circlator.assembly.Error

[fengyuchengdu]

Hi, there I tested circlator with test command and it worked perfect. However, when I entered the following commands circlator all --verbose --threads 8 --merge_min_id 85 --merge_breaklen 1000 96200minion_mc10.fasta minion_trimmedReads.fasta ./spades/ it stopped at somewhere near "Making ACT files from 04.merge.merge.iter.2.merged.fasta"

please see the detailed information below

_____ Checking external programs __ Circlator version: 1.5.1

External dependencies: bwa 0.7.15 /home/linuxbrew/.linuxbrew/bin/bwa canu 1.5 /home/linuxbrew/.linuxbrew/bin/canu nucmer 3.1 /home/linuxbrew/.linuxbrew/bin/nucmer prodigal 2.6.2 /home/linuxbrew/.linuxbrew/bin/prodigal samtools 1.4.1 /home/linuxbrew/.linuxbrew/bin/samtools WARNING: SPAdes version 3.10.1 is being used. It will work, but better results are usually obtained from Circlator using SPAdes version 3.7.1. Although 3.7.1 is not the latest version, we recommend it for Circlator. spades 3.10.1 /home/linuxbrew/.linuxbrew/bin/spades.py

Python version: 3.6.1 (default, Apr 8 2017, 07:19:26) [GCC 4.8.4]

Python dependencies: openpyxl 2.4.1 /home/linuxbrew/.linuxbrew/Cellar/circlator/1.5.1/libexec/lib/python3.6/site-packages/openpyxl/init.py pyfastaq 3.14.0 /home/linuxbrew/.linuxbrew/Cellar/circlator/1.5.1/libexec/lib/python3.6/site-packages/pyfastaq/init.py pymummer 0.10.1 /home/linuxbrew/.linuxbrew/Cellar/circlator/1.5.1/libexec/lib/python3.6/site-packages/pymummer/init.py pysam 0.8.4 /home/linuxbrew/.linuxbrew/Cellar/circlator/1.5.1/libexec/lib/python3.6/site-packages/pysam/init.py WARNING: SPAdes version 3.10.1 is being used. It will work, but better results are usually obtained from Circlator using SPAdes version 3.7.1. Although 3.7.1 is not the latest version, we recommend it for Circlator. __ Running mapreads _ samtools 1.4.1 /home/linuxbrew/.linuxbrew/bin/samtools bwa 0.7.15 /home/linuxbrew/.linuxbrew/bin/bwa syscall: bwa index -p 01.mapreads.bam.tmp.bwa_index 00.input_assembly.fasta syscall: bwa mem -x pacbio -t 8 01.mapreads.bam.tmp.bwa_index /home/zong/Desktop/666/96200/circlator/minion_trimmedReads.fasta | samtools view -F 0x0800 -T 00.input_assembly.fasta -b -o 01.mapreads.bam.tmp.unsorted.bam - syscall: samtools sort -@ 4 -m 125M 01.mapreads.bam.tmp.unsorted.bam -o 01.mapreads.bam syscall: samtools index 01.mapreads.bam Running bam2reads __ Getting reads from BAM file /home/zong/Desktop/666/96200/circlator/spades/01.mapreads.bam Getting all reads that map to ends of contig 96200minion_mc10_1. Coords: 1-50000;5022640-5072639 Getting all reads that map to contig 96200minion_mc10_10 Getting all reads that map to contig 96200minion_mc10_11 Getting all reads that map to contig 96200minion_mc10_12 Getting all reads that map to contig 96200minion_mc10_13 Getting all reads that map to contig 96200minion_mc10_14 Getting all reads that map to contig 96200minion_mc10_15 Getting all reads that map to contig 96200minion_mc10_16 Getting all reads that map to contig 96200minion_mc10_17 Getting all reads that map to contig 96200minion_mc10_18 Getting all reads that map to contig 96200minion_mc10_19 Getting all reads that map to ends of contig 96200minion_mc10_2. Coords: 1-50000;113721-163720 Getting all reads that map to contig 96200minion_mc10_20 Getting all reads that map to contig 96200minion_mc10_21 Getting all reads that map to contig 96200minion_mc10_22 Getting all reads that map to contig 96200minion_mc10_23 Getting all reads that map to contig 96200minion_mc10_24 Getting all reads that map to contig 96200minion_mc10_25 Getting all reads that map to contig 96200minion_mc10_26 Getting all reads that map to contig 96200minion_mc10_27 Getting all reads that map to contig 96200minion_mc10_28 Getting all reads that map to contig 96200minion_mc10_29 Getting all reads that map to ends of contig 96200minion_mc10_3. Coords: 1-50000;54749-104748 Getting all reads that map to contig 96200minion_mc10_30 Getting all reads that map to contig 96200minion_mc10_31 Getting all reads that map to contig 96200minion_mc10_32 Getting all reads that map to contig 96200minion_mc10_33 Getting all reads that map to contig 96200minion_mc10_34 Getting all reads that map to contig 96200minion_mc10_35 Getting all reads that map to contig 96200minion_mc10_36 Getting all reads that map to contig 96200minion_mc10_37 Getting all reads that map to contig 96200minion_mc10_38 Getting all reads that map to contig 96200minion_mc10_4 Getting all reads that map to contig 96200minion_mc10_5 Getting all reads that map to contig 96200minion_mc10_6 Getting all reads that map to contig 96200minion_mc10_7 Getting all reads that map to contig 96200minion_mc10_8 Getting all reads that map to contig 96200minion_mc109 Getting all unmapped reads Finished getting reads. Log file: /home/zong/Desktop/666/96200/circlator/spades/02.bam2reads.log Reads file: /home/zong/Desktop/666/96200/circlator/spades/02.bam2reads.fasta __ Running assemble __ samtools 1.4.1 /home/linuxbrew/.linuxbrew/bin/samtools WARNING: SPAdes version 3.10.1 is being used. It will work, but better results are usually obtained from Circlator using SPAdes version 3.7.1. Although 3.7.1 is not the latest version, we recommend it for Circlator. spades 3.10.1 /home/linuxbrew/.linuxbrew/bin/spades.py syscall: spades.py -s /home/zong/Desktop/666/96200/circlator/spades/02.bam2reads.fasta -o /home/zong/Desktop/666/96200/circlator/spades/03.assemble.tmp.spades.127.zja_p98v -t 8 -k 127 --careful --only-assembler syscall: samtools faidx /home/zong/Desktop/666/96200/circlator/spades/03.assemble.tmp.spades.127.zja_p98v/contigs.fasta syscall: spades.py -s /home/zong/Desktop/666/96200/circlator/spades/02.bam2reads.fasta -o /home/zong/Desktop/666/96200/circlator/spades/03.assemble.tmp.spades.117.zl1gtppk -t 8 -k 117 --careful --only-assembler syscall: samtools faidx /home/zong/Desktop/666/96200/circlator/spades/03.assemble.tmp.spades.117.zl1gtppk/contigs.fasta syscall: spades.py -s /home/zong/Desktop/666/96200/circlator/spades/02.bam2reads.fasta -o /home/zong/Desktop/666/96200/circlator/spades/03.assemble.tmp.spades.107.t_iaspce -t 8 -k 107 --careful --only-assembler syscall: samtools faidx /home/zong/Desktop/666/96200/circlator/spades/03.assemble.tmp.spades.107.t_iaspce/contigs.fasta syscall: spades.py -s /home/zong/Desktop/666/96200/circlator/spades/02.bam2reads.fasta -o /home/zong/Desktop/666/96200/circlator/spades/03.assemble.tmp.spades.97.4_cfct66 -t 8 -k 97 --careful --only-assembler syscall: samtools faidx /home/zong/Desktop/666/96200/circlator/spades/03.assemble.tmp.spades.97.4_cfct66/contigs.fasta syscall: spades.py -s /home/zong/Desktop/666/96200/circlator/spades/02.bam2reads.fasta -o /home/zong/Desktop/666/96200/circlator/spades/03.assemble.tmp.spades.87.wuyfga3j -t 8 -k 87 --careful --only-assembler syscall: samtools faidx /home/zong/Desktop/666/96200/circlator/spades/03.assemble.tmp.spades.87.wuyfga3j/contigs.fasta syscall: spades.py -s /home/zong/Desktop/666/96200/circlator/spades/02.bam2reads.fasta -o /home/zong/Desktop/666/96200/circlator/spades/03.assemble.tmp.spades.77.1_sat3zg -t 8 -k 77 --careful --only-assembler syscall: samtools faidx /home/zong/Desktop/666/96200/circlator/spades/03.assemble.tmp.spades.77.1_sat3zg/contigs.fasta [assemble] kmer N50 [assemble] 77 53776 [assemble] 87 53792 [assemble] 97 37763 [assemble] 107 39658 [assemble] 117 44019 [assemble] 127 53758 [assemble] using assembly with kmer 87 ____ Running merge ____ Running command: bash run_nucmer.sh 1: PREPARING DATA 2,3: RUNNING mummer AND CREATING CLUSTERS

reading input file "p.ntref" of length 6680340

construct suffix tree for sequence of length 6680340

(maximum reference length is 536870908)

(maximum query length is 4294967295)

process 66803 characters per dot

....................................................................................................

CONSTRUCTIONTIME /home/linuxbrew/.linuxbrew/Cellar/mummer/3.23_1/mummer p.ntref 2.84

reading input file "/home/zong/Desktop/666/96200/circlator/spades/03.assemble/contigs.fasta" of length 1067392

matching query-file "/home/zong/Desktop/666/96200/circlator/spades/03.assemble/contigs.fasta"

against subject-file "p.ntref"

COMPLETETIME /home/linuxbrew/.linuxbrew/Cellar/mummer/3.23_1/mummer p.ntref 3.81

SPACE /home/linuxbrew/.linuxbrew/Cellar/mummer/3.23_1/mummer p.ntref 7.51

4: FINISHING DATA

Making ACT files from 00.input_assembly.fasta /home/zong/Desktop/666/96200/circlator/spades/03.assemble/contigs.fasta 04.merge.merge.iter.1.coords samtools 1.4.1 /home/linuxbrew/.linuxbrew/bin/samtools bwa 0.7.15 /home/linuxbrew/.linuxbrew/bin/bwa syscall: bwa index -p 04.merge.merge.iter.2.bam.tmp.bwa_index 04.merge.merge.iter.2.merged.fasta syscall: bwa mem -x pacbio -t 8 04.merge.merge.iter.2.bam.tmp.bwa_index 02.bam2reads.fasta | samtools view -F 0x0800 -T 04.merge.merge.iter.2.merged.fasta -b -o 04.merge.merge.iter.2.bam.tmp.unsorted.bam - syscall: samtools sort -@ 4 -m 125M 04.merge.merge.iter.2.bam.tmp.unsorted.bam -o 04.merge.merge.iter.2.bam syscall: samtools index 04.merge.merge.iter.2.bam samtools 1.4.1 /home/linuxbrew/.linuxbrew/bin/samtools WARNING: SPAdes version 3.10.1 is being used. It will work, but better results are usually obtained from Circlator using SPAdes version 3.7.1. Although 3.7.1 is not the latest version, we recommend it for Circlator. spades 3.10.1 /home/linuxbrew/.linuxbrew/bin/spades.py syscall: spades.py -s /home/zong/Desktop/666/96200/circlator/spades/04.merge.merge.iter.2.reads.fasta -o /home/zong/Desktop/666/96200/circlator/spades/04.merge.merge.iter.2.assembly.tmp.spades.127.4ujuu8og -t 8 -k 127 --careful --only-assembler syscall: samtools faidx /home/zong/Desktop/666/96200/circlator/spades/04.merge.merge.iter.2.assembly.tmp.spades.127.4ujuu8og/contigs.fasta syscall: spades.py -s /home/zong/Desktop/666/96200/circlator/spades/04.merge.merge.iter.2.reads.fasta -o /home/zong/Desktop/666/96200/circlator/spades/04.merge.merge.iter.2.assembly.tmp.spades.117.xprip4ey -t 8 -k 117 --careful --only-assembler syscall: samtools faidx /home/zong/Desktop/666/96200/circlator/spades/04.merge.merge.iter.2.assembly.tmp.spades.117.xprip4ey/contigs.fasta syscall: spades.py -s /home/zong/Desktop/666/96200/circlator/spades/04.merge.merge.iter.2.reads.fasta -o /home/zong/Desktop/666/96200/circlator/spades/04.merge.merge.iter.2.assembly.tmp.spades.107.nfcjenuc -t 8 -k 107 --careful --only-assembler syscall: samtools faidx /home/zong/Desktop/666/96200/circlator/spades/04.merge.merge.iter.2.assembly.tmp.spades.107.nfcjenuc/contigs.fasta syscall: spades.py -s /home/zong/Desktop/666/96200/circlator/spades/04.merge.merge.iter.2.reads.fasta -o /home/zong/Desktop/666/96200/circlator/spades/04.merge.merge.iter.2.assembly.tmp.spades.97.8ormd5qy -t 8 -k 97 --careful --only-assembler syscall: samtools faidx /home/zong/Desktop/666/96200/circlator/spades/04.merge.merge.iter.2.assembly.tmp.spades.97.8ormd5qy/contigs.fasta syscall: spades.py -s /home/zong/Desktop/666/96200/circlator/spades/04.merge.merge.iter.2.reads.fasta -o /home/zong/Desktop/666/96200/circlator/spades/04.merge.merge.iter.2.assembly.tmp.spades.87.v4phbqci -t 8 -k 87 --careful --only-assembler syscall: samtools faidx /home/zong/Desktop/666/96200/circlator/spades/04.merge.merge.iter.2.assembly.tmp.spades.87.v4phbqci/contigs.fasta syscall: spades.py -s /home/zong/Desktop/666/96200/circlator/spades/04.merge.merge.iter.2.reads.fasta -o /home/zong/Desktop/666/96200/circlator/spades/04.merge.merge.iter.2.assembly.tmp.spades.77.ljnbbsrb -t 8 -k 77 --careful --only-assembler syscall: samtools faidx /home/zong/Desktop/666/96200/circlator/spades/04.merge.merge.iter.2.assembly.tmp.spades.77.ljnbbsrb/contigs.fasta [assemble] kmer N50 [assemble] 77 55319 [assemble] 87 55381 [assemble] 97 37763 [assemble] 107 39658 [assemble] 117 53751 [assemble] 127 53758 [assemble] using assembly with kmer 87 Running command: bash run_nucmer.sh 1: PREPARING DATA 2,3: RUNNING mummer AND CREATING CLUSTERS

reading input file "p.ntref" of length 6669533

construct suffix tree for sequence of length 6669533

(maximum reference length is 536870908)

(maximum query length is 4294967295)

process 66695 characters per dot

....................................................................................................

CONSTRUCTIONTIME /home/linuxbrew/.linuxbrew/Cellar/mummer/3.23_1/mummer p.ntref 2.69

reading input file "/home/zong/Desktop/666/96200/circlator/spades/04.merge.merge.iter.2.assembly/contigs.fasta" of length 1188473

matching query-file "/home/zong/Desktop/666/96200/circlator/spades/04.merge.merge.iter.2.assembly/contigs.fasta"

against subject-file "p.ntref"

COMPLETETIME /home/linuxbrew/.linuxbrew/Cellar/mummer/3.23_1/mummer p.ntref 3.77

SPACE /home/linuxbrew/.linuxbrew/Cellar/mummer/3.23_1/mummer p.ntref 7.62

4: FINISHING DATA

Making ACT files from 04.merge.merge.iter.2.merged.fasta /home/zong/Desktop/666/96200/circlator/spades/04.merge.merge.iter.2.assembly/contigs.fasta 04.merge.merge.iter.2.coords Traceback (most recent call last): File "/home/linuxbrew/.linuxbrew/bin/circlator", line 58, in exec('circlator.tasks.' + task + '.run()') File "", line 1, in File "/home/linuxbrew/.linuxbrew/Cellar/circlator/1.5.1/libexec/lib/python3.6/site-packages/circlator/tasks/all.py", line 212, in run m.run() File "/home/linuxbrew/.linuxbrew/Cellar/circlator/1.5.1/libexec/lib/python3.6/site-packages/circlator/merge.py", line 825, in run self._circularise_contigs(nucmer_hits) File "/home/linuxbrew/.linuxbrew/Cellar/circlator/1.5.1/libexec/lib/python3.6/site-packages/circlator/merge.py", line 351, in _circularise_contigs called_as_circular_by_spades = self.reassembly.circular_contigs() File "/home/linuxbrew/.linuxbrew/Cellar/circlator/1.5.1/libexec/lib/python3.6/site-packages/circlator/assembly.py", line 183, in circular_contigs return self._circular_contigs_from_spades_after_3_6_1(self.assembly_graph_fastg, self.contigs_paths) File "/home/linuxbrew/.linuxbrew/Cellar/circlator/1.5.1/libexec/lib/python3.6/site-packages/circlator/assembly.py", line 129, in _circular_contigs_from_spades_after_3_6_1 paths_dict = Assembly._spades_contigs_paths_to_dict(contigs_paths) File "/home/linuxbrew/.linuxbrew/Cellar/circlator/1.5.1/libexec/lib/python3.6/site-packages/circlator/assembly.py", line 106, in _spades_contigs_paths_to_dict raise Error('Error loading info from SPAdes contigs path file ' + filename) circlator.assembly.Error: Error loading info from SPAdes contigs path file /home/zong/Desktop/666/96200/circlator/spades/04.merge.merge.iter.2.assembly/contigs.paths

Could someone help me to solve this? Thanks so much.

Circlator version: 1.5.1

External dependencies: bwa 0.7.15 /home/linuxbrew/.linuxbrew/bin/bwa canu 1.5 /home/linuxbrew/.linuxbrew/bin/canu nucmer 3.1 /home/linuxbrew/.linuxbrew/bin/nucmer prodigal 2.6.2 /home/linuxbrew/.linuxbrew/bin/prodigal samtools 1.4.1 /home/linuxbrew/.linuxbrew/bin/samtools WARNING: SPAdes version 3.10.1 is being used. It will work, but better results are usually obtained from Circlator using SPAdes version 3.7.1. Although 3.7.1 is not the latest version, we recommend it for Circlator. spades 3.10.1 /home/linuxbrew/.linuxbrew/bin/spades.py

Python version: 3.6.1 (default, Apr 8 2017, 07:19:26) [GCC 4.8.4]

Python dependencies: openpyxl 2.4.1 /home/linuxbrew/.linuxbrew/Cellar/circlator/1.5.1/libexec/lib/python3.6/site-packages/openpyxl/init.py pyfastaq 3.14.0 /home/linuxbrew/.linuxbrew/Cellar/circlator/1.5.1/libexec/lib/python3.6/site-packages/pyfastaq/init.py pymummer 0.10.1 /home/linuxbrew/.linuxbrew/Cellar/circlator/1.5.1/libexec/lib/python3.6/site-packages/pymummer/init.py pysam 0.8.4 /home/linuxbrew/.linuxbrew/Cellar/circlator/1.5.1/libexec/lib/python3.6/site-packages/pysam/init.py

[martinghunt]

Could you copy + paste the contents of /home/zong/Desktop/666/96200/circlator/spades/04.merge.merge.iter.2.assembly/contigs.paths here please?

[fengyuchengdu]

it seems like I didn't save that folder, anyway I ran it with canu as the assembler and it went well without any error. I checked the spade log file and found it saying the reads I used were at poor quality and failed the reads error correction. Maybe this was the reason? Thanks