0.66 9966 9980

ENST00000655252.1 1003 ACCAGCCTG 213 t 2071 101.11 2.194 0.00900 ACCAGCCTG 97.88 2.92 0.95 9930 9966

ENST00000655252.1 1004 CCAGCCTGA 213 t 2072 105.47 4.120 0.00325 CCAGCCTGA 102.65 2.41 1.00 9917 9930

I tried to run m6Anet dataprep with both eventalign inputs but I got empty files.

Looking forward to your response,

Nick

From: Yuk Kei Wan @.> Date: Tuesday, June 4, 2024 at 4:54 PM To: GoekeLab/m6anet @.> Cc: Settas, Nikolaos @.>, Mention @.> Subject: [EXT] Re: [GoekeLab/m6anet] empty dataprep data.json and data.log (Issue #165) ATTENTION: External Email! Do not click attachments/links unless sender is known.

---

Hi Nick (tagging you here @nickst85 [github. com]), Sorry for the delayed reply (was out of town and will be on vacation)! Do you mind showing my the first ten lines of your eventalign file head eventalign. txt please? Thanks! Best wishes, Yuk

Hi Nick (tagging you here @nickst85 [github.com]https://urldefense.com/v3/__https:/github.com/nickst85__;!!FMDslA!fifnACR2I0P29sHbcm_MSEo1rdxcXMQl0mwJUCWiu1nZV2qVr27IAYrK8PCC47raSKHFTV27KZRzKxlUPlZFH4yMQSuR84k$),

Sorry for the delayed reply (was out of town and will be on vacation)!

Do you mind showing my the first ten lines of your eventalign file head eventalign.txt 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/m6anet/issues/165*issuecomment-2148399756__;Iw!!FMDslA!fifnACR2I0P29sHbcm_MSEo1rdxcXMQl0mwJUCWiu1nZV2qVr27IAYrK8PCC47raSKHFTV27KZRzKxlUPlZFH4yMATMj8Bw$, or unsubscribe [github.com]https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/A5QGITVJPLNCYKX7R3VL2ATZFYSP5AVCNFSM6AAAAABICLDMJSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNBYGM4TSNZVGY__;!!FMDslA!fifnACR2I0P29sHbcm_MSEo1rdxcXMQl0mwJUCWiu1nZV2qVr27IAYrK8PCC47raSKHFTV27KZRzKxlUPlZFH4yMTSoaFWM$. You are receiving this because you were mentioned.Message ID: @.***>

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[yuukiiwa]

Hi Nick (@nickst85),

You will have to change the reference_kmer and the model_kmer columns from 9mers to 5mers:

GATAAGGAT --> TAAGG
ATAAGGATT --> AAGGA

I will update m6anet this month for converting 9mer to 5mer within.

Thanks!

Best wishes, Yuk Kei

[nickst85]

Hi Yuk Kei,

Thank you for your response. Can you share any sample script for the conversion, maybe in python?

Best,

Nick

From: Yuk Kei Wan @.> Date: Wednesday, June 5, 2024 at 5:21 PM To: GoekeLab/m6anet @.> Cc: Settas, Nikolaos @.>, Mention @.> Subject: [EXT] Re: [GoekeLab/m6anet] empty dataprep data.json and data.log (Issue #165) ATTENTION: External Email! Do not click attachments/links unless sender is known.

---

Hi Nick (@ nickst85 [github. com]), You will have to change the reference_kmer and the model_kmer columns from 9mers to 5mers: GATAAGGAT --> TAAGG ATAAGGATT --> AAGGA I will update m6anet this month for converting 9mer to 5mer within. Thanks!

Hi Nick @.*** [github.com]https://urldefense.com/v3/__https:/github.com/nickst85__;!!FMDslA!dKiJH28yCSDOOtyMYJI8MoTs2GyWRP1MvgLtIlDU92UEiV0PN6xMXPoCi3vyJV__pLXWBoq4G3IGGgnWrLtRDzXyfUlME4c$),

You will have to change the reference_kmer and the model_kmer columns from 9mers to 5mers:

GATAAGGAT --> TAAGG

ATAAGGATT --> AAGGA

I will update m6anet this month for converting 9mer to 5mer within.

Thanks!

Best wishes, Yuk Kei

— Reply to this email directly, view it on GitHub [github.com]https://urldefense.com/v3/__https:/github.com/GoekeLab/m6anet/issues/165*issuecomment-2150984072__;Iw!!FMDslA!dKiJH28yCSDOOtyMYJI8MoTs2GyWRP1MvgLtIlDU92UEiV0PN6xMXPoCi3vyJV__pLXWBoq4G3IGGgnWrLtRDzXy9G4yGLM$, or unsubscribe [github.com]https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/A5QGITU6PIXKYFEZ5L6GBLLZF56N3AVCNFSM6AAAAABICLDMJSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNJQHE4DIMBXGI__;!!FMDslA!dKiJH28yCSDOOtyMYJI8MoTs2GyWRP1MvgLtIlDU92UEiV0PN6xMXPoCi3vyJV__pLXWBoq4G3IGGgnWrLtRDzXywYau2rU$. 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]

Hi Nick (tagging you here @nickst85),

Sorry for the delayed reply! You can use the code below (not tested):

file=open('eventalign.txt', 'r') ##change eventalign.txt to the name of the eventalign file accordingly if needed
outfile=open('5mer_eventalign.txt','w')
outfile.write(file.readline())
for ln in file:
    ln=ln.strip().split('\t')
    outfile.write('\t'.join(ln[:2]+[ln[2][2:7]]+ln[3:])+'\n')
outfile.close()

Thanks!

Best wishes, Yuk Kei