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liangclab / HERA

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Use of uninitialized value #9

Open chopra29 opened 4 years ago

chopra29 commented 4 years ago

Scripts in ParseLA.pl and Daligner_Reformate.pl are giving this error or uninitialized value.

Please let me know if you have a quick fix for this.

GRGong commented 4 years ago

same problem """ $ cat Super-Scaffold_6-1-2.out Use of uninitialized value within %ContigNameHash in concatenation (.) or string at /public/home/grgong/software/HERA-master//ParseLA.pl line 86, line 5. Use of uninitialized value within %ContigLengthHash in concatenation (.) or string at /public/home/grgong/software/HERA-master//ParseLA.pl line 89, line 5. Use of uninitialized value within %ContigNameHash in concatenation (.) or string at /public/home/grgong/software/HERA-master//ParseLA.pl line 90, line 5. Use of uninitialized value within %ContigLengthHash in concatenation (.) or string at /public/home/grgong/software/HERA-master//ParseLA.pl line 93, line 5.

"""

liangclab commented 4 years ago

Hi, are you runnning the new scripts? if not please download them and try again.

GRGong commented 4 years ago

yes, I downloaded yesterday

chopra29 commented 4 years ago

Even with the new scripts for some reason uninitialized value error is recurring

dej-deng commented 4 years ago

same problem. I find "DBdump -rh Super-Scaffold_1-1-2.dam" do nothing and the file "ParseDAZZDB.txt" is null.

sunnycqcn commented 4 years ago

same problem. I find "DBdump -rh Super-Scaffold_1-1-2.dam" do nothing and the file "ParseDAZZDB.txt" is null.

Me too. I met the same issue. Did you solve this problem?

dej-deng commented 4 years ago

same problem. I find "DBdump -rh Super-Scaffold_1-1-2.dam" do nothing and the file "ParseDAZZDB.txt" is null.

Me too. I met the same issue. Did you solve this problem?

modified line 511 of the DB.c in DAZZ_DB-master/ then rebuild the code, it seems solved: 509 if (what & DB_STUB_NREADS) 510 { stub->nreads = ((int ) Malloc(sizeof(int)(nfiles+1),"Allocating DB stub record"))+1; 511 if (stub->nreads == NULL || stub->fname == NULL) 512 goto stub_error; 513 } line 511 change to: 511 if (stub->nreads == NULL)

But after rerun the pipline, the N50 of final ctg only improve little and I don't known whether it's normal. Both in test data and my real data.