[2024-01-25 18:02:05,572] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:02:05,574] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:02:05,574] [INFO] DQC Reference Directory: /var/lib/cwl/stg9659671c-3fa4-4ddb-86d8-1ea43ed8457c/dqc_reference
[2024-01-25 18:02:06,768] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:02:06,769] [INFO] Task started: Prodigal
[2024-01-25 18:02:06,769] [INFO] Running command: gunzip -c /var/lib/cwl/stgc1f1f422-11b1-4098-a5f9-e34c4864d21f/GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna/cds.fna -a GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:02:16,450] [INFO] Task succeeded: Prodigal
[2024-01-25 18:02:16,450] [INFO] Task started: HMMsearch
[2024-01-25 18:02:16,450] [INFO] Running command: hmmsearch --tblout GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9659671c-3fa4-4ddb-86d8-1ea43ed8457c/dqc_reference/reference_markers.hmm GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:02:16,672] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:02:16,673] [INFO] Found 6/6 markers.
[2024-01-25 18:02:16,703] [INFO] Query marker FASTA was written to GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 18:02:16,703] [INFO] Task started: Blastn
[2024-01-25 18:02:16,703] [INFO] Running command: blastn -query GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9659671c-3fa4-4ddb-86d8-1ea43ed8457c/dqc_reference/reference_markers.fasta -out GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:17,543] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:17,546] [INFO] Selected 18 target genomes.
[2024-01-25 18:02:17,546] [INFO] Target genome list was writen to GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 18:02:17,554] [INFO] Task started: fastANI
[2024-01-25 18:02:17,554] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1f1f422-11b1-4098-a5f9-e34c4864d21f/GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna.gz --refList GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:02:34,196] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:34,196] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9659671c-3fa4-4ddb-86d8-1ea43ed8457c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:02:34,197] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9659671c-3fa4-4ddb-86d8-1ea43ed8457c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:02:34,208] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:02:34,208] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:02:34,208] [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
Methylocapsa palsarum	strain=NE2	GCA_900114285.1	1612308	1612308	type	True	100.0	1325	1328	95	conclusive
Methylocapsa aurea	strain=KYG	GCA_000746085.1	663610	663610	type	True	78.6242	470	1328	95	below_threshold
Methylocella silvestris	strain=BL2	GCA_000021745.1	199596	199596	type	True	78.4187	392	1328	95	below_threshold
Methylocapsa acidiphila	strain=B2	GCA_000427445.1	133552	133552	type	True	78.2661	415	1328	95	below_threshold
Beijerinckia indica subsp. indica	strain=ATCC 9039	GCA_000019845.1	31994	533	type	True	77.8101	173	1328	95	below_threshold
Methylovirgula ligni	strain=BW863	GCA_003387225.1	569860	569860	type	True	77.657	260	1328	95	below_threshold
Candidatus Rhodoblastus alkanivorans		GCA_022760755.1	2954117	2954117	type	True	77.5034	229	1328	95	below_threshold
Methyloferula stellata	strain=AR4T	GCA_000385335.1	876270	876270	type	True	77.4586	253	1328	95	below_threshold
Rhabdaerophilum calidifontis	strain=SYSU G02060	GCA_008641065.1	2604328	2604328	type	True	77.1407	168	1328	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	77.0829	180	1328	95	below_threshold
Beijerinckia mobilis	strain=UQM 1969	GCA_000745425.1	231434	231434	type	True	77.063	182	1328	95	below_threshold
Bradyrhizobium huanghuaihaiense	strain=CGMCC 1.10948	GCA_007830635.1	990078	990078	type	True	76.8768	183	1328	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	76.8693	158	1328	95	below_threshold
Roseiarcus fermentans	strain=DSM 24875	GCA_003315135.1	1473586	1473586	type	True	76.7207	237	1328	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	76.5983	210	1328	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.5909	212	1328	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	76.471	172	1328	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	76.3229	219	1328	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:02:34,209] [INFO] DFAST Taxonomy check result was written to GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 18:02:34,209] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:02:34,210] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:02:34,210] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9659671c-3fa4-4ddb-86d8-1ea43ed8457c/dqc_reference/checkm_data
[2024-01-25 18:02:34,211] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:02:34,254] [INFO] Task started: CheckM
[2024-01-25 18:02:34,254] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna/checkm_input GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 18:03:05,031] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:05,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:05,051] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:05,052] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:05,052] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 18:03:05,052] [INFO] Task started: Blastn
[2024-01-25 18:03:05,052] [INFO] Running command: blastn -query GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9659671c-3fa4-4ddb-86d8-1ea43ed8457c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:06,738] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:06,741] [INFO] Selected 14 target genomes.
[2024-01-25 18:03:06,741] [INFO] Target genome list was writen to GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:06,754] [INFO] Task started: fastANI
[2024-01-25 18:03:06,754] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1f1f422-11b1-4098-a5f9-e34c4864d21f/GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna.gz --refList GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:03:18,001] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:18,011] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:03:18,011] [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_900114285.1	s__Methylocella palsarum	100.0	1325	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000746085.1	s__Methylocella aurea	78.6151	471	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021745.1	s__Methylocella silvestris	78.4084	393	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901905185.1	s__Methylocella tundrae	78.3345	380	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	97.31	97.31	0.88	0.88	2	-
GCF_000427445.1	s__Methylocella acidiphila	78.2661	415	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002891535.1	s__Methylocella silvestris_A	78.2608	407	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003244015.1	s__Methylocella sp003244015	77.469	237	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_901457705.2	s__RH-AL1 sp901457705	77.419	241	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__RH-AL1	95.0	99.94	99.94	0.99	0.99	3	-
GCA_006514895.1	s__Methylocella sp006514895	77.3385	232	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003837805.1	s__Bradyrhizobium sp003837805	77.1786	156	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009720755.1	s__Rhodoplanes serenus	76.8559	170	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	97.72	97.48	0.91	0.88	4	-
GCA_019242655.1	s__JAFASC01 sp019242655	76.7963	135	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__JAFASC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019233695.1	s__JAFAME01 sp019233695	76.5193	148	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__JAFAME01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655535.1	s__Methyloferula sp015655535	76.4916	177	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methyloferula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:03:18,014] [INFO] GTDB search result was written to GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 18:03:18,014] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:03:18,017] [INFO] DFAST_QC result json was written to GCF_900114285.1_IMG-taxon_2675903028_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 18:03:18,018] [INFO] DFAST_QC completed!
[2024-01-25 18:03:18,018] [INFO] Total running time: 0h1m12s