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From: Priscila K. <pri...@ya...> - 2018-08-28 16:08:59
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I am using OPERA-LG to scaffolding an Illumina genome assembled using pacbio data. The program finished to run, but actually there is no change between the fasta file I use as input and the output fasta file. The only "error" that I saw is: "rm: cannot remove ‘*.sai’: No such file or directory". Follow are the output messages. " [...] [bwa_aln_core] refine gapped alignments... 0.31 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 563502918 sequences have been processed. [main] Version: 0.7.17-r1188 [main] CMD: bwa samse -n 1 Tetrapedia_SOAPdenovo.fasta read.sai - [main] Real time: 13206.938 sec; CPU: 6838.958 sec [bam_sort_core] merging from 120 files... PREPROCESS: Fastq format is recognized [Tue Aug 21 20:33:10 2018] Building bwa index... bwa index -p Tetrapedia_SOAPdenovo.fasta /scratch/8172532/Tetrapedia_SOAPdenovo.fasta [Tue Aug 21 20:41:00 2018] Finding the SA coordinates of the reads using BWA aln... [Wed Aug 22 19:19:16 2018] Generate alignments of reads using bwa sampe... bwa samse -n 1 Tetrapedia_SOAPdenovo.fasta read.sai - | grep '(^@|XT:A:U)' | samtools view -S -h -b -F 0x4 - | samtools sort -@ 20 -no - temporarySam > SOAP-opera2.bam [Wed Aug 22 23:16:10 2018] Preprocessing done! Mapping long-reads using blasr... /scratch/apps/blasrbinary/blasr -nproc 1 -m 1 -minMatch 5 -bestn 10 -noSplitSubreads -advanceExactMatches 1 -nCandidates 1 -maxAnchorsPerPosition 1 -sdpTupleSize 7 /scratch/8172532/All_pacbio_SMRT.fasta /scratch/8172532/Tetrapedia_SOAPdenovo.fasta | cut -d ' ' -f1-5,7-12 | sed 's/ /\t/g' > SOAP-opera2.map Sorting mapping results... sort -k1,1 -k9,9g SOAP-opera2.map > SOAP-opera2.map.sort N50: 127830250 i1 300 1000 i3 2000 5000 i5 15000 40000 i0 -200 300 i2 1000 2000 i4 5000 15000 Analyzing sorted results... Extracting linking information... Repeat detection... /scratch/apps/OPERA-LG_v2.0.6/bin//filter_conflicting_edge.pl pairedEdges_i0 contig_length.dat 100 2 *** 344 edges filtered from 1440 (0.238888888888889) rm anchor_contig_info.dat contig_length.dat filtered_edges.dat filtered_edges_cov.dat .sai rm: cannot remove ‘.sai’: No such file or directory mv SOAP-opera2.bam SOAP-opera2-with-repeat.bam /scratch/apps/OPERA-LG_v2.0.6/bin//filter_repeat.pl SOAP-opera2-with-repeat.bam repeat.dat | samtools view - -h -S -b > SOAP-opera2.bam [samopen] SAM header is present: 15508 sequences. rm SOAP-opera2-with-repeat.bam /scratch/apps/OPERA-LG_v2.0.6/bin/OPERA-LG config > log Analyzing 1 library: SOAP-opera2.bam min library mean : 250 minimum contig length is 500 Current library: 1 out of 7 Analyzing file: pairedEdges_no_repeat_i0 Analyzing file: pairedEdges_no_repeat_i1 Analyzing file: pairedEdges_no_repeat_i2 Analyzing file: pairedEdges_no_repeat_i3 Analyzing file: pairedEdges_no_repeat_i4 Analyzing file: pairedEdges_no_repeat_i5 ln -s results/scaffoldSeq.fasta scaffoldSeq.fasta" Follow is input command line: OPERA-long-read.pl --blasr /apps/blasrbinary --opera /apps/OPERA-LG_v2.0.6/bin --contig-file contig.fasta --kmer 63 --illumina-read1 /scratch/8172532/All_reads_1.fastq --illumina-read2 /scratch/8172532/All_reads_2.fastq --long-read-file All_pacbio_SMRT.fasta --output-prefix SOAP-opera2 --output-directory SOAP-opera2 Could someone help me? What is wrong? Priscila |
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From: Amandine V. <Ama...@in...> - 2018-04-03 15:00:13
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Hi, I have a question about OPERA-LG. Is it possible that in addition to scaffolding, OPERA made changes in the sequence? Because I found differences between my sequence before and after OPERA, but I thought that OPERA was only linking my contigs with some N ... The problem is that when I run a BUSCO on my assembly before OPERA and after OPERA, I lose genes after OPERA. Have you ever seen this? OPERA makes changes in the sequence? How to avoid that? Best, Amandine |
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From: Amandine V. <Ama...@in...> - 2018-03-08 08:45:02
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Hi, I found the solution to my problem, it was the version of blasr I was using. This is not the first time I have a problem with this tool. I was using blasr version 5.3 which takes two "-" for the options. However, OPERA launches blasr with one dash for the options, but no blasr error is displayed. It was only by launching the blasr command of OPERA "by hand" that I realized it. Now I use blasr version 1.3 and OPERA works very well, because the old versions of blasr use one dash for the options. I advise you to check the version of blasr and launch the blasr command with one or two dashes depending on the version. Best, Amandine De : Amandine Velt Envoyé : mercredi 28 février 2018 10:34 À : 'ope...@li...' <ope...@li...> Objet : Error with OPERA-LG Hi, When I launch OPERA-LG, I have an error : [bwa_aln_core] 121110528 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 17.84 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 121227290 sequences have been processed. [main] Version: 0.7.15-r1142-dirty [main] CMD: bwa aln -t 30 VV_12X_embl_102_Scaffolds.fasta - [main] Real time: 1452.929 sec; CPU: 21372.185 sec [E::hts_open_format] fail to open file 'temporarySam' [bam_sort_core] fail to open 'temporarySam': No such file or directory [bam_sort] Note the <out.prefix> argument has been replaced by -T/-o options [bwa_aln_core] convert to sequence coordinate... 1.46 sec [bwa_aln_core] refine gapped alignments... 0.29 sec [bwa_aln_core] print alignments... PREPROCESS: Fasta format is recognized [Wed Feb 28 09:42:33 2018] Building bwa index... bwa index -p VV_12X_embl_102_Scaffolds.fasta /path_to/ contigs.fasta [Wed Feb 28 09:49:57 2018] Finding the SA coordinates of the reads using BWA aln... [Wed Feb 28 10:14:10 2018] Generate alignments of reads using bwa sampe... bwa samse -n 1 VV_12X_embl_102_Scaffolds.fasta read.sai - | grep '\(^@\|XT:A:U\)' | samtools view -S -h -b -F 0x4 - | samtools sort -@ 20 -no - temporarySam > mapping_files.bam Mapping long-reads using blasr... blasr -nproc 16 -m 1 -minMatch 5 -bestn 10 -noSplitSubreads -advanceExactMatches 1 -nCandidates 1 -maxAnchorsPerPosition 1 -sdpTupleSize 7 /path_to/pacbio_corrected_reads.fasta /path_to/contigs.fasta | cut -d ' ' -f1-5,7-12 | sed 's/ /\t/g' > mapping_files.map Sorting mapping results... sort -k1,1 -k9,9g mapping_files.map > mapping_files.map.sort Analyzing sorted results... Argument "have" isn't numeric in numeric lt (<) at /path_to/OPERA-long-read.pl line 537, <MAP> line 205. Argument "overlap" isn't numeric in numeric lt (<) at /path_to/OPERA-long-read.pl line 537, <MAP> line 207. Argument "Tesler" isn't numeric in numeric lt (<) at /path_to/OPERA-long-read.pl line 537, <MAP> line 236. Use of uninitialized value $data[9] in join or string at /path_to/OPERA-long-read.pl line 538, <MAP> line 236. Extracting linking information... i2 1000 2000 i5 15000 40000 i3 2000 5000 i4 5000 15000 i0 -200 300 i1 300 1000 Repeat detection... /path_to/filter_conflicting_edge.pl pairedEdges_i0 contig_length.dat 100 2 Illegal division by zero at /path_to/filter_conflicting_edge.pl line 93. readline() on closed filehandle FILE at /path_to/OPERA-long-read.pl line 250. rm anchor_contig_info.dat contig_length.dat filtered_edges.dat filtered_edges_cov.dat *.sai rm: cannot remove `anchor_contig_info.dat': No such file or directory mv mapping_files.bam mapping_files-with-repeat.bam /path_to/filter_repeat.pl mapping_files-with-repeat.bam repeat.dat | samtools view - -h -S -b > mapping_files.bam rm mapping_files-with-repeat.bam /path_to/OPERA-LG config > log Analyzing 1 library: mapping_files.bam min library mean : 0 minimum contig length is 500 Current library: 1 out of 7 Analyzing file: pairedEdges_no_repeat_i0 Analyzing file: pairedEdges_no_repeat_i1 Analyzing file: pairedEdges_no_repeat_i2 Analyzing file: pairedEdges_no_repeat_i3 Analyzing file: pairedEdges_no_repeat_i4 Analyzing file: pairedEdges_no_repeat_i5 ln -s results/scaffoldSeq.fasta scaffoldSeq.fasta Out of the 5 runs I launched, only one worked without error. Here an example of my command : perl /path_to/OPERA-long-read.pl --contig-file /path_to/contigs.fasta --kmer 18 \ --illumina-read1 /path_to/Illumina.1.fasta --illumina-read2 /path_to/Illumina.2.fasta \ --long-read-file /path_to/pacbio_corrected_reads.fasta --num-of-processors 16 --output-prefix mapping_files \ --output-directory /path_to/OPERA_LG_output/ Have you an idea about this ? Best, Amandine |
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From: Amandine V. <Ama...@in...> - 2018-02-28 09:34:07
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Hi, When I launch OPERA-LG, I have an error : [bwa_aln_core] 121110528 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 17.84 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 121227290 sequences have been processed. [main] Version: 0.7.15-r1142-dirty [main] CMD: bwa aln -t 30 VV_12X_embl_102_Scaffolds.fasta - [main] Real time: 1452.929 sec; CPU: 21372.185 sec [E::hts_open_format] fail to open file 'temporarySam' [bam_sort_core] fail to open 'temporarySam': No such file or directory [bam_sort] Note the <out.prefix> argument has been replaced by -T/-o options [bwa_aln_core] convert to sequence coordinate... 1.46 sec [bwa_aln_core] refine gapped alignments... 0.29 sec [bwa_aln_core] print alignments... PREPROCESS: Fasta format is recognized [Wed Feb 28 09:42:33 2018] Building bwa index... bwa index -p VV_12X_embl_102_Scaffolds.fasta /path_to/ contigs.fasta [Wed Feb 28 09:49:57 2018] Finding the SA coordinates of the reads using BWA aln... [Wed Feb 28 10:14:10 2018] Generate alignments of reads using bwa sampe... bwa samse -n 1 VV_12X_embl_102_Scaffolds.fasta read.sai - | grep '\(^@\|XT:A:U\)' | samtools view -S -h -b -F 0x4 - | samtools sort -@ 20 -no - temporarySam > mapping_files.bam Mapping long-reads using blasr... blasr -nproc 16 -m 1 -minMatch 5 -bestn 10 -noSplitSubreads -advanceExactMatches 1 -nCandidates 1 -maxAnchorsPerPosition 1 -sdpTupleSize 7 /path_to/pacbio_corrected_reads.fasta /path_to/contigs.fasta | cut -d ' ' -f1-5,7-12 | sed 's/ /\t/g' > mapping_files.map Sorting mapping results... sort -k1,1 -k9,9g mapping_files.map > mapping_files.map.sort Analyzing sorted results... Argument "have" isn't numeric in numeric lt (<) at /path_to/OPERA-long-read.pl line 537, <MAP> line 205. Argument "overlap" isn't numeric in numeric lt (<) at /path_to/OPERA-long-read.pl line 537, <MAP> line 207. Argument "Tesler" isn't numeric in numeric lt (<) at /path_to/OPERA-long-read.pl line 537, <MAP> line 236. Use of uninitialized value $data[9] in join or string at /path_to/OPERA-long-read.pl line 538, <MAP> line 236. Extracting linking information... i2 1000 2000 i5 15000 40000 i3 2000 5000 i4 5000 15000 i0 -200 300 i1 300 1000 Repeat detection... /path_to/filter_conflicting_edge.pl pairedEdges_i0 contig_length.dat 100 2 Illegal division by zero at /path_to/filter_conflicting_edge.pl line 93. readline() on closed filehandle FILE at /path_to/OPERA-long-read.pl line 250. rm anchor_contig_info.dat contig_length.dat filtered_edges.dat filtered_edges_cov.dat *.sai rm: cannot remove `anchor_contig_info.dat': No such file or directory mv mapping_files.bam mapping_files-with-repeat.bam /path_to/filter_repeat.pl mapping_files-with-repeat.bam repeat.dat | samtools view - -h -S -b > mapping_files.bam rm mapping_files-with-repeat.bam /path_to/OPERA-LG config > log Analyzing 1 library: mapping_files.bam min library mean : 0 minimum contig length is 500 Current library: 1 out of 7 Analyzing file: pairedEdges_no_repeat_i0 Analyzing file: pairedEdges_no_repeat_i1 Analyzing file: pairedEdges_no_repeat_i2 Analyzing file: pairedEdges_no_repeat_i3 Analyzing file: pairedEdges_no_repeat_i4 Analyzing file: pairedEdges_no_repeat_i5 ln -s results/scaffoldSeq.fasta scaffoldSeq.fasta Out of the 5 runs I launched, only one worked without error. Here an example of my command : perl /path_to/OPERA-long-read.pl --contig-file /path_to/contigs.fasta --kmer 18 \ --illumina-read1 /path_to/Illumina.1.fasta --illumina-read2 /path_to/Illumina.2.fasta \ --long-read-file /path_to/pacbio_corrected_reads.fasta --num-of-processors 16 --output-prefix mapping_files \ --output-directory /path_to/OPERA_LG_output/ Have you an idea about this ? Best, Amandine |
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From: Abbott, J. <j.a...@im...> - 2017-12-05 11:24:15
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Hello, I've a couple of queries relating to running opera-LG on a genome I've been working on. Firstly, we have some 5kb and 2kb libraries which I believe were sequenced using the jumping library protocols. The reads aligned using bwa mem show the correct insert size, but are orientated 'RF' according picard's CollectInsertSizeMetrics. It seems opera has a problem with this however, reporting: > ERROR: The orientation of reads is not "in", "out", neither "forward", > Opera could not handle such orientation. Please check the mapping > files. From what I can see mate-pair libraries should be supported - is there anything I can do to make these acceptable to opera? The initial bam files included a large number of short-insert pairs in FR orientation in addition to the correct RF pairs, so I've tried removing the reads with short inserts from the bam files in case those were confusing things but with no effect. Secondly, the wiki states that blasr versions of 1.3.1 or lower only are supported, however since the blasr github repo is not tagged with versions and fixed releases do not seem to be available, tracking down an appropriate version does not look straightforward. Is the reason for the required version the command line changes from '-' to '--' for arguments, or is there more to it than that? Best Regards James -- Dr. James Abbott Lead Bioinformatician Bioinformatics Data Science Group Imperial College, London |
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From: Edi S. <edi...@gm...> - 2016-12-06 05:38:44
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Hi, I am interested to try your OPERA-long-reads to scaffold contigs using both short and long reads. But I am currently encountering some problem while running the program. I tried to run the test dataset from your website, but it seems that I could not get the expected results. Copied below is the outcome of the run: perl ./bin/OPERA-long-read.pl --blasr > /home/andrew/bioinformatics/blasr_install/blasr/ --opera > /home/andrew/bioinformatics/OPERA-LG_v2.0.6/bin/ --contig-file > /home/andrew/bioinformatics/OPERA-LG_v2.0.6/test_dataset_long_reads/contigs.fa > --illumina-read1 > /home/andrew/bioinformatics/OPERA-LG_v2.0.6/test_dataset_long_reads/illumina_1.fastq.gz > --illumina-read2 > /home/andrew/bioinformatics/OPERA-LG_v2.0.6/test_dataset_long_reads/illumina_2.fastq.gz > --long-read-file > /home/andrew/bioinformatics/OPERA-LG_v2.0.6/test_dataset_long_reads/nanopore.fa > --output-prefix opera-lr --output-directory RESULTS --num-of-processors 15 > > log_test_dataset.txt mkdir RESULTS/ perl /home/andrew/bioinformatics/OPERA-LG_v2.0.6/bin//preprocess_reads.pl > --map-tool bwa --contig > /home/andrew/bioinformatics/OPERA-LG_v2.0.6/test_dataset_long_reads/contigs.fa > --illumina-read1 > /home/andrew/bioinformatics/OPERA-LG_v2.0.6/test_dataset_long_reads/illumina_1.fastq.gz > --illumina-read2 > /home/andrew/bioinformatics/OPERA-LG_v2.0.6/test_dataset_long_reads/illumina_2.fastq.gz > --out opera-lr.bam [bwa_index] Pack FASTA... 0.35 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 7.60 seconds elapse. [bwa_index] Update BWT... 0.16 sec [bwa_index] Pack forward-only FASTA... 0.25 sec [bwa_index] Construct SA from BWT and Occ... 3.98 sec [main] Version: 0.7.5a-r405 [main] CMD: bwa index -p contigs.fa > /home/andrew/bioinformatics/OPERA-LG_v2.0.6/test_dataset_long_reads/contigs.fa [main] Real time: 12.834 sec; CPU: 12.347 sec [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwa_aln_core] calculate SA coordinate... 1675.24 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 251894 sequences have been processed. [main] Version: 0.7.5a-r405 [main] CMD: bwa aln -t 30 contigs.fa - [main] Real time: 84.121 sec; CPU: 1676.439 sec [E::hts_open_format] fail to open file 'temporarySam' [bam_sort_core] fail to open 'temporarySam': No such file or directory [bam_sort] Note the <out.prefix> argument has been replaced by -T/-o options [bwa_aln_core] convert to sequence coordinate... 0.73 sec [bwa_aln_core] refine gapped alignments... 0.96 sec [bwa_aln_core] print alignments... PREPROCESS: Fastq format is recognized [Mon Dec 5 23:28:39 2016] Building bwa index... bwa index -p contigs.fa > /home/andrew/bioinformatics/OPERA-LG_v2.0.6/test_dataset_long_reads/contigs.fa [Mon Dec 5 23:28:52 2016] Finding the SA coordinates of the reads using > BWA aln... [Mon Dec 5 23:30:16 2016] Generate alignments of reads using bwa sampe... bwa samse -n 1 contigs.fa read.sai - | grep '\(^@\|XT:A:U\)' | samtools > view -S -h -b -F 0x4 - | samtools sort -@ 20 -no - temporarySam > > opera-lr.bam [Mon Dec 5 23:30:19 2016] Preprocessing done! /home/andrew/bioinformatics/blasr_install/blasr/blasr -nproc 15 -m 1 > -minMatch 5 -bestn 10 -noSplitSubreads -advanceExactMatches 1 -nCandidates > 1 -maxAnchorsPerPosition 1 -sdpTupleSize 7 > /home/andrew/bioinformatics/OPERA-LG_v2.0.6/test_dataset_long_reads/nanopore.fa > /home/andrew/bioinformatics/OPERA-LG_v2.0.6/test_dataset_long_reads/contigs.fa > | cut -d ' ' -f1-5,7-12 | sed 's/ /\t/g' > opera-lr.map sort -k1,1 -k9,9g opera-lr.map > opera-lr.map.sort Argument "have" isn't numeric in numeric lt (<) at ./bin/OPERA-long-read.pl > line 537, <MAP> line 204. Argument "overlap" isn't numeric in numeric lt (<) at > ./bin/OPERA-long-read.pl line 537, <MAP> line 206. Argument "Tesler" isn't numeric in numeric lt (<) at > ./bin/OPERA-long-read.pl line 537, <MAP> line 234. Use of uninitialized value $data[9] in join or string at > ./bin/OPERA-long-read.pl line 538, <MAP> line 234. i3 2000 5000 i0 -200 300 i4 5000 15000 i5 15000 40000 i1 300 1000 i2 1000 2000 /home/andrew/bioinformatics/OPERA-LG_v2.0.6/bin//filter_conflicting_edge.pl > pairedEdges_i0 contig_length.dat 100 2 Illegal division by zero at > /home/andrew/bioinformatics/OPERA-LG_v2.0.6/bin// > filter_conflicting_edge.pl line 93. readline() on closed filehandle FILE at ./bin/OPERA-long-read.pl line 250. rm anchor_contig_info.dat contig_length.dat filtered_edges.dat > filtered_edges_cov.dat *.sai rm: cannot remove ‘anchor_contig_info.dat’: No such file or directory rm: cannot remove ‘*.sai’: No such file or directory mv opera-lr.bam opera-lr-with-repeat.bam /home/andrew/bioinformatics/OPERA-LG_v2.0.6/bin//filter_repeat.pl > opera-lr-with-repeat.bam repeat.dat | samtools view - -h -S -b > > opera-lr.bam rm opera-lr-with-repeat.bam /home/andrew/bioinformatics/OPERA-LG_v2.0.6/bin/OPERA-LG config > log Analyzing 1 library: opera-lr.bam min library mean : 0 minimum contig length is 500 Current library: 1 out of 7 Analyzing file: pairedEdges_no_repeat_i0 Analyzing file: pairedEdges_no_repeat_i1 Analyzing file: pairedEdges_no_repeat_i2 Analyzing file: pairedEdges_no_repeat_i3 Analyzing file: pairedEdges_no_repeat_i4 Analyzing file: pairedEdges_no_repeat_i5 ln -s results/scaffoldSeq.fasta scaffoldSeq.fasta Would you have idea on how to solve this? Thanks a lot for your help. Regards, Edi |
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From: Jianquan C. <cao...@gm...> - 2016-10-22 02:03:39
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Hello Sir, I'm running "OPERA-LG_v2.0.5/bin/preprocess_reads.pl" and have the following error: "[Fri Oct 21 16:56:44 2016] Generate alignments of reads using bwa sampe... bwa samse -n 1 ./assembly.fasta ./read.sai - | grep '\(^@\|XT:A:U\)' | samtools view -S -h -b -F 0x4 - | samtools sort -@ 20 -no - ./temporarySam > ./map.sam [E::hts_open_format] fail to open file './temporarySam' [bam_sort_core] fail to open './temporarySam': No such file or directory [bam_sort] Note the <out.prefix> argument has been replaced by -T/-o options" I guess that this problem is probably caused by bwa or samtools, but I'm not sure. I'm using samtools Version: 1.3.1 and bwa Version: 0.7.12-r1039. Any idea how to get over it? Which versions of samtools and bwa are preferred? Thanks Quan |
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From: sangramjit b. <off...@gm...> - 2016-09-13 04:54:33
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Hello Sir, I am trying to run OPERA-LG with bacterial data (short reads: Illumina PE and long reads: PacBio) like more like a test run. Now the contig were assembled using velvet from PE data. Now I am trying to scaffold them (38 contig) and resolve the gaps using pacbio reads using OPERA-LG. And I just encountered this error which is becoming a little difficult to decipher for me :( .... mkdir opera_test/RESULTS/ Mapping short-reads using bowtie... preprocess_reads.pl --map-tool bowtie --contig /home/bioinfo15.corp/Tools/OPERA-LG_v2.0.5/bin/opera_test/data/velvet_contigs.fasta --illumina-read1 /home/bioinfo15.corp/Tools/OPERA-LG_v2.0.5/bin/opera_test/data/illumina_shrt_rds_1.fastq --illumina-read2 /home/bioinfo15.corp/Tools/OPERA-LG_v2.0.5/bin/opera_test/data/illumina_shrt_rds_2.fastq --out opera-lr.bam PREPROCESS: Fastq format is recognized [Mon Sep 12 17:45:33 2016] Building bowtie index... [Mon Sep 12 17:45:36 2016] Mapping reads using bowtie... [Mon Sep 12 18:04:38 2016] Preprocessing done! Mapping long-reads using blasr... blasr --nproc 6 -m 1 --minMatch 5 --bestn 10 --noSplitSubreads --advanceExactMatches 1 --nCandidates 1 --maxAnchorsPerPosition 1 --sdpTupleSize 7 /home/bioinfo15.corp/Tools/OPERA-LG_v2.0.5/bin/opera_test/data/pacbio_lng_rds.fastq /home/bioinfo15.corp/Tools/OPERA-LG_v2.0.5/bin/opera_test/data/velvet_contigs.fasta | cut -d ' ' -f1-5,7-12 | sed 's/ /\t/g' > opera-lr.map [INFO] 2016-09-12T18:04:38 [blasr] started. Warning: resetting nCandidates to nBest 10 [INFO] 2016-09-12T19:02:07 [blasr] ended. Sorting mapping results... sort -k1,1 -k9,9g opera-lr.map > opera-lr.map.sort Analyzing sorted results... Extracting linking information... i1 300 1000 i3 2000 5000 i5 15000 40000 i0 -200 300 i2 1000 2000 i4 5000 15000 Repeat detection... filter_conflicting_edge.pl pairedEdges_i0 contig_length.dat 100 2 *** 13 edges filtered from 21 (0.619047619047619) rm anchor_contig_info.dat contig_length.dat filtered_edges.dat filtered_edges_cov.dat *.sai rm: cannot remove `*.sai': No such file or directory mv opera-lr.bam opera-lr-with-repeat.bam filter_repeat.pl opera-lr-with-repeat.bam repeat.dat | samtools view - -h -S -b > opera-lr.bam [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [main_samview] fail to read the header from "opera-lr-with-repeat.bam". [samopen] no @SQ lines in the header. [sam_read1] missing header? Abort! rm opera-lr-with-repeat.bam OPERA-LG config > log [bam_header_read] EOF marker is absent. The input is probably truncated. Analyzing 1 library: opera-lr.bam [bam_header_read] EOF marker is absent. The input is probably truncated. min library mean : 0 minimum contig length is 500 Current library: 1 out of 7 Analyzing file: pairedEdges_no_repeat_i0 Analyzing file: pairedEdges_no_repeat_i1 Analyzing file: pairedEdges_no_repeat_i2 Analyzing file: pairedEdges_no_repeat_i3 Analyzing file: pairedEdges_no_repeat_i4 Analyzing file: pairedEdges_no_repeat_i5 ln -s results/scaffoldSeq.fasta scaffoldSeq.fasta I would appreciate any kind of suggestion and thanks in advance for the help. -- With best regards Sangramjit Basu |
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From: Sean S. <sea...@ic...> - 2016-06-09 19:29:59
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Hi! I have just finished using Opera-LG to scaffold my assembly and would like to generate an AGP file. Does Opera LG create this file, or do you have any plans to add this feature to the software? |
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From: song g. <gao...@gm...> - 2014-09-18 00:00:22
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Dear Jean-Paul, Thank you for your interests in using Opera. For the cluster_threshold, by default it will be 5, which should be a good value for Illumina/Solexa data, since their coverage is high enough (for instance, >40X for 300bp library or >2X for 10000bp library) in most cases. Opera will also automatically increase the threshold if needed during calculation. The cluster_threshold should be linked to each library. It might be useful if some of your library has such low coverage (e.g. less than 5X coverage for a 300bp library) that smaller threshold (such as 3 or 2) should be used. In most cases, you can just use the default value (5) to use Opera. Hope that will help. Please let me know if there are any other questions. Sincerely Song Gao On Tue, Sep 16, 2014 at 11:05 PM, Jean-Paul Bouchet < jea...@av...> wrote: > Hello, > How can we determine for the parameter "cluster_threshold" a value well > adapted to a given set of data ? > In test_dataset/multiLib.config file, this parameter is linked to each > library, but in the file test_dataset/advanced.config this parameter is > described as determining the scaffolding and not linked to libraries. Is > it useful to assign a value to this parameter for each library ? If yes, > on which criteria ? > Thanks in advance for your answers. > Best regards, > > Jean-Paul Bouchet > Institut National de la Recherche Agronomique - Centre de Provence, > Alpes, Côte d'Azur > UR 1052 <http://w3.avignon.inra.fr/gafl/en> - Génétique et Amélioration > des Fruits et Légumes > Domaine Saint-Maurice - CS 60094 - F-84143 Montfavet cedex - France > E-mail : <mailto:Jea...@av...> > Phone : +33-(0)4-3272-2723 - Fax : +33-(0)4-3272-2702 > > > > ------------------------------------------------------------------------------ > Want excitement? > Manually upgrade your production database. > When you want reliability, choose Perforce. > Perforce version control. Predictably reliable. > > http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk > _______________________________________________ > Operasf-updates mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/operasf-updates > -- Song GAO Post-doc Fellow of EMBL Australia Tel: (61)-0416 452 922 Email: gao...@gm... South Australian Health & Medical Research Institute North Terrace, Adelaide SA 5000 Australia |
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From: Jean-Paul B. <jea...@av...> - 2014-09-16 14:00:13
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Hello, How can we determine for the parameter "cluster_threshold" a value well adapted to a given set of data ? In test_dataset/multiLib.config file, this parameter is linked to each library, but in the file test_dataset/advanced.config this parameter is described as determining the scaffolding and not linked to libraries. Is it useful to assign a value to this parameter for each library ? If yes, on which criteria ? Thanks in advance for your answers. Best regards, Jean-Paul Bouchet Institut National de la Recherche Agronomique - Centre de Provence, Alpes, Côte d'Azur UR 1052 <http://w3.avignon.inra.fr/gafl/en> - Génétique et Amélioration des Fruits et Légumes Domaine Saint-Maurice - CS 60094 - F-84143 Montfavet cedex - France E-mail : <mailto:Jea...@av...> Phone : +33-(0)4-3272-2723 - Fax : +33-(0)4-3272-2702 |
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From: song g. <gao...@gm...> - 2011-07-14 01:12:32
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This is a testing email for opera updates list. Sorry for the inconvinience and thank you for subscribing this list. Sincerely Song Gao |
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From: song g. <gao...@gm...> - 2011-07-14 01:09:28
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This is a testing email for opera updates list. Sorry for the inconvinience and thank you for subscribing this list. Sincerely Song Gao |
