[2024-01-24 13:01:12,489] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:12,492] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:12,493] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ba4494b-3ab9-475f-b02b-58ed2f078205/dqc_reference
[2024-01-24 13:01:13,857] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:13,861] [INFO] Task started: Prodigal
[2024-01-24 13:01:13,861] [INFO] Running command: gunzip -c /var/lib/cwl/stge5718973-e646-4c40-9b85-fd3dced4c869/GCF_000733855.1_ASM73385v1_genomic.fna.gz | prodigal -d GCF_000733855.1_ASM73385v1_genomic.fna/cds.fna -a GCF_000733855.1_ASM73385v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:28,714] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:28,714] [INFO] Task started: HMMsearch
[2024-01-24 13:01:28,714] [INFO] Running command: hmmsearch --tblout GCF_000733855.1_ASM73385v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ba4494b-3ab9-475f-b02b-58ed2f078205/dqc_reference/reference_markers.hmm GCF_000733855.1_ASM73385v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:29,025] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:29,026] [INFO] Found 6/6 markers.
[2024-01-24 13:01:29,067] [INFO] Query marker FASTA was written to GCF_000733855.1_ASM73385v1_genomic.fna/markers.fasta
[2024-01-24 13:01:29,067] [INFO] Task started: Blastn
[2024-01-24 13:01:29,067] [INFO] Running command: blastn -query GCF_000733855.1_ASM73385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ba4494b-3ab9-475f-b02b-58ed2f078205/dqc_reference/reference_markers.fasta -out GCF_000733855.1_ASM73385v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:29,894] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:29,898] [INFO] Selected 20 target genomes.
[2024-01-24 13:01:29,899] [INFO] Target genome list was writen to GCF_000733855.1_ASM73385v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:29,907] [INFO] Task started: fastANI
[2024-01-24 13:01:29,907] [INFO] Running command: fastANI --query /var/lib/cwl/stge5718973-e646-4c40-9b85-fd3dced4c869/GCF_000733855.1_ASM73385v1_genomic.fna.gz --refList GCF_000733855.1_ASM73385v1_genomic.fna/target_genomes.txt --output GCF_000733855.1_ASM73385v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:45,127] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:45,127] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ba4494b-3ab9-475f-b02b-58ed2f078205/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:45,128] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ba4494b-3ab9-475f-b02b-58ed2f078205/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:45,141] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:01:45,141] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:01:45,142] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Methylomicrobium lacus	strain=LW14	GCA_000527095.1	136992	136992	type	True	82.9476	812	1507	95	below_threshold
Methylosarcina fibrata	strain=AML-C10	GCA_000372865.1	105972	105972	type	True	79.8844	498	1507	95	below_threshold
Methylobacter marinus	strain=A45	GCA_000383855.1	34058	34058	type	True	77.6058	286	1507	95	below_threshold
Methylomonas koyamae	strain=Fw12E-Y	GCA_019669905.1	702114	702114	suspected-type	True	77.551	237	1507	95	below_threshold
Methylomonas rhizoryzae	strain=GJ1	GCA_008632455.1	2608981	2608981	type	True	77.4012	162	1507	95	below_threshold
Methylomonas koyamae	strain=JCM 16701	GCA_001312005.1	702114	702114	suspected-type	True	77.3066	222	1507	95	below_threshold
Methylomonas albis	strain=EbA	GCA_014850955.1	1854563	1854563	type	True	76.9772	149	1507	95	below_threshold
Methylomarinum vadi	strain=IT-4	GCA_000733935.1	438855	438855	type	True	76.9745	190	1507	95	below_threshold
Methylotuvimicrobium alcaliphilum	strain=20Z	GCA_000968535.1	271065	271065	type	True	76.9338	156	1507	95	below_threshold
Methylomonas denitrificans	strain=FJG1	GCA_000785705.2	1538553	1538553	type	True	76.9302	184	1507	95	below_threshold
Methylococcus geothermalis	strain=IM1	GCA_012769535.1	2681310	2681310	type	True	76.7081	142	1507	95	below_threshold
Methylogaea oryzae	strain=E10	GCA_019669985.1	1295382	1295382	type	True	76.6717	114	1507	95	below_threshold
Methylomagnum ishizawai	strain=RS11D-Pr	GCA_019670005.1	1760988	1760988	type	True	76.5656	126	1507	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	76.2198	50	1507	95	below_threshold
Methyloterricola oryzae	strain=73a	GCA_000934725.1	1495050	1495050	type	True	76.071	104	1507	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.0259	110	1507	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	75.4168	120	1507	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:45,144] [INFO] DFAST Taxonomy check result was written to GCF_000733855.1_ASM73385v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:45,144] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:45,144] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:45,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ba4494b-3ab9-475f-b02b-58ed2f078205/dqc_reference/checkm_data
[2024-01-24 13:01:45,146] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:45,189] [INFO] Task started: CheckM
[2024-01-24 13:01:45,189] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000733855.1_ASM73385v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000733855.1_ASM73385v1_genomic.fna/checkm_input GCF_000733855.1_ASM73385v1_genomic.fna/checkm_result
[2024-01-24 13:02:28,878] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:28,880] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:28,900] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:28,900] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:28,900] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000733855.1_ASM73385v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:28,900] [INFO] Task started: Blastn
[2024-01-24 13:02:28,901] [INFO] Running command: blastn -query GCF_000733855.1_ASM73385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ba4494b-3ab9-475f-b02b-58ed2f078205/dqc_reference/reference_markers_gtdb.fasta -out GCF_000733855.1_ASM73385v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:30,298] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:30,303] [INFO] Selected 12 target genomes.
[2024-01-24 13:02:30,303] [INFO] Target genome list was writen to GCF_000733855.1_ASM73385v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:30,312] [INFO] Task started: fastANI
[2024-01-24 13:02:30,312] [INFO] Running command: fastANI --query /var/lib/cwl/stge5718973-e646-4c40-9b85-fd3dced4c869/GCF_000733855.1_ASM73385v1_genomic.fna.gz --refList GCF_000733855.1_ASM73385v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000733855.1_ASM73385v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:41,321] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:41,331] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:41,331] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000733855.1	s__Methylomicrobium agile	100.0	1507	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomicrobium	95.0	99.08	99.08	0.92	0.92	2	conclusive
GCF_016745425.1	s__Methylomicrobium sp016745425	91.2909	1084	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000527095.1	s__Methylomicrobium lacus	82.9677	812	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372865.1	s__Methylosarcina fibrata	79.8858	499	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006483455.1	s__Methylomonas koyamae_B	77.4248	229	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001312005.1	s__Methylomonas koyamae	77.3186	222	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	96.46	95.49	0.87	0.86	5	-
GCF_001644025.1	s__Methylomonas koyamae_A	77.17	230	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	97.40	97.36	0.85	0.85	3	-
GCF_903064715.1	s__Methylomonas sp903064715	76.8699	147	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002934365.1	s__Methylobacter_A tundripaludum_A	76.8513	202	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004299305.1	s__Methylobacter_A sp004299305	76.3954	131	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874115.1	s__Methyloglobulus sp016874115	76.0585	92	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloglobulus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:41,333] [INFO] GTDB search result was written to GCF_000733855.1_ASM73385v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:41,333] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:41,338] [INFO] DFAST_QC result json was written to GCF_000733855.1_ASM73385v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:41,338] [INFO] DFAST_QC completed!
[2024-01-24 13:02:41,338] [INFO] Total running time: 0h1m29s