How to improve final alignement

[MonicaSteffi]

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 --out_dir /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 --input_fastq /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 --out_dir /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 --input_fastq /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, [email protected]
Laurent Noé, [email protected]
Hélène Touzet, [email protected]

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_SSURef_NR95.clustered.fasta
PARAM: Sam file: /nfs/home/users/monica188/cohort/CRC/shotgun/filtering/matam/EXX478962_.fastq_output/workdir/EXX478962_.sortmerna_vs_SILVA_128_SSURef_NR95_b10_m10.scr_filt_geo_90pct.sam
PARAM: Output basename: /nfs/home/users/monica188/cohort/CRC/shotgun/filtering/matam/EXX478962_.fastq_output/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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INFO: Compatibility graph building progress at 1.1%
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INFO: Compatibility graph building progress at 2%
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INFO: Compatibility graph building progress at 3.1%
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INFO: Compatibility graph building progress at 4.1%
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INFO: Compatibility graph building progress at 5.1%
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INFO: Compatibility graph building progress at 6.1%
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INFO: Compatibility graph building progress at 7.1%
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INFO: Compatibility graph building progress at 8.1%
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INFO: Compatibility graph building progress at 9%
INFO: Compatibility graph building progress at 9.1%
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INFO: Compatibility graph building progress at 10%
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INFO: Compatibility graph building progress at 11%
INFO: Compatibility graph building progress at 11.1%
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INFO: Compatibility graph building progress at 12.1%
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INFO: Compatibility graph building progress at 13.1%
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INFO: Compatibility graph building progress at 14.1%
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INFO: Compatibility graph building progress at 15%
INFO: Compatibility graph building progress at 15.1%
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INFO: Compatibility graph building progress at 16.1%
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INFO: Compatibility graph building progress at 17.1%
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INFO: Compatibility graph building progress at 18.1%
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INFO: Compatibility graph building progress at 19.1%
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INFO: Compatibility graph building progress at 20.1%
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INFO: Compatibility graph building progress at 21.1%
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INFO: Compatibility graph building progress at 22.1%
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INFO: Compatibility graph building progress at 23.1%
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INFO: Compatibility graph building progress at 24.1%
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INFO: Compatibility graph building progress at 25.1%
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INFO: Compatibility graph building progress at 26.1%
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INFO: Compatibility graph building progress at 27.1%
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INFO: Compatibility graph building progress at 28%
INFO: Compatibility graph building progress at 28.1%
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INFO: Compatibility graph building progress at 29%
INFO: Compatibility graph building progress at 29.1%
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INFO: Compatibility graph building progress at 30%
INFO: Compatibility graph building progress at 30.1%
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INFO: Compatibility graph building progress at 31%
INFO: Compatibility graph building progress at 31.1%
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INFO: Compatibility graph building progress at 32%
INFO: Compatibility graph building progress at 32.1%
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INFO: Compatibility graph building progress at 33%
INFO: Compatibility graph building progress at 33.1%
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INFO: Compatibility graph building progress at 34%
INFO: Compatibility graph building progress at 34.1%
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INFO: Compatibility graph building progress at 35%
INFO: Compatibility graph building progress at 35.1%
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INFO: Compatibility graph building progress at 36%
INFO: Compatibility graph building progress at 36.1%
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INFO: Compatibility graph building progress at 37%
INFO: Compatibility graph building progress at 37.1%
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INFO: Compatibility graph building progress at 37.4%
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INFO: Compatibility graph building progress at 38%
INFO: Compatibility graph building progress at 38.1%
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INFO: Compatibility graph building progress at 39%
INFO: Compatibility graph building progress at 39.1%
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INFO: Compatibility graph building progress at 40%
INFO: Compatibility graph building progress at 40.1%
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INFO: Compatibility graph building progress at 41%
INFO: Compatibility graph building progress at 41.1%
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INFO: Compatibility graph building progress at 41.4%
INFO: Compatibility graph building progress at 41.5%
INFO: Compatibility graph building progress at 41.6%
INFO: Compatibility graph building progress at 41.7%
INFO: Compatibility graph building progress at 41.8%
INFO: Compatibility graph building progress at 41.9%
INFO: Compatibility graph building progress at 42%
INFO: Compatibility graph building progress at 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%
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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%
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INFO: Compatibility graph building progress at 43.3%
INFO: Compatibility graph building progress at 43.4%
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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%
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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%
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INFO: Compatibility graph building progress at 45.8%
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INFO: Compatibility graph building progress at 46%
INFO: Compatibility graph building progress at 46.1%
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INFO: Compatibility graph building progress at 47%
INFO: Compatibility graph building progress at 47.1%
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INFO: Compatibility graph building progress at 48%
INFO: Compatibility graph building progress at 48.1%
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INFO: Compatibility graph building progress at 49%
INFO: Compatibility graph building progress at 49.1%
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INFO: Compatibility graph building progress at 50.1%
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INFO: Compatibility graph building progress at 51%
INFO: Compatibility graph building progress at 51.1%
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INFO: Compatibility graph building progress at 52.1%
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INFO: Compatibility graph building progress at 53%
INFO: Compatibility graph building progress at 53.1%
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INFO: Compatibility graph building progress at 54%
INFO: Compatibility graph building progress at 54.1%
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INFO: Compatibility graph building progress at 55%
INFO: Compatibility graph building progress at 55.1%
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INFO: Compatibility graph building progress at 56%
INFO: Compatibility graph building progress at 56.1%
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INFO: Compatibility graph building progress at 57%
INFO: Compatibility graph building progress at 57.1%
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INFO: Compatibility graph building progress at 58%
INFO: Compatibility graph building progress at 58.1%
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INFO: Compatibility graph building progress at 59%
INFO: Compatibility graph building progress at 59.1%
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INFO: Compatibility graph building progress at 60%
INFO: Compatibility graph building progress at 60.1%
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INFO: Compatibility graph building progress at 60.3%
INFO: Compatibility graph building progress at 60.4%
INFO: Compatibility graph building progress at 60.5%
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INFO: Compatibility graph building progress at 60.8%
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INFO: Compatibility graph building progress at 61%
INFO: Compatibility graph building progress at 61.1%
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INFO: Compatibility graph building progress at 61.3%
INFO: Compatibility graph building progress at 61.4%
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INFO: Compatibility graph building progress at 62%
INFO: Compatibility graph building progress at 62.1%
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INFO: Compatibility graph building progress at 63%
INFO: Compatibility graph building progress at 63.1%
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INFO: Compatibility graph building progress at 63.4%
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INFO: Compatibility graph building progress at 64%
INFO: Compatibility graph building progress at 64.1%
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INFO: Compatibility graph building progress at 65%
INFO: Compatibility graph building progress at 65.1%
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INFO: Compatibility graph building progress at 66%
INFO: Compatibility graph building progress at 66.1%
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INFO: Compatibility graph building progress at 67%
INFO: Compatibility graph building progress at 67.1%
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INFO: Compatibility graph building progress at 68%
INFO: Compatibility graph building progress at 68.1%
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INFO: Compatibility graph building progress at 68.3%
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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%
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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 progress at 70.4%
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INFO: Compatibility graph building progress at 71%
INFO: Compatibility graph building progress at 71.1%
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INFO: Compatibility graph building progress at 71.3%
INFO: Compatibility graph building progress at 71.4%
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INFO: Compatibility graph building progress at 72%
INFO: Compatibility graph building progress at 72.1%
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INFO: Compatibility graph building progress at 72.3%
INFO: Compatibility graph building progress at 72.4%
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INFO: Compatibility graph building progress at 73%
INFO: Compatibility graph building progress at 73.1%
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INFO: Compatibility graph building progress at 73.3%
INFO: Compatibility graph building progress at 73.4%
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INFO: Compatibility graph building progress at 74%
INFO: Compatibility graph building progress at 74.1%
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INFO: Compatibility graph building progress at 75%
INFO: Compatibility graph building progress at 75.1%
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INFO: Compatibility graph building progress at 76%
INFO: Compatibility graph building progress at 76.1%
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INFO: Compatibility graph building progress at 76.3%
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INFO: Compatibility graph building progress at 76.5%
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INFO: Compatibility graph building progress at 76.9%
INFO: Compatibility graph building progress at 77%
INFO: Compatibility graph building progress at 77.1%
INFO: Compatibility graph building progress at 77.2%
INFO: Compatibility graph building progress at 77.3%
INFO: Compatibility graph building progress at 77.4%
INFO: Compatibility graph building progress at 77.5%
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INFO: Compatibility graph building progress at 77.8%
INFO: Compatibility graph building progress at 77.9%
INFO: Compatibility graph building progress at 78%
INFO: Compatibility graph building progress at 78.1%
INFO: Compatibility graph building progress at 78.2%
INFO: Compatibility graph building progress at 78.3%
INFO: Compatibility graph building progress at 78.4%
INFO: Compatibility graph building progress at 78.5%
INFO: Compatibility graph building progress at 78.6%
INFO: Compatibility graph building progress at 78.7%
INFO: Compatibility graph building progress at 78.8%
INFO: Compatibility graph building progress at 78.9%
INFO: Compatibility graph building progress at 79%
INFO: Compatibility graph building progress at 79.1%
INFO: Compatibility graph building progress at 79.2%
INFO: Compatibility graph building progress at 79.3%
INFO: Compatibility graph building progress at 79.4%
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INFO: Compatibility graph building progress at 79.8%
INFO: Compatibility graph building progress at 79.9%
INFO: Compatibility graph building progress at 80%
INFO: Compatibility graph building progress at 80.1%
INFO: Compatibility graph building progress at 80.2%
INFO: Compatibility graph building progress at 80.3%
INFO: Compatibility graph building progress at 80.4%
INFO: Compatibility graph building progress at 80.5%
INFO: Compatibility graph building progress at 80.6%
INFO: Compatibility graph building progress at 80.7%
INFO: Compatibility graph building progress at 80.8%
INFO: Compatibility graph building progress at 80.9%
INFO: Compatibility graph building progress at 81%
INFO: Compatibility graph building progress at 81.1%
INFO: Compatibility graph building progress at 81.2%
INFO: Compatibility graph building progress at 81.3%
INFO: Compatibility graph building progress at 81.4%
INFO: Compatibility graph building progress at 81.5%
INFO: Compatibility graph building progress at 81.6%
INFO: Compatibility graph building progress 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 progress at 83.6%
INFO: Compatibility graph building progress at 83.7%
INFO: Compatibility graph building progress at 83.8%
INFO: Compatibility graph building progress at 83.9%
INFO: Compatibility graph building progress at 84%
INFO: Compatibility graph building progress at 84.1%
INFO: Compatibility graph building progress at 84.2%
INFO: Compatibility graph building progress at 84.3%
INFO: Compatibility graph building progress at 84.4%
INFO: Compatibility graph building progress at 84.5%
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INFO: Compatibility graph building progress at 84.7%
INFO: Compatibility graph building progress at 84.8%
INFO: Compatibility graph building progress at 84.9%
INFO: Compatibility graph building progress at 85%
INFO: Compatibility graph building progress at 85.1%
INFO: Compatibility graph building progress at 85.2%
INFO: Compatibility graph building progress at 85.3%
INFO: Compatibility graph building progress at 85.4%
INFO: Compatibility graph building progress at 85.5%
INFO: Compatibility graph building progress at 85.6%
INFO: Compatibility graph building progress at 85.7%
INFO: Compatibility graph building progress at 85.8%
INFO: Compatibility graph building progress at 85.9%
INFO: Compatibility graph building progress at 86%
INFO: Compatibility graph building progress at 86.1%
INFO: Compatibility graph building progress at 86.2%
INFO: Compatibility graph building progress at 86.3%
INFO: Compatibility graph building progress at 86.4%
INFO: Compatibility graph building progress at 86.5%
INFO: Compatibility graph building progress at 86.6%
INFO: Compatibility graph building progress at 86.7%
INFO: Compatibility graph building progress at 86.8%
INFO: Compatibility graph building progress at 86.9%
INFO: Compatibility graph building progress at 87%
INFO: Compatibility graph building progress at 87.1%
INFO: Compatibility graph building progress at 87.2%
INFO: Compatibility graph building progress at 87.3%
INFO: Compatibility graph building progress at 87.4%
INFO: Compatibility graph building progress at 87.5%
INFO: Compatibility graph building progress at 87.6%
INFO: Compatibility graph building progress at 87.7%
INFO: Compatibility graph building progress at 87.8%
INFO: Compatibility graph building progress at 87.9%
INFO: Compatibility graph building progress at 88%
INFO: Compatibility graph building progress at 88.1%
INFO: Compatibility graph building progress at 88.2%
INFO: Compatibility graph building progress at 88.3%
INFO: Compatibility graph building progress at 88.4%
INFO: Compatibility graph building progress at 88.5%
INFO: Compatibility graph building progress at 88.6%
INFO: Compatibility graph building progress at 88.7%
INFO: Compatibility graph building progress at 88.8%
INFO: Compatibility graph building progress at 88.9%
INFO: Compatibility graph building progress at 89%
INFO: Compatibility graph building progress at 89.1%
INFO: Compatibility graph building progress at 89.2%
INFO: Compatibility graph building progress at 89.3%
INFO: Compatibility graph building progress at 89.4%
INFO: Compatibility graph building progress at 89.5%
INFO: Compatibility graph building progress at 89.6%
INFO: Compatibility graph building progress at 89.7%
INFO: Compatibility graph building progress at 89.8%
INFO: Compatibility graph building progress at 89.9%
INFO: Compatibility graph building progress at 90%
INFO: Compatibility graph building progress at 90.1%
INFO: Compatibility graph building progress at 90.2%
INFO: Compatibility graph building progress at 90.3%
INFO: Compatibility graph building progress at 90.4%
INFO: Compatibility graph building progress at 90.5%
INFO: Compatibility graph building progress at 90.6%
INFO: Compatibility graph building progress at 90.7%
INFO: Compatibility graph building progress at 90.8%
INFO: Compatibility graph building progress at 90.9%
INFO: Compatibility graph building progress at 91%
INFO: Compatibility graph building progress at 91.1%
INFO: Compatibility graph building progress at 91.2%
INFO: Compatibility graph building progress at 91.3%
INFO: Compatibility graph building progress at 91.4%
INFO: Compatibility graph building progress at 91.5%
INFO: Compatibility graph building progress at 91.6%
INFO: Compatibility graph building progress at 91.7%
INFO: Compatibility graph building progress at 91.8%
INFO: Compatibility graph building progress at 91.9%
INFO: Compatibility graph building progress at 92%
INFO: Compatibility graph building progress at 92.1%
INFO: Compatibility graph building progress at 92.2%
INFO: Compatibility graph building progress at 92.3%
INFO: Compatibility graph building progress at 92.4%
INFO: Compatibility graph building progress at 92.5%
INFO: Compatibility graph building progress at 92.6%
INFO: Compatibility graph building progress at 92.7%
INFO: Compatibility graph building progress at 92.8%
INFO: Compatibility graph building progress at 92.9%
INFO: Compatibility graph building progress at 93%
INFO: Compatibility graph building progress at 93.1%
INFO: Compatibility graph building progress at 93.2%
INFO: Compatibility graph building progress at 93.3%
INFO: Compatibility graph building progress at 93.4%
INFO: Compatibility graph building progress at 93.5%
INFO: Compatibility graph building progress at 93.6%
INFO: Compatibility graph building progress at 93.7%
INFO: Compatibility graph building progress at 93.8%
INFO: Compatibility graph building progress at 93.9%
INFO: Compatibility graph building progress at 94%
INFO: Compatibility graph building progress at 94.1%
INFO: Compatibility graph building progress at 94.2%
INFO: Compatibility graph building progress at 94.3%
INFO: Compatibility graph building progress at 94.4%
INFO: Compatibility graph building progress at 94.5%
INFO: Compatibility graph building progress at 94.6%
INFO: Compatibility graph building progress at 94.7%
INFO: Compatibility graph building progress at 94.8%
INFO: Compatibility graph building progress 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 progress at 96.8%
INFO: Compatibility graph building progress at 96.9%
INFO: Compatibility graph building progress at 97%
INFO: Compatibility graph building progress at 97.1%
INFO: Compatibility graph building progress at 97.2%
INFO: Compatibility graph building progress at 97.3%
INFO: Compatibility graph building progress at 97.4%
INFO: Compatibility graph building progress at 97.5%
INFO: Compatibility graph building progress at 97.6%
INFO: Compatibility graph building progress at 97.7%
INFO: Compatibility graph building progress at 97.8%
INFO: Compatibility graph building progress at 97.9%
INFO: Compatibility graph building progress at 98%
INFO: Compatibility graph building progress at 98.1%
INFO: Compatibility graph building progress at 98.2%
INFO: Compatibility graph building progress at 98.3%
INFO: Compatibility graph building progress at 98.4%
INFO: Compatibility graph building progress at 98.5%
INFO: Compatibility graph building progress at 98.6%
INFO: Compatibility graph building progress at 98.7%
INFO: Compatibility graph building progress at 98.8%
INFO: Compatibility graph building progress at 98.9%
INFO: Compatibility graph building progress at 99%
INFO: Compatibility graph building progress at 99.1%
INFO: Compatibility graph building progress at 99.2%
INFO: Compatibility graph building progress at 99.3%
INFO: Compatibility graph building progress at 99.4%
INFO: Compatibility graph building progress at 99.5%
INFO: Compatibility graph building progress at 99.6%
INFO: Compatibility graph building progress at 99.7%
INFO: Compatibility graph building progress at 99.8%
INFO: Compatibility graph building progress at 99.9%
INFO: Compatibility graph building progress at 100%
INFO: Compatibility graph building progress at 100%

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, [email protected]
Laurent Noé, [email protected]
Hélène Touzet, [email protected]

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, [email protected]
Laurent Noé, [email protected]
Hélène Touzet, [email protected]

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, [email protected]
Laurent Noé, [email protected]
Hélène Touzet, [email protected]

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". I couldnt perform further analysis. How do I get improve aligned sequence from matam