gavinmdouglas
commented
2 years ago I'm not familiar with the matam output specifically, but you could take a look here to see if these answers help: https://github.com/picrust/picrust2/wiki/Frequently-Asked-Questions#why-am-i-getting-the-error-stopping---all-x-input-sequences-aligned-poorly-to-reference-sequences
Cheers,
Gavin
Dear All,
I am trying to reconstruct 16S rRNA gene sequences from metagenome and then use those predicted 16S to find functional profiling using picrust2. So I followed the following steps
matam_assembly.py -d SILVA_128_SSURef_NR95 -i read.fastq --cpu 5 --max_memory 10000 -v --perform_taxonomic_assignment -o output
`INFO - === MATAM assembly === INFO - CMD: /nfs/home/users/monica188/cohort/CRC/shotgun/filtering/matam/scripts/matam_assembly.py --verbose --cpu 25 --max_memory 10000 --best 10 --evalue 1.00e-05 --score_threshold 0.90 --coverage_threshold 0 --min_identity 1.00 --min_overlap_length 50 --min_read_node 1 --min_overlap_edge 1 --quorum 0.51 --read_correction auto --contig_coverage_threshold 20 --min_scaffold_length 500 --perform_taxonomic_assignment --training_model 16srrna --rdp_cutoff 0.8 --outdir /nfs/home/users/monica188/cohort/CRC/shotgun/filtering/matam/EXX478962.fastq_output --ref_db /nfs/home/users/monica188/cohort/CRC/shotgun/filtering/matam/SILVA_128_SSURef_NR95 --inputfastq /nfs/home/users/monica188/cohort/CRC/shotgun/filtering/matam/EXX478962.fastq.fastq INFO - === MATAM assembly === INFO - CMD: /nfs/home/users/monica188/cohort/CRC/shotgun/filtering/matam/scripts/matam_assembly.py --verbose --cpu 25 --max_memory 10000 --best 10 --evalue 1.00e-05 --score_threshold 0.90 --coverage_threshold 0 --min_identity 1.00 --min_overlap_length 50 --min_read_node 1 --min_overlap_edge 1 --quorum 0.51 --read_correction auto --contig_coverage_threshold 20 --min_scaffold_length 500 --perform_taxonomic_assignment --training_model 16srrna --rdp_cutoff 0.8 --outdir /nfs/home/users/monica188/cohort/CRC/shotgun/filtering/matam/EXX478962.fastq_output --ref_db /nfs/home/users/monica188/cohort/CRC/shotgun/filtering/matam/SILVA_128_SSURef_NR95 --inputfastq /nfs/home/users/monica188/cohort/CRC/shotgun/filtering/matam/EXX478962.fastq INFO - === Input === INFO - Input file: /nfs/home/users/monica188/cohort/CRC/shotgun/filtering/matam/EXX478962_.fastq INFO - Input file reads nb: 19620360 reads INFO - === Reads mapping against ref db ===
Program: SortMeRNA version 2.1b, 03/03/2016 Copyright: 2012-16 Bonsai Bioinformatics Research Group: LIFL, University Lille 1, CNRS UMR 8022, INRIA Nord-Europe 2014-16 Knight Lab: Department of Pediatrics, UCSD, La Jolla, Disclaimer: SortMeRNA comes with ABSOLUTELY NO WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. Contact: Evguenia Kopylova, jenya.kopylov@gmail.com Laurent Noé, laurent.noe@lifl.fr Hélène Touzet, helene.touzet@lifl.fr
Computing read file statistics ... done [9.74 sec] size of reads file: 3882561748 bytes partial section(s) to be executed: 4 of size 1073741824 bytes Parameters summary: Number of seeds = 2 Edges = 4 (as integer) SW match = 2 SW mismatch = -3 SW gap open penalty = 5 SW gap extend penalty = 2 SW ambiguous nucleotide = -3 SQ tags are not output Number of threads = 25
�[4mBegin mmap reads section # 1�[0m: Time to mmap reads and set up pointers [1.50 sec]
Begin analysis of: �[0;34m/nfs/home/users/monica188/cohort/CRC/shotgun/filtering/matam/SILVA_128_SSURef_NR95.clustered.fasta�[0m Seed length = 18 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3 Gumbel lambda = 0.605719 Gumbel K = 0.333508 Minimal SW score based on E-value = 82 Loading index part 1/1 ... done [4.45 sec] Begin index search ... done [28.62 sec] Freeing index ... done [0.80 sec] Total number of reads mapped (incl. all reads file sections searched): 10424 Writing alignments ... done [2.92 sec] Writing aligned FASTA/FASTQ ... done [0.08 sec]
�[4mBegin mmap reads section # 2�[0m: Time to mmap reads and set up pointers [1.47 sec]
Begin analysis of: �[0;34m/nfs/home/users/monica188/cohort/CRC/shotgun/filtering/matam/SILVA_128_SSURef_NR95.clustered.fasta�[0m Loading index part 1/1 ... done [5.70 sec] Begin index search ... done [27.37 sec] Freeing index ... done [0.74 sec] Total number of reads mapped (incl. all reads file sections searched): 20370 Writing alignments ... done [2.87 sec] Writing aligned FASTA/FASTQ ... done [0.08 sec]
�[4mBegin mmap reads section # 3�[0m: Time to mmap reads and set up pointers [1.46 sec]
Begin analysis of: �[0;34m/nfs/home/users/monica188/cohort/CRC/shotgun/filtering/matam/SILVA_128_SSURef_NR95.clustered.fasta�[0m Loading index part 1/1 ... done [5.40 sec] Begin index search ... done [27.61 sec] Freeing index ... done [0.71 sec] Total number of reads mapped (incl. all reads file sections searched): 30578 Writing alignments ... done [2.89 sec] Writing aligned FASTA/FASTQ ... done [0.08 sec]
�[4mBegin mmap reads section # 4�[0m: Time to mmap reads and set up pointers [0.90 sec]
Begin analysis of: �[0;34m/nfs/home/users/monica188/cohort/CRC/shotgun/filtering/matam/SILVA_128_SSURef_NR95.clustered.fasta�[0m Loading index part 1/1 ... done [5.40 sec] Begin index search ... done [16.86 sec] Freeing index ... done [0.73 sec] Total number of reads mapped (incl. all reads file sections searched): 36586 Writing alignments ... done [2.53 sec] Writing aligned FASTA/FASTQ ... done [0.05 sec] INFO - Reads mapping completed in 151.7875 seconds wall time INFO - Identified as marker: 36586 / 19620360 reads (0.19%) INFO - === Alignment filtering === INFO - Good alignments filtering completed in 1.8397 seconds wall time INFO - === Overlap-graph building ===
PARAM: References: /nfs/home/users/monica188/cohort/CRC/shotgun/filtering/matam/SILVA_128_SSURefNR95.clustered.fasta PARAM: Sam file: /nfs/home/users/monica188/cohort/CRC/shotgun/filtering/matam/EXX478962.fastqoutput/workdir/EXX478962.sortmerna_vs_SILVA_128_SSURef_NR95_b10_m10.scr_filt_geo90pct.sam PARAM: Output basename: /nfs/home/users/monica188/cohort/CRC/shotgun/filtering/matam/EXX478962.fastqoutput/workdir/EXX478962.sortmerna_vs_SILVA_128_SSURef_NR95_b10_m10.scr_filt_geo_90pct.ovgb_i100_o50 PARAM: ASQG output: 0 PARAM: CSV output: 1 PARAM: Min Overlap: 50 PARAM: Id Threshold: 1 PARAM: NoIndel: 0 PARAM: Debug: 0 PARAM: Verbose: 1 PARAM: Test: 0
TIME: Reference fasta file read in 1.18978 seconds. INFO: 76956 reference sequences were loaded
TIME: References names loaded from the SAM file in 0.256116 seconds. INFO: 11176 references are present in the SAM file
TIME: SAM file reading finished in 1.32384 seconds. INFO: 197002 bam records were read, representing 22529 reads INFO: 197002 bam record were mapped on a reference, representing 22529 mapped reads
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building progress at 0.94175% INFO: Compatibility graph building progress at 0.94275% INFO: Compatibility graph building progress at 0.94375% INFO: Compatibility graph building progress at 0.94475% INFO: Compatibility graph building progress at 0.94575% INFO: Compatibility graph building progress at 0.94675% INFO: Compatibility graph building progress at 0.94775% INFO: Compatibility graph building progress at 0.94875% INFO: Compatibility graph building progress at 0.94975% INFO: Compatibility graph building progress at 0.95075% INFO: Compatibility graph building progress at 0.95175% INFO: Compatibility graph building progress at 0.95275% INFO: Compatibility graph building progress at 0.95375% INFO: Compatibility graph building progress at 0.95475% INFO: Compatibility graph building progress at 0.95575% INFO: Compatibility graph building progress at 0.95675% INFO: Compatibility graph building progress at 0.95775% INFO: Compatibility graph building progress at 0.95875% INFO: Compatibility graph building progress at 0.95975% INFO: Compatibility graph building progress at 0.96075% INFO: Compatibility graph building progress at 0.96175% INFO: Compatibility graph building progress at 0.96275% INFO: Compatibility graph building progress at 0.96375% INFO: Compatibility graph building progress at 0.96475% INFO: Compatibility graph building progress at 0.96575% INFO: Compatibility graph building progress at 0.96675% INFO: Compatibility graph building progress at 0.96775% INFO: Compatibility graph building progress at 0.96875% INFO: Compatibility graph building progress at 0.96975% INFO: Compatibility graph building progress at 0.97074% INFO: Compatibility graph building progress at 0.97174% INFO: Compatibility graph building progress at 0.97274% INFO: Compatibility graph building progress at 0.97374% INFO: Compatibility graph building progress at 0.97474% INFO: Compatibility graph building progress at 0.97574% INFO: Compatibility graph building progress at 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progress at 0.99474% INFO: Compatibility graph building progress at 0.99574% INFO: Compatibility graph building progress at 0.99674% INFO: Compatibility graph building progress at 0.99774% INFO: Compatibility graph building progress at 0.99874% INFO: Compatibility graph building progress at 0.99974% INFO: Compatibility graph building progress at 1.1% INFO: Compatibility graph building progress at 1.2% INFO: Compatibility graph building progress at 1.3% INFO: Compatibility graph building progress at 1.4% INFO: Compatibility graph building progress at 1.5% INFO: Compatibility graph building progress at 1.6% INFO: Compatibility graph building progress at 1.7% INFO: Compatibility graph building progress at 1.8% INFO: Compatibility graph building progress at 1.9% INFO: Compatibility graph building progress at 2% INFO: Compatibility graph building progress at 2.1% INFO: Compatibility graph building progress at 2.2% INFO: Compatibility graph building progress at 2.3% INFO: Compatibility graph building progress at 2.4% INFO: Compatibility graph building progress at 2.5% INFO: Compatibility graph building progress at 2.6% INFO: Compatibility graph building progress at 2.7% INFO: Compatibility graph building progress at 2.8% INFO: Compatibility graph building progress at 2.9% INFO: Compatibility graph building progress at 3% INFO: Compatibility graph building progress at 3.1% INFO: Compatibility graph building progress at 3.2% INFO: Compatibility graph building progress at 3.3% INFO: Compatibility graph building progress at 3.4% INFO: Compatibility graph building progress at 3.5% INFO: Compatibility graph building progress at 3.6% INFO: Compatibility graph building progress at 3.7% INFO: Compatibility graph building progress at 3.8% INFO: Compatibility graph building progress at 3.9% INFO: Compatibility graph building progress at 4% INFO: Compatibility graph building progress at 4.1% INFO: Compatibility graph building progress at 4.2% INFO: Compatibility graph building progress at 4.3% INFO: Compatibility graph building progress at 4.4% INFO: Compatibility graph building progress at 4.5% INFO: Compatibility graph building progress at 4.6% INFO: Compatibility graph building progress at 4.7% INFO: Compatibility graph building progress at 4.8% INFO: Compatibility graph building progress at 4.9% INFO: Compatibility graph building progress at 5% INFO: Compatibility graph building progress at 5.1% INFO: Compatibility graph building progress at 5.2% INFO: Compatibility graph building progress at 5.3% INFO: Compatibility graph building progress at 5.4% INFO: Compatibility graph building progress at 5.5% INFO: Compatibility graph building progress at 5.6% INFO: Compatibility graph building progress at 5.7% INFO: Compatibility graph building progress at 5.8% INFO: Compatibility graph building progress at 5.9% INFO: Compatibility graph building progress at 6% INFO: Compatibility graph building progress at 6.1% INFO: Compatibility graph building progress at 6.2% 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graph building progress at 10.1% INFO: Compatibility graph building progress at 10.2% INFO: Compatibility graph building progress at 10.3% INFO: Compatibility graph building progress at 10.4% INFO: Compatibility graph building progress at 10.5% INFO: Compatibility graph building progress at 10.6% INFO: Compatibility graph building progress at 10.7% INFO: Compatibility graph building progress at 10.8% INFO: Compatibility graph building progress at 10.9% INFO: Compatibility graph building progress at 11% INFO: Compatibility graph building progress at 11.1% INFO: Compatibility graph building progress at 11.2% INFO: Compatibility graph building progress at 11.3% INFO: Compatibility graph building progress at 11.4% INFO: Compatibility graph building progress at 11.5% INFO: Compatibility graph building progress at 11.6% INFO: Compatibility graph building progress at 11.7% INFO: Compatibility graph building progress at 11.8% INFO: Compatibility graph building progress at 11.9% INFO: Compatibility graph building progress at 12% INFO: Compatibility graph building progress at 12.1% INFO: Compatibility graph building progress at 12.2% INFO: Compatibility graph building progress at 12.3% INFO: Compatibility graph building progress at 12.4% INFO: Compatibility graph building progress at 12.5% INFO: Compatibility graph building progress at 12.6% INFO: Compatibility graph building progress at 12.7% INFO: Compatibility graph building progress at 12.8% INFO: Compatibility graph building progress at 12.9% INFO: Compatibility graph building progress at 13% INFO: Compatibility graph building progress at 13.1% INFO: Compatibility graph building progress at 13.2% INFO: Compatibility graph building progress at 13.3% INFO: Compatibility graph building progress at 13.4% INFO: Compatibility graph building progress at 13.5% INFO: Compatibility graph building progress at 13.6% INFO: Compatibility graph building progress at 13.7% INFO: Compatibility graph building progress at 13.8% 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15.7% INFO: Compatibility graph building progress at 15.8% INFO: Compatibility graph building progress at 15.9% INFO: Compatibility graph building progress at 16% INFO: Compatibility graph building progress at 16.1% INFO: Compatibility graph building progress at 16.2% INFO: Compatibility graph building progress at 16.3% INFO: Compatibility graph building progress at 16.4% INFO: Compatibility graph building progress at 16.5% INFO: Compatibility graph building progress at 16.6% INFO: Compatibility graph building progress at 16.7% INFO: Compatibility graph building progress at 16.8% INFO: Compatibility graph building progress at 16.9% INFO: Compatibility graph building progress at 17% INFO: Compatibility graph building progress at 17.1% INFO: Compatibility graph building progress at 17.2% INFO: Compatibility graph building progress at 17.3% INFO: Compatibility graph building progress at 17.4% INFO: Compatibility graph building progress at 17.5% INFO: Compatibility graph building progress at 17.6% INFO: Compatibility graph building progress at 17.7% INFO: Compatibility graph building progress at 17.8% INFO: Compatibility graph building progress at 17.9% INFO: Compatibility graph building progress at 18% INFO: Compatibility graph building progress at 18.1% INFO: Compatibility graph building progress at 18.2% INFO: Compatibility graph building progress at 18.3% INFO: Compatibility graph building progress at 18.4% INFO: Compatibility graph building progress at 18.5% INFO: Compatibility graph building progress at 18.6% INFO: Compatibility graph building progress at 18.7% INFO: Compatibility graph building progress at 18.8% INFO: Compatibility graph building progress at 18.9% INFO: Compatibility graph building progress at 19% INFO: Compatibility graph building progress at 19.1% INFO: Compatibility graph building progress at 19.2% INFO: Compatibility graph building progress at 19.3% INFO: Compatibility graph building progress at 19.4% INFO: Compatibility graph building progress at 19.5% INFO: Compatibility graph building progress at 19.6% INFO: Compatibility graph building progress at 19.7% INFO: Compatibility graph building progress at 19.8% INFO: Compatibility graph building progress at 19.9% INFO: Compatibility graph building progress at 20% INFO: Compatibility graph building progress at 20.1% INFO: Compatibility graph building progress at 20.2% INFO: Compatibility graph building progress at 20.3% INFO: Compatibility graph building progress at 20.4% INFO: Compatibility graph building progress at 20.5% INFO: Compatibility graph building progress at 20.6% INFO: Compatibility graph building progress at 20.7% INFO: Compatibility graph building progress at 20.8% INFO: Compatibility graph building progress at 20.9% INFO: Compatibility graph building progress at 21% INFO: Compatibility graph building progress at 21.1% INFO: Compatibility graph building progress at 21.2% INFO: Compatibility graph building progress at 21.3% INFO: Compatibility graph building progress at 21.4% INFO: Compatibility graph building progress at 21.5% INFO: Compatibility graph building progress at 21.6% INFO: Compatibility graph building progress at 21.7% INFO: Compatibility graph building progress at 21.8% INFO: Compatibility graph building progress at 21.9% INFO: Compatibility graph building progress at 22% INFO: Compatibility graph building progress at 22.1% INFO: Compatibility graph building progress at 22.2% INFO: Compatibility graph building progress at 22.3% INFO: Compatibility graph building progress at 22.4% INFO: Compatibility graph building progress at 22.5% INFO: Compatibility graph building progress at 22.6% INFO: Compatibility graph building progress at 22.7% INFO: Compatibility graph building progress at 22.8% INFO: Compatibility graph building progress at 22.9% INFO: Compatibility graph building progress at 23% INFO: Compatibility graph building progress at 23.1% INFO: Compatibility graph building progress at 23.2% INFO: Compatibility graph building progress at 23.3% INFO: Compatibility graph building progress at 23.4% INFO: Compatibility graph building progress at 23.5% INFO: Compatibility graph building progress at 23.6% INFO: Compatibility graph building progress at 23.7% INFO: Compatibility graph building progress at 23.8% INFO: Compatibility graph building progress at 23.9% INFO: Compatibility graph building progress at 24% INFO: Compatibility graph building progress at 24.1% INFO: Compatibility graph building progress at 24.2% INFO: Compatibility graph building progress at 24.3% INFO: Compatibility graph building progress at 24.4% INFO: Compatibility graph building progress at 24.5% INFO: Compatibility graph building progress at 24.6% INFO: Compatibility graph building progress at 24.7% INFO: Compatibility graph building progress at 24.8% INFO: Compatibility graph building progress at 24.9% INFO: Compatibility graph building progress at 25% INFO: Compatibility graph building progress at 25.1% INFO: 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28.9% INFO: Compatibility graph building progress at 29% INFO: Compatibility graph building progress at 29.1% INFO: Compatibility graph building progress at 29.2% INFO: Compatibility graph building progress at 29.3% INFO: Compatibility graph building progress at 29.4% INFO: Compatibility graph building progress at 29.5% INFO: Compatibility graph building progress at 29.6% INFO: Compatibility graph building progress at 29.7% INFO: Compatibility graph building progress at 29.8% INFO: Compatibility graph building progress at 29.9% INFO: Compatibility graph building progress at 30% INFO: Compatibility graph building progress at 30.1% INFO: Compatibility graph building progress at 30.2% INFO: Compatibility graph building progress at 30.3% INFO: Compatibility graph building progress at 30.4% INFO: Compatibility graph building progress at 30.5% INFO: Compatibility graph building progress at 30.6% INFO: Compatibility graph building progress at 30.7% INFO: Compatibility graph building progress at 30.8% INFO: Compatibility graph building progress at 30.9% INFO: Compatibility graph building progress at 31% INFO: Compatibility graph building progress at 31.1% INFO: Compatibility graph building progress at 31.2% INFO: Compatibility graph building progress at 31.3% INFO: Compatibility graph building progress at 31.4% INFO: Compatibility graph building progress at 31.5% INFO: Compatibility graph building progress at 31.6% INFO: Compatibility graph building progress at 31.7% INFO: Compatibility graph building progress at 31.8% INFO: Compatibility graph building progress at 31.9% INFO: Compatibility graph building progress at 32% INFO: Compatibility graph building progress at 32.1% INFO: Compatibility graph building progress at 32.2% INFO: Compatibility graph building progress at 32.3% INFO: Compatibility graph building progress at 32.4% INFO: Compatibility graph building progress at 32.5% INFO: Compatibility graph building progress at 32.6% INFO: Compatibility graph building progress at 32.7% INFO: Compatibility graph building progress at 32.8% INFO: Compatibility graph building progress at 32.9% INFO: Compatibility graph building progress at 33% INFO: Compatibility graph building progress at 33.1% INFO: Compatibility graph building progress at 33.2% INFO: Compatibility graph building progress at 33.3% INFO: Compatibility graph building progress at 33.4% INFO: Compatibility graph building progress at 33.5% INFO: Compatibility graph building progress at 33.6% INFO: Compatibility graph building progress at 33.7% INFO: Compatibility graph building progress at 33.8% INFO: Compatibility graph building progress at 33.9% INFO: Compatibility graph building progress at 34% INFO: Compatibility graph building progress at 34.1% INFO: Compatibility graph building progress at 34.2% INFO: Compatibility graph building progress at 34.3% INFO: Compatibility graph building progress at 34.4% INFO: Compatibility graph building progress at 34.5% INFO: Compatibility graph building progress at 34.6% INFO: Compatibility graph building progress at 34.7% INFO: Compatibility graph building progress at 34.8% INFO: Compatibility graph building progress at 34.9% INFO: Compatibility graph building progress at 35% INFO: Compatibility graph building progress at 35.1% INFO: Compatibility graph building progress at 35.2% INFO: Compatibility graph building progress at 35.3% INFO: Compatibility graph building progress at 35.4% INFO: Compatibility graph building progress at 35.5% INFO: Compatibility graph building progress at 35.6% INFO: Compatibility graph building progress at 35.7% INFO: Compatibility graph building progress at 35.8% INFO: Compatibility graph building progress at 35.9% INFO: Compatibility graph building progress at 36% INFO: Compatibility graph building progress at 36.1% INFO: Compatibility graph building progress at 36.2% INFO: Compatibility graph building progress at 36.3% INFO: Compatibility graph building progress at 36.4% INFO: Compatibility graph building progress at 36.5% INFO: Compatibility graph building progress at 36.6% INFO: Compatibility graph building progress at 36.7% INFO: Compatibility graph building progress at 36.8% INFO: Compatibility graph building progress at 36.9% INFO: Compatibility graph building progress at 37% INFO: Compatibility graph building progress at 37.1% INFO: Compatibility graph building progress at 37.2% INFO: Compatibility graph building progress at 37.3% INFO: Compatibility graph building progress at 37.4% INFO: Compatibility graph building progress at 37.5% INFO: Compatibility graph building progress at 37.6% INFO: Compatibility graph building progress at 37.7% INFO: Compatibility graph building progress at 37.8% INFO: Compatibility graph building progress at 37.9% INFO: Compatibility graph building progress at 38% INFO: Compatibility graph building progress at 38.1% INFO: Compatibility graph building progress at 38.2% INFO: Compatibility graph building progress at 38.3% INFO: 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42.1% INFO: Compatibility graph building progress at 42.2% INFO: Compatibility graph building progress at 42.3% INFO: Compatibility graph building progress at 42.4% INFO: Compatibility graph building progress at 42.5% INFO: Compatibility graph building progress at 42.6% INFO: Compatibility graph building progress at 42.7% INFO: Compatibility graph building progress at 42.8% INFO: Compatibility graph building progress at 42.9% INFO: Compatibility graph building progress at 43% INFO: Compatibility graph building progress at 43.1% INFO: Compatibility graph building progress at 43.2% INFO: Compatibility graph building progress at 43.3% INFO: Compatibility graph building progress at 43.4% INFO: Compatibility graph building progress at 43.5% INFO: Compatibility graph building progress at 43.6% INFO: Compatibility graph building progress at 43.7% INFO: Compatibility graph building progress at 43.8% INFO: Compatibility graph building progress at 43.9% INFO: Compatibility graph building progress at 44% INFO: Compatibility graph building progress at 44.1% INFO: Compatibility graph building progress at 44.2% INFO: Compatibility graph building progress at 44.3% INFO: Compatibility graph building progress at 44.4% INFO: Compatibility graph building progress at 44.5% INFO: Compatibility graph building progress at 44.6% INFO: Compatibility graph building progress at 44.7% INFO: Compatibility graph building progress at 44.8% INFO: Compatibility graph building progress at 44.9% INFO: Compatibility graph building progress at 45% INFO: Compatibility graph building progress at 45.1% INFO: Compatibility graph building progress at 45.2% INFO: Compatibility graph building progress at 45.3% INFO: Compatibility graph building progress at 45.4% INFO: Compatibility graph building progress at 45.5% INFO: Compatibility graph building progress at 45.6% INFO: Compatibility graph building progress at 45.7% INFO: Compatibility graph building progress at 45.8% INFO: Compatibility graph building progress at 45.9% INFO: Compatibility graph building progress at 46% INFO: Compatibility graph building progress at 46.1% INFO: Compatibility graph building progress at 46.2% INFO: Compatibility graph building progress at 46.3% INFO: Compatibility graph building progress at 46.4% INFO: Compatibility graph building progress at 46.5% INFO: Compatibility graph building progress at 46.6% INFO: Compatibility graph building progress at 46.7% INFO: Compatibility graph building progress at 46.8% INFO: Compatibility graph building progress at 46.9% INFO: Compatibility graph building progress at 47% INFO: Compatibility graph building progress at 47.1% INFO: Compatibility graph building progress at 47.2% INFO: Compatibility graph building progress at 47.3% INFO: Compatibility graph building progress at 47.4% INFO: Compatibility graph building progress at 47.5% INFO: Compatibility graph building progress at 47.6% INFO: Compatibility graph building progress at 47.7% INFO: Compatibility graph building progress at 47.8% INFO: Compatibility graph building progress at 47.9% INFO: Compatibility graph building progress at 48% INFO: Compatibility graph building progress at 48.1% INFO: Compatibility graph building progress at 48.2% INFO: Compatibility graph building progress at 48.3% INFO: Compatibility graph building progress at 48.4% INFO: Compatibility graph building progress at 48.5% INFO: Compatibility graph building progress at 48.6% INFO: Compatibility graph building progress at 48.7% INFO: Compatibility graph building progress at 48.8% INFO: Compatibility graph building progress at 48.9% INFO: Compatibility graph building progress at 49% INFO: Compatibility graph building progress at 49.1% INFO: Compatibility graph building progress at 49.2% INFO: Compatibility graph building progress at 49.3% INFO: Compatibility graph building progress at 49.4% INFO: Compatibility graph building progress at 49.5% INFO: Compatibility graph building progress at 49.6% INFO: 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at 55.3% INFO: Compatibility graph building progress at 55.4% INFO: Compatibility graph building progress at 55.5% INFO: Compatibility graph building progress at 55.6% INFO: Compatibility graph building progress at 55.7% INFO: Compatibility graph building progress at 55.8% INFO: Compatibility graph building progress at 55.9% INFO: Compatibility graph building progress at 56% INFO: Compatibility graph building progress at 56.1% INFO: Compatibility graph building progress at 56.2% INFO: Compatibility graph building progress at 56.3% INFO: Compatibility graph building progress at 56.4% INFO: Compatibility graph building progress at 56.5% INFO: Compatibility graph building progress at 56.6% INFO: Compatibility graph building progress at 56.7% INFO: Compatibility graph building progress at 56.8% INFO: Compatibility graph building progress at 56.9% INFO: Compatibility graph building progress at 57% INFO: Compatibility graph building progress at 57.1% INFO: Compatibility graph building 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building progress at 59.1% INFO: Compatibility graph building progress at 59.2% INFO: Compatibility graph building progress at 59.3% INFO: Compatibility graph building progress at 59.4% INFO: Compatibility graph building progress at 59.5% INFO: Compatibility graph building progress at 59.6% INFO: Compatibility graph building progress at 59.7% INFO: Compatibility graph building progress at 59.8% INFO: Compatibility graph building progress at 59.9% INFO: Compatibility graph building progress at 60% INFO: Compatibility graph building progress at 60.1% INFO: Compatibility graph building progress at 60.2% INFO: Compatibility graph building progress at 60.3% INFO: Compatibility graph building progress at 60.4% INFO: Compatibility graph building progress at 60.5% INFO: Compatibility graph building progress at 60.6% INFO: Compatibility graph building progress at 60.7% INFO: Compatibility graph building progress at 60.8% INFO: Compatibility graph building progress at 60.9% INFO: Compatibility graph building progress at 61% INFO: Compatibility graph building progress at 61.1% INFO: Compatibility graph building progress at 61.2% INFO: Compatibility graph building progress at 61.3% INFO: Compatibility graph building progress at 61.4% INFO: Compatibility graph building progress at 61.5% INFO: Compatibility graph building progress at 61.6% INFO: Compatibility graph building progress at 61.7% INFO: Compatibility graph building progress at 61.8% INFO: Compatibility graph building progress at 61.9% INFO: Compatibility graph building progress at 62% INFO: Compatibility graph building progress at 62.1% INFO: Compatibility graph building progress at 62.2% INFO: Compatibility graph building progress at 62.3% INFO: Compatibility graph building progress at 62.4% INFO: Compatibility graph building progress at 62.5% INFO: Compatibility graph building progress at 62.6% INFO: Compatibility graph building progress at 62.7% INFO: Compatibility graph building progress at 62.8% INFO: 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at 68.5% INFO: Compatibility graph building progress at 68.6% INFO: Compatibility graph building progress at 68.7% INFO: Compatibility graph building progress at 68.8% INFO: Compatibility graph building progress at 68.9% INFO: Compatibility graph building progress at 69% INFO: Compatibility graph building progress at 69.1% INFO: Compatibility graph building progress at 69.2% INFO: Compatibility graph building progress at 69.3% INFO: Compatibility graph building progress at 69.4% INFO: Compatibility graph building progress at 69.5% INFO: Compatibility graph building progress at 69.6% INFO: Compatibility graph building progress at 69.7% INFO: Compatibility graph building progress at 69.8% INFO: Compatibility graph building progress at 69.9% INFO: Compatibility graph building progress at 70% INFO: Compatibility graph building progress at 70.1% INFO: Compatibility graph building progress at 70.2% INFO: Compatibility graph building progress at 70.3% INFO: Compatibility graph building 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at 81.7% INFO: Compatibility graph building progress at 81.8% INFO: Compatibility graph building progress at 81.9% INFO: Compatibility graph building progress at 82% INFO: Compatibility graph building progress at 82.1% INFO: Compatibility graph building progress at 82.2% INFO: Compatibility graph building progress at 82.3% INFO: Compatibility graph building progress at 82.4% INFO: Compatibility graph building progress at 82.5% INFO: Compatibility graph building progress at 82.6% INFO: Compatibility graph building progress at 82.7% INFO: Compatibility graph building progress at 82.8% INFO: Compatibility graph building progress at 82.9% INFO: Compatibility graph building progress at 83% INFO: Compatibility graph building progress at 83.1% INFO: Compatibility graph building progress at 83.2% INFO: Compatibility graph building progress at 83.3% INFO: Compatibility graph building progress at 83.4% INFO: Compatibility graph building progress at 83.5% INFO: Compatibility graph building 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at 94.9% INFO: Compatibility graph building progress at 95% INFO: Compatibility graph building progress at 95.1% INFO: Compatibility graph building progress at 95.2% INFO: Compatibility graph building progress at 95.3% INFO: Compatibility graph building progress at 95.4% INFO: Compatibility graph building progress at 95.5% INFO: Compatibility graph building progress at 95.6% INFO: Compatibility graph building progress at 95.7% INFO: Compatibility graph building progress at 95.8% INFO: Compatibility graph building progress at 95.9% INFO: Compatibility graph building progress at 96% INFO: Compatibility graph building progress at 96.1% INFO: Compatibility graph building progress at 96.2% INFO: Compatibility graph building progress at 96.3% INFO: Compatibility graph building progress at 96.4% INFO: Compatibility graph building progress at 96.5% INFO: Compatibility graph building progress at 96.6% INFO: Compatibility graph building progress at 96.7% INFO: Compatibility graph building 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TIME: Compatibility graph was build in 73.498 seconds. INFO: 253766656 reads pairs were considered INFO: Of which 695728 were found compatible INFO: 252550233 were found incompatible INFO: and 229131178 were neither compatible nor incompatible
INFO - Overlap-graph building completed in 76.9970 seconds wall time INFO - Overlap graph stats: 22529 nodes, 695728 edges INFO - === Graph compaction & Components identification ===
--- Loading --- 22529 nodes loaded
--- Run algorithms --- -> BFS... -> Contraction... 7127 nodes in the contracted graph 3198 edges in the contracted graph -> Absorb fingers... 6150 nodes in the contracted graph 2221 edges in the contracted graph
--- Filtering --- -> Filtering nodes... 1356 nodes in the filtered graph -> Filtering edges... 683 edges in the filtered graph
--- Splicing ---
--- Saving results --- -> Saving components -> Saving meta graph
--- Program ended ---
INFO - Graph compaction & Components identification completed in 1.6436 seconds wall time INFO - Compressed graph: 985 components INFO - === LCA labelling === INFO - LCA labelling completed in 1.4708 seconds wall time INFO - === Contigs assembly === INFO - Save components to fastq files INFO - Assemble components WARNING - Number of non empty components: 216/984 INFO - Contigs assembly completed in 82.4199 seconds wall time INFO - === Scaffolding ===
Program: SortMeRNA version 2.1b, 03/03/2016 Copyright: 2012-16 Bonsai Bioinformatics Research Group: LIFL, University Lille 1, CNRS UMR 8022, INRIA Nord-Europe 2014-16 Knight Lab: Department of Pediatrics, UCSD, La Jolla, Disclaimer: SortMeRNA comes with ABSOLUTELY NO WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. Contact: Evguenia Kopylova, jenya.kopylov@gmail.com Laurent Noé, laurent.noe@lifl.fr Hélène Touzet, helene.touzet@lifl.fr
Computing read file statistics ... done [0.00 sec] size of reads file: 82633 bytes partial section(s) to be executed: 1 of size 82633 bytes Parameters summary: Number of seeds = 2 Edges = 4 (as integer) SW match = 2 SW mismatch = -3 SW gap open penalty = 5 SW gap extend penalty = 2 SW ambiguous nucleotide = -3 SQ tags are not output Number of threads = 25
�[4mBegin mmap reads section # 1�[0m: Time to mmap reads and set up pointers [0.00 sec]
Begin analysis of: �[0;34m/nfs/home/users/monica188/cohort/CRC/shotgun/filtering/matam/SILVA_128_SSURef_NR95.complete.fasta�[0m Seed length = 18 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3 Gumbel lambda = 0.604560 Gumbel K = 0.332261 Minimal SW score based on E-value = 68 Loading index part 1/1 ... done [13.48 sec] Begin index search ... done [98.92 sec] Freeing index ... done [2.42 sec] Total number of reads mapped (incl. all reads file sections searched): 352 INFO - Contig mapping completed in 115.5272 seconds wall time [mpileup] 1 samples in 1 input files INFO - Scaffolding completed in 11.7839 seconds wall time INFO - === Abundance calculation === INFO - --- Indexing scaffolds ---
Program: SortMeRNA version 2.1b, 03/03/2016 Copyright: 2012-16 Bonsai Bioinformatics Research Group: LIFL, University Lille 1, CNRS UMR 8022, INRIA Nord-Europe 2014-16 Knight Lab: Department of Pediatrics, UCSD, La Jolla, Disclaimer: SortMeRNA comes with ABSOLUTELY NO WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. Contact: Evguenia Kopylova, jenya.kopylov@gmail.com Laurent Noé, laurent.noe@lifl.fr Hélène Touzet, helene.touzet@lifl.fr
Parameters summary: K-mer size: 19 K-mer interval: 1 Maximum positions to store per unique K-mer: 10000
Total number of databases to index: 1
Begin indexing file �[0;34m/nfs/home/users/monica188/cohort/CRC/shotgun/filtering/matam/EXX478962_.fastq_output/workdir/scaffolds.NR.min_500bp.fa�[0m under index name �[0;34m/nfs/INFO - --- Reads mapping against scaffolds ---
Program: SortMeRNA version 2.1b, 03/03/2016 Copyright: 2012-16 Bonsai Bioinformatics Research Group: LIFL, University Lille 1, CNRS UMR 8022, INRIA Nord-Europe 2014-16 Knight Lab: Department of Pediatrics, UCSD, La Jolla, Disclaimer: SortMeRNA comes with ABSOLUTELY NO WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. Contact: Evguenia Kopylova, jenya.kopylov@gmail.com Laurent Noé, laurent.noe@lifl.fr Hélène Touzet, helene.touzet@lifl.fr
Computing read file statistics ... done [0.02 sec] size of reads file: 6960417 bytes partial section(s) to be executed: 1 of size 6960417 bytes Parameters summary: Number of seeds = 2 Edges = 4 (as integer) SW match = 2 SW mismatch = -3 SW gap open penalty = 5 SW gap extend penalty = 2 SW ambiguous nucleotide = -3 SQ tags are not output Number of threads = 25
�[4mBegin mmap reads section # 1�[0m: Time to mmap reads and set up pointers [0.01 sec]
Begin analysis of: �[0;34m/nfs/home/users/monica188/cohort/CRC/shotgun/filtering/matam/EXX478962_.fastq_output/workdir/scaffolds.NR.min_500bp.fa�[0m Seed length = 18 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3 Gumbel lambda = 0.605082 Gumbel K = 0.334257 Minimal SW score based on E-value = 56 Loading index part 1/1 ... done [0.03 sec] Begin index search ... done [0.13 sec] Freeing index ... done [0.00 sec] Total number of reads mapped (incl. all reads file sections searched): 28207 Writing alignments ... done [1.04 sec] Writing aligned FASTA/FASTQ ... done [0.17 sec] INFO - Abundance calculation completed in 2.5576 seconds wall time INFO - === Taxonomic assignment & Krona visualization === INFO - Make krona plot INFO - Taxonomic assignment & Krona visualization completed in 5.2968 seconds wall time INFO - === MATAM Statistics ===
Input reads nb: 19620360 Selected reads nb: 36586
Ov. Graph nodes nb: 22529 Ov. Graph edges nb: 695728
Compressed Graph nodes nb: 1356 Compressed Graph edges nb: 374 Compressed Graph reads nb: 17735 Compr. Graph excluded reads nb: 4794 (21.28% of total reads) Compr. Graph components nb: 985
Contigs assembly: Seq nb: 352 Seq min size: 86 nt Seq max size: 334 nt Seq avg. size: 132.24 nt Seq total size: 46548 nt
Large NR Contigs assembly: Seq nb: 0 Seq min size: -1 nt Seq max size: -1 nt Seq avg. size: -1.00 nt Seq total size: 0 nt
Scaffolds assembly: Seq nb: 208 Seq min size: 67 nt Seq max size: 1252 nt Seq avg. size: 223.38 nt Seq total size: 46462 nt
Large NR Scaffolds assembly: Seq nb: 12 Seq min size: 527 nt Seq max size: 1252 nt Seq avg. size: 896.17 nt Seq total size: 10754 nt
INFO - Removing tmp files INFO - matam_assembly.py terminated with no error INFO - Run completed in 458.0690 seconds wall time `
I got the final assembly file fasta and i tried picrust but I got the error stating that "all the sequences are aligned poorly to reference sequences ones". Is there any way I can work with the results from matam?