[maker-devel] blast error in maker

[chen wang]

Dear professor


maker is a great annotation software, when i using it, i have some strange problems. i added in the google group and browsed many questions, but i didnt get useful message for my question. 

**By the way, i can not submit new question in google group(although i have added the group and subscribed), so i send this email to you.** 


I check the log file, i found somehow a file was removed, but then it cannot find this file. Then the strange error happened.


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Removing file: /xtdisk/xueyb_group/wangchenA/Petunia_denovo/HiFi/09.anno/04.maker/part-hp1/hp1_HiC1/hp1_HiC1_rnd1.make

r.output/hp1_HiC1_rnd1_datastore/1D/F6/HiC_1//theVoid.HiC_1/HiC_1.35.end.blastx.holdover

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ERROR: No such file or directory at /xtdisk/xueyb_group/wangchenA/Petunia_denovo/HiFi/09.anno/04.maker/part-hp1/hp1_Hi
C1/hp1_HiC1_rnd1.maker.output/hp1_HiC1_rnd1_datastore/1D/F6/HiC_1//theVoid.HiC_1/HiC_1.35.end.blastx.holdover


ERROR: Failed while collecting blastx reports
ERROR: Chunk failed at level:9, tier_type:3
FAILED CONTIG:HiC_1


merging blast reports...
doing blastn of ESTs
ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:HiC_1

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any advice would be highly appreciated, i have been stopped in this strange errors for days.

I submit my job at PBS. (one node, 20cpu, mpiexec -n 20).  max_dna_len=100000. TMP=/tmp/

i dont know why the .blastx.holdover file was removed by maker/bin/../lib/Process/MpiChunk.pm?  the blast start or end coordinate is removed because of uncomplete blast? so the blast report is truncated? 

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ncbi-blast-2.12.0+

RepeatMasker was installed with rmblast-2.2.28


thank u


best regards


wangchen


student in chinese academy of sciences