[2024-01-24 14:05:34,365] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:34,367] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:34,367] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8eedb0f-4863-46ef-ad0c-21f315dcd6db/dqc_reference
[2024-01-24 14:05:35,636] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:35,637] [INFO] Task started: Prodigal
[2024-01-24 14:05:35,637] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d3d1cd2-5740-48ef-8c2d-832e5ced9a76/GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna/cds.fna -a GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:48,056] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:48,057] [INFO] Task started: HMMsearch
[2024-01-24 14:05:48,057] [INFO] Running command: hmmsearch --tblout GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8eedb0f-4863-46ef-ad0c-21f315dcd6db/dqc_reference/reference_markers.hmm GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:48,442] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:48,444] [INFO] Found 6/6 markers.
[2024-01-24 14:05:48,505] [INFO] Query marker FASTA was written to GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:05:48,505] [INFO] Task started: Blastn
[2024-01-24 14:05:48,505] [INFO] Running command: blastn -query GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8eedb0f-4863-46ef-ad0c-21f315dcd6db/dqc_reference/reference_markers.fasta -out GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:49,357] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:49,361] [INFO] Selected 18 target genomes.
[2024-01-24 14:05:49,361] [INFO] Target genome list was writen to GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:05:49,367] [INFO] Task started: fastANI
[2024-01-24 14:05:49,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d3d1cd2-5740-48ef-8c2d-832e5ced9a76/GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna.gz --refList GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:01,316] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:01,316] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8eedb0f-4863-46ef-ad0c-21f315dcd6db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:01,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8eedb0f-4863-46ef-ad0c-21f315dcd6db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:01,334] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:01,334] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:01,335] [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
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	100.0	1180	1182	95	conclusive
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	80.3948	605	1182	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	80.0084	563	1182	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	78.2161	420	1182	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	78.0352	305	1182	95	below_threshold
Sulfitobacter donghicola	strain=JCM 14565	GCA_000712275.1	421000	421000	type	True	77.9089	310	1182	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.7949	363	1182	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	77.7756	360	1182	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	77.7462	389	1182	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.7091	404	1182	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.6615	408	1182	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	76.7988	132	1182	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.6656	155	1182	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	76.6104	127	1182	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.5586	141	1182	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.5586	141	1182	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	76.2188	143	1182	95	below_threshold
Paracoccus aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	76.1889	116	1182	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:01,337] [INFO] DFAST Taxonomy check result was written to GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:06:01,337] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:01,338] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:01,338] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8eedb0f-4863-46ef-ad0c-21f315dcd6db/dqc_reference/checkm_data
[2024-01-24 14:06:01,340] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:01,378] [INFO] Task started: CheckM
[2024-01-24 14:06:01,378] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna/checkm_input GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:06:41,005] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:41,006] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:41,032] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:41,032] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:41,033] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:06:41,033] [INFO] Task started: Blastn
[2024-01-24 14:06:41,033] [INFO] Running command: blastn -query GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8eedb0f-4863-46ef-ad0c-21f315dcd6db/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:42,484] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:42,487] [INFO] Selected 11 target genomes.
[2024-01-24 14:06:42,488] [INFO] Target genome list was writen to GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:42,502] [INFO] Task started: fastANI
[2024-01-24 14:06:42,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d3d1cd2-5740-48ef-8c2d-832e5ced9a76/GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna.gz --refList GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:51,263] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:51,273] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:51,274] [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_900116285.1	s__Sulfitobacter marinus	100.0	1181	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013139555.1	s__Sulfitobacter sp013139555	87.2453	813	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282155.1	s__Sulfitobacter sp013282155	83.9735	848	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_000156335.1	s__Sulfitobacter sp000156335	81.3433	714	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106935.1	s__Sulfitobacter pontiacus	80.3948	605	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_900103185.1	s__Sulfitobacter litoralis	80.0084	563	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.10	98.53	0.92	0.85	6	-
GCF_006064855.1	s__Sulfitobacter sp006064855	79.8612	564	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054325.1	s__Sulfitobacter mediterraneus	78.2161	420	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.52	96.39	0.88	0.86	71	-
GCF_001650875.1	s__Sulfitobacter sp001650875	77.9209	441	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743885.1	s__Sulfitobacter sp001635605	77.8391	368	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	-
GCA_017854855.1	s__Sulfitobacter sp017854855	77.8189	408	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:51,275] [INFO] GTDB search result was written to GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:51,276] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:51,282] [INFO] DFAST_QC result json was written to GCF_900116285.1_IMG-taxon_2619619641_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:06:51,282] [INFO] DFAST_QC completed!
[2024-01-24 14:06:51,283] [INFO] Total running time: 0h1m17s