[2024-01-24 13:49:19,264] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:19,266] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:19,266] [INFO] DQC Reference Directory: /var/lib/cwl/stg87298ef8-5335-4a90-99aa-2cbd15f67783/dqc_reference
[2024-01-24 13:49:20,695] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:20,696] [INFO] Task started: Prodigal
[2024-01-24 13:49:20,696] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e2ddad1-57c3-43f7-8832-d5c34a0713f8/GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna/cds.fna -a GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:32,865] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:32,865] [INFO] Task started: HMMsearch
[2024-01-24 13:49:32,865] [INFO] Running command: hmmsearch --tblout GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87298ef8-5335-4a90-99aa-2cbd15f67783/dqc_reference/reference_markers.hmm GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:33,141] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:33,143] [INFO] Found 6/6 markers.
[2024-01-24 13:49:33,181] [INFO] Query marker FASTA was written to GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:49:33,182] [INFO] Task started: Blastn
[2024-01-24 13:49:33,182] [INFO] Running command: blastn -query GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg87298ef8-5335-4a90-99aa-2cbd15f67783/dqc_reference/reference_markers.fasta -out GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:34,302] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:34,305] [INFO] Selected 17 target genomes.
[2024-01-24 13:49:34,306] [INFO] Target genome list was writen to GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:49:34,312] [INFO] Task started: fastANI
[2024-01-24 13:49:34,312] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e2ddad1-57c3-43f7-8832-d5c34a0713f8/GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna.gz --refList GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:49,178] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:49,178] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87298ef8-5335-4a90-99aa-2cbd15f67783/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:49,179] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87298ef8-5335-4a90-99aa-2cbd15f67783/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:49,193] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:49,193] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:49,194] [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
Roseivivax marinus	strain=DSM 27511	GCA_900109705.1	1379903	1379903	type	True	100.0	1318	1321	95	conclusive
Roseivivax halodurans	strain=JCM 10272	GCA_000521785.1	93683	93683	type	True	81.8236	765	1321	95	below_threshold
Roseivivax jejudonensis	strain=CECT 8625	GCA_900172265.1	1529041	1529041	type	True	81.7207	830	1321	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	81.649	815	1321	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	80.5496	688	1321	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	80.0754	676	1321	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	79.6053	513	1321	95	below_threshold
Roseivivax halotolerans	strain=JCM 10271	GCA_900115815.1	93684	93684	type	True	79.5348	588	1321	95	below_threshold
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	78.8717	451	1321	95	below_threshold
Limimaricola soesokkakensis	strain=CECT 8367	GCA_900172345.1	1343159	1343159	type	True	78.7998	457	1321	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	78.4712	421	1321	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.4619	433	1321	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.2441	402	1321	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.1903	524	1321	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.9636	404	1321	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.9251	368	1321	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	77.5473	346	1321	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:49,195] [INFO] DFAST Taxonomy check result was written to GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:49:49,196] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:49,196] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:49,196] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87298ef8-5335-4a90-99aa-2cbd15f67783/dqc_reference/checkm_data
[2024-01-24 13:49:49,198] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:49,240] [INFO] Task started: CheckM
[2024-01-24 13:49:49,240] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna/checkm_input GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:50:29,083] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:29,085] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:29,103] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:29,103] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:29,104] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:50:29,104] [INFO] Task started: Blastn
[2024-01-24 13:50:29,104] [INFO] Running command: blastn -query GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg87298ef8-5335-4a90-99aa-2cbd15f67783/dqc_reference/reference_markers_gtdb.fasta -out GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:31,116] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:31,119] [INFO] Selected 11 target genomes.
[2024-01-24 13:50:31,120] [INFO] Target genome list was writen to GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:31,130] [INFO] Task started: fastANI
[2024-01-24 13:50:31,130] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e2ddad1-57c3-43f7-8832-d5c34a0713f8/GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna.gz --refList GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:41,515] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:41,530] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:41,530] [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_900109705.1	s__Roseivivax marinus	100.0	1318	1321	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	97.84	97.84	0.91	0.91	2	conclusive
GCF_900112685.1	s__Roseivivax sediminis	81.88	824	1321	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521785.1	s__Roseivivax halodurans	81.8101	766	1321	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172265.1	s__Roseivivax jejudonensis	81.735	829	1321	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	81.6254	818	1321	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	80.3428	671	1321	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156805.1	s__Roseivivax lentus	80.0732	676	1321	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	79.6134	637	1321	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169415.1	s__Sagittula stellata	78.7259	543	1321	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689745.1	s__Roseicyclus sp015689745	78.6808	449	1321	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053725.1	s__Rhodovulum kholense	78.2173	460	1321	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:41,539] [INFO] GTDB search result was written to GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:41,540] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:41,545] [INFO] DFAST_QC result json was written to GCF_900109705.1_IMG-taxon_2693429879_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:50:41,546] [INFO] DFAST_QC completed!
[2024-01-24 13:50:41,546] [INFO] Total running time: 0h1m22s