ERROR LOADING TRANSCRIPT LENGTH FILE ; UNKNOWN HAPLOTYPE NAME: PAR

[jon4thin]

Hello! I am running into an issue with emase-zero as implemented in kbchoi/emase:latest, getting the error:
ERROR LOADING TRANSCRIPT LENGTH FILE ; UNKNOWN HAPLOTYPE NAME: PAR

The issue is that if I remove these transcripts from the TRANSCRIPT LENGTH FILE, I get the WARNGING:

2024-08-15T19:22:18.685284122Z WARNING!
2024-08-15T19:22:18.685304588Z LOADING TRANSCRIPT LENGTH FILE /sbgenomics/Projects/daa73588-c56b-406b-95d0-845b472104dc/_1_Diploid_noHLA_1-01553_Asterisks.txlengths_noPAR.txt
2024-08-15T19:22:18.685308557Z EXPECTED 473950 VALUES BUT FILE CONTAINS 473632
2024-08-15T19:22:19.034095545Z No mapping information for ENST00000431238.7_PAR_Y

The warning lines keep printing ("No mapping information for" + the next ENST in the .EC file that has such label) 162 times, prints an empty line, and then the command fails on me with error code 1.

Any insights?

[jon4thin]

Jerry-rigged solution (still needs to be tested, will update afterwords):
I can go into the .bam and grep out the ENSTs that are PAR_Y and the original ENST, so that when I use samtools Faidx to get the .fai file to get the transcript length from, neither file has these transcripts. Then, when I make the gene mapping files with biomaRt in R, I can filter out all the transcripts that are not present in the transcripts length file.