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TERefiner_1 error #11
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And I have this in my repertory ! |
Hi @Milad021 , |
I tried to recompile TERefiner_1, but I got an error. In fact it seems that it doesn't found the api/BamReader.h . when i do REPdenovo/bamtools$ find ./ -name lib, i get nothing and it's asked when i do make for TERefiner. Thanks for your time |
I think you need to set the bamtools path in the makefile (under TERefiner folder). Usually, it works well and don't need to re-compile. But I do need to release a user-friendly installation package. |
In fact there is ( maybe since recently ) two separated include folders for bamtools.
now it's compiled without errors, but i'm not sure everything is right. |
Unfortunately still the same problem. And the same files are generated in my directory My directory """""""""""""""" |
Can you post the reported errors by running this command?
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Thank you for the speedy respons ! I will do it tomorrow, as soon as I have access to my PC. |
In case you will meet other issues, you can similarly compile ContigsMerger on your server. Then copy the newly compiled TERefiner_1 and ContigsMerger to the same level as main.py. Then try again. |
Hi @ReedWarbler , |
I think the error is caused before this step. The /Siek14_Repeatelm_12X/contigs.fa.itself.sort.bam is empty? |
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 I can not manage TERefiner and ContigsMerger, can I send you my original_contigs_before_merging.fa ? And My question is ,will I need TERefiner and ContigsMerger for Scaffolding step? |
Hi,
the head is :
The ContigsMerger is compiled on the machine without error, I'm not sure if the error can from the change I made on the makefile for TERefiner. If not, I have no idea where does it came from. |
Can u view this file?
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I mean this file: ./Siek14_Repeatelm_12X/contigs.fa.itself.sort.bam, because u said:
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Sorry I did n't understand.
Thanks for responding fast each time ! I did again all the REPdenovo commands and now i get a strange error :
I get a lot of free RAM |
Hi @ReedWarbler do you have any idea ? |
Hi Chong,
I'am from France and I think I have some problems with TERefiner_1. I wanted to know is it important for the rest of my analyzes? I obtain my contigs.fa but after Scaffolding I have zero informations in my X_contig_pairs_info.txt_cov_info_with_cutoff.txt .
Running command: /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_n o_dup.fa -c 0.9 -g ... rm: impossible de supprimer './Siek14_Repeatelm_12X/contigs.fa.itself.bam': Aucun fichier ou dossier de ce type rm: impossible de supprimer './Siek14_Repeatelm_12X/contigs.fa.itself.bam': Aucun fichier ou dossier de ce type rm: impossible de supprimer './Siek14_Repeatelm_12X/contigs.fa.itself.bam': Aucun fichier ou dossier de ce type Running command: /usr/local/src/REPdenovo/ContigsMerger -s 0.2 -i1 -6.0 -i2 -6.0 -x 15 -y 50 -k 10 -t 15 -m 1 -o ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merge.info ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa > ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa ... Running command: Running command: samtools faidx ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa ... [bwa_index] Pack FASTA... 0.12 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 5.07 seconds elapse. [bwa_index] Update BWT... 0.09 sec [bwa_index] Pack forward-only FASTA... 0.07 sec [bwa_index] Construct SA from BWT and Occ... 2.19 sec [main] Version: 0.7.15-r1140 [main] CMD: bwa index ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa [main] Real time: 8.361 sec; CPU: 7.540 sec [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 4034 sequences (10001826 bp)... [M::process] read 5595 sequences (6324459 bp)... [M::mem_process_seqs] Processed 4034 reads in 71.228 CPU sec, 71.386 real sec [M::mem_process_seqs] Processed 5595 reads in 46.156 CPU sec, 46.256 real sec [main] Version: 0.7.15-r1140 [main] CMD: bwa mem -a ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa [main] Real time: 117.819 sec; CPU: 117.456 sec Running command: /usr/local/src/REPdenovo/TERefiner_1 -P -b ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.itself.sort.bam -r ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa -o ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -c 0.85 -g ... rm: impossible de supprimer './Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.itself.bam': Aucun fichier ou dossier de ce type rm: impossible de supprimer './Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.itself.bam': Aucun fichier ou dossier de ce type rm: impossible de supprimer './Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.itself.bam': Aucun fichier ou dossier de ce type Running command: Running command: samtools faidx ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.no_dup.fa ... [bwa_index] Pack FASTA... 0.08 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 2.97 seconds elapse. [bwa_index] Update BWT... 0.06 sec [bwa_index] Pack forward-only FASTA... 0.05 sec [bwa_index] Construct SA from BWT and Occ... 1.39 sec [main] Version: 0.7.15-r1140 [main] CMD: bwa index ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.no_dup.fa [main] Real time: 5.104 sec; CPU: 4.552 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs[M::process] read 4162 sequences (10002529 bp)...
[M::process] read 1173 sequences (877888 bp)...
[M::mem_process_seqs] Processed 4162 reads in 64.264 CPU sec, 64.418 real sec
[M::mem_process_seqs] Processed 1173 reads in 7.060 CPU sec, 7.065 real sec
[main] Version: 0.7.15-r1140
[main] CMD: bwa mem -a ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.no_dup.fa ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.no_dup.fa
[main] Real time: 71.635 sec; CPU: 71.368 sec
Running command: /usr/local/src/REPdenovo/TERefiner_1 -P -b ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.itself.sort.bam -r ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -o ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.no_contained.fa -c 0.85 ...
rm: impossible de supprimer './Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.itself.bam': Aucun fichier ou dossier de ce type
rm: impossible de supprimer './Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.itself.bam': Aucun fichier ou dossier de ce type
rm: impossible de supprimer './Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.itself.bam': Aucun fichier ou dossier de ce type
It's very emergency because I need to finish my intenrship, Thank you so much !
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