Milad021
Milad021
I found a workaround for this compilation issue : [https://github.com/Reedwarbler/REPdenovo/issues/11#issuecomment-393540162](https://github.com/Reedwarbler/REPdenovo/issues/11#issuecomment-393540162)
And I have this in my repertory ! `30mer.temp_contigs.fa Asm_30_4880_29 Asm_40_64434_39 Asm_60_112338_59 contigs.fa.itself.sort.bam contigs.fa_no_dup.fa.merge.info 40mer.temp_contigs.fa Asm_30_610_29 Asm_40_8054_39 Asm_60_14042_59 contigs.fa.itself.sort.bam.bai dumped_30mers.txt 50mer.temp_contigs.fa Asm_30_78089_29 Asm_50_119523_49 Asm_60_1755_59 contigs.fa_no_dup.fa dumped_40mers.txt 60mer.temp_contigs.fa Asm_30_9761_29 Asm_50_14940_49 Asm_60_28084_59...
I tried to recompile TERefiner_1, but I got an error. In fact it seems that it doesn't found the api/BamReader.h . I tried multiple links from bamtools repository and build...
In fact there is ( maybe since recently ) two separated include folders for bamtools. I did a little modification in your Makefile before to success compiling with lot of...
Unfortunately still the same problem. And the same files are generated in my directory """"""""""""" [bwa_index] Pack FASTA... 0.01 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 0.11 seconds...
Thank you for the speedy respons ! I will do it tomorrow, as soon as I have access to my PC.
Hi @Reedwarbler , By running this command, I have this error message : """""""""""" $ /usr/local/src/REPdenovo/TERefiner_1 /usr/local/src/REPdenovo/TERefiner_1 -P -b ./Siek14_Repeatelm_12X/contigs.fa.itself.sort.bam -r ./Siek14_Repeatelm_12X/contigs.fa -o ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa -c 0.9 -g Index file not...
Hi @Reedwarbler I'm so sorry for my late response, because I will not be in the lab until Tuesday. As soon as I'm there I'll let you know. But if...
Hi, the file doesn't look empty : ``` 678K mai 31 17:30 contigs.fa.itself.sort.bam ``` the head is : ``` BAMsl@HD VN:1.3 SO:coordinate @SQ SN:NODE_1_length_176_cov_1.988636_30_31235_312356 LN:204 @SQ SN:NODE_2_length_106_cov_2.000000_30_31235_312356 LN:134 @SQ SN:NODE_6_length_76_cov_1.973684_30_31235_312356...
``` NODE_1_length_176_cov_1.988636_30_31235_312356 256 NODE_1_length_176_cov_1.988636_30_31235_312356 1 0 204M * 0 0 * * NM:i:0 MD:Z:204 AS:i:204 NODE_2_length_236_cov_2.258475_30_15617_312356 256 NODE_1_length_176_cov_1.988636_30_31235_312356 1 0 204M60H * 0 0 * * NM:i:1 MD:Z:8A195 AS:i:199 NODE_3_length_161_cov_2.869565_30_7808_312356...