how to convert Plink files to Merlin format

[Ana Marija]

Hello,

I was running Mega2
(mega2_v6.0.0_linux ) following these instructions:

https://docs.google.com/viewer?a=v&pid=forums&srcid=MDU3MzMwODU3ODIzNjAwNDk5NzIBMTQ5MDI0MjYxMTE3ODQxNDM3MDgBMHhObXRNRkRFUUFKATAuMQEBdjI&authuser=0&urp=gmail_link

and I got these errors:

Typed, ext_ped_num, ext_per_num, MZTwin, DZTwin, GroupX, rec_num, loopbreakers, pedigree_link, person_link   FROM person_brkloop_table;" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "INSERT INTO canonicalallele_table(key, value) VALUES(?, ?);" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "SELECT key, value FROM canonicalallele_table;" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "INSERT INTO markerscheme_table(key, allele1, allele2) VALUES(?, ?, ?);" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "SELECT key, allele1, allele2 FROM markerscheme_table;" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "INSERT INTO locus_table( LocusName, Type, Class, number, col_num, AlleleCnt, locus_link)   VALUES(?, ?, ?, ?, ?, ?, ?);" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "SELECT  LocusName, Type, Class, number, col_num, AlleleCnt, locus_link   FROM locus_table;" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "INSERT INTO allele_table( AlleleName, Frequency, indexX, locus_link)   VALUES(?, ?, ?, ?);" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "SELECT  AlleleName, Frequency, indexX, locus_link   FROM allele_table;" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "INSERT INTO marker_table( MarkerName, Recoded, NumAlleles, SelectOpt, EstFreq, pos_avg, pos_male, pos_female, error_prob, chromosome, col_num, locus_link)   VALUES(?, ?, ?, ?, ?, ?, ?, ?, ?, ?,   ?, ?);" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "INSERT INTO marker_table( MarkerName, Recoded, NumAlleles, SelectOpt, EstFreq, pos_avg, pos_male, pos_female, error_prob, chromosome, col_num, locus_link)   VALUES(?, ?, ?, ?, ?, ?, NULL, NULL, ?, ?,   ?, ?);" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "SELECT  MarkerName, Recoded, NumAlleles, SelectOpt, EstFreq, pos_avg, ifnull(pos_male,-99.99), ifnull(pos_female,-99.99), error_prob, chromosome, col_num, locus_link   FROM marker_table;" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "INSERT INTO traitaff_table( ClassCnt, PenCnt, NumLabels, Labels, locus_link)   VALUES(?, ?, ?, ?, ?);" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "SELECT  ClassCnt, PenCnt, NumLabels, Labels, locus_link   FROM traitaff_table;" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "INSERT INTO affectclass_table( MaleDef, FemaleDef, AutoDef, MalePen, FemalePen, AutoPen, locus_link, class_link)   VALUES(?, ?, ?, ?, ?, ?, ?, ?);" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "SELECT  MaleDef, FemaleDef, AutoDef, MalePen, FemalePen, AutoPen, locus_link, class_link   FROM affectclass_table;" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "INSERT INTO traitquant_table( ClassCnt, Mean, Variance, Multiplier, locus_link)   VALUES(?, ?, ?, ?, ?);" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "SELECT  ClassCnt, Mean, Variance, Multiplier, locus_link   FROM traitquant_table;" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "INSERT INTO mapnames_table( map, sex_averaged_map, male_sex_map, female_sex_map, name) VALUES(?, ?, ?, ?, ?);" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "SELECT map, sex_averaged_map, male_sex_map, female_sex_map, name FROM mapnames_table;" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "INSERT INTO map_table(marker, map, position, pos_female, pos_male) VALUES(?, ?, ?, ?, ?);" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "INSERT INTO map_table(marker, map, position, pos_female, pos_male) VALUES(?, ?, ?, NULL, NULL);" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "SELECT marker, map, position, ifnull(pos_female,-99.99), ifnull(pos_male,-99.99) FROM map_table;" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "INSERT INTO phenotype_table( person_link, bytes, data)  VALUES(?, ?, ?);" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "SELECT  person_link, bytes, data  FROM phenotype_table;" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "INSERT INTO genotype_table( person_link, chr, bytes, data)  VALUES(?, ?, ?, ?);" (file "dbmega2.db") failed: #10:disk I/O error
DB prep "SELECT  person_link, chr, bytes, data  FROM genotype_table;" (file "dbmega2.db") failed: #10:disk I/O error
Dumping SQLite3 DB to file "dbmega2.db"
DB sqlite3_exec (file "dbmega2.db") failed: #10:disk I/O error
SQLite3 database "dbmega2.db" was processed to generate this output.
===========================================================
Run parameters stored in batch file 2020-9-18-11-51/MEGA2.BATCH
See run summaries in directory
   MEGA2.LOG, MEGA2.RECODE, MEGA2.ERR, MEGA2.KEYS
The script 'mega2log2html.pl' exited normally.
To view the HTML-formatted run summaries, open
/projects/com_grassim/anamaria/anamaria/anamaria/merlin/2020-9-18-11-51/MEGA2run.html
in a web browser.

Please advise,

Ana

[Dan Weeks]

Dear Ana,

I'm sorry - we discussed and explored your report of this type of "(file "dbmega2.db") failed: #10:disk I/O error" error earlier this year, and as I was not able to reproduce your problem on a similar Centos machine, I wasn't able to figure out why you are encountering such an error.  At the time, you said you'd ask your systems administrator for help - did they have any insights?

You could try recompiling Mega2 from the source code - maybe a freshly re-compiled executable would work properly on your machine.

Sincerely,

Dan