[2024-01-24 13:40:44,560] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:44,563] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:44,563] [INFO] DQC Reference Directory: /var/lib/cwl/stg385dc944-2d05-42b5-98ec-5eb34da3a611/dqc_reference
[2024-01-24 13:40:45,898] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:45,898] [INFO] Task started: Prodigal
[2024-01-24 13:40:45,899] [INFO] Running command: gunzip -c /var/lib/cwl/stg60e44490-ab05-4424-a25a-72153fce1cff/GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna/cds.fna -a GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:01,870] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:01,870] [INFO] Task started: HMMsearch
[2024-01-24 13:41:01,870] [INFO] Running command: hmmsearch --tblout GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg385dc944-2d05-42b5-98ec-5eb34da3a611/dqc_reference/reference_markers.hmm GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:02,221] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:02,222] [INFO] Found 6/6 markers.
[2024-01-24 13:41:02,277] [INFO] Query marker FASTA was written to GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:41:02,278] [INFO] Task started: Blastn
[2024-01-24 13:41:02,278] [INFO] Running command: blastn -query GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg385dc944-2d05-42b5-98ec-5eb34da3a611/dqc_reference/reference_markers.fasta -out GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:03,237] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:03,240] [INFO] Selected 23 target genomes.
[2024-01-24 13:41:03,241] [INFO] Target genome list was writen to GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:41:03,248] [INFO] Task started: fastANI
[2024-01-24 13:41:03,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg60e44490-ab05-4424-a25a-72153fce1cff/GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna.gz --refList GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:24,163] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:24,164] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg385dc944-2d05-42b5-98ec-5eb34da3a611/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:24,165] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg385dc944-2d05-42b5-98ec-5eb34da3a611/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:24,186] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:24,186] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:24,186] [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
Tropicimonas isoalkanivorans	strain=DSM 19548	GCA_900112335.1	441112	441112	type	True	100.0	1630	1632	95	conclusive
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	79.6086	317	1632	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	79.2539	315	1632	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	79.2075	317	1632	95	below_threshold
Aliiruegeria sabulilitoris	strain=GJMS-35	GCA_001558155.1	1510458	1510458	type	True	79.1064	563	1632	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	78.9541	451	1632	95	below_threshold
Aliiruegeria lutimaris	strain=DSM 25294	GCA_900099935.1	571298	571298	type	True	78.8674	555	1632	95	below_threshold
Aliiruegeria haliotis	strain=DSM 29328	GCA_003003255.1	1280846	1280846	type	True	78.7217	499	1632	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	78.4496	383	1632	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	78.4078	370	1632	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.4036	338	1632	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	78.3889	271	1632	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.0922	303	1632	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.0413	441	1632	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	77.9648	359	1632	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	77.9408	326	1632	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.8893	323	1632	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	77.8146	342	1632	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	77.7942	330	1632	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.7901	344	1632	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.5402	335	1632	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	77.4705	352	1632	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.3351	311	1632	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:24,188] [INFO] DFAST Taxonomy check result was written to GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:41:24,189] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:24,189] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:24,189] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg385dc944-2d05-42b5-98ec-5eb34da3a611/dqc_reference/checkm_data
[2024-01-24 13:41:24,190] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:24,240] [INFO] Task started: CheckM
[2024-01-24 13:41:24,240] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna/checkm_input GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:42:12,733] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:12,735] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:12,759] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:12,760] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:12,760] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:42:12,761] [INFO] Task started: Blastn
[2024-01-24 13:42:12,761] [INFO] Running command: blastn -query GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg385dc944-2d05-42b5-98ec-5eb34da3a611/dqc_reference/reference_markers_gtdb.fasta -out GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:14,283] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:14,286] [INFO] Selected 13 target genomes.
[2024-01-24 13:42:14,287] [INFO] Target genome list was writen to GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:14,325] [INFO] Task started: fastANI
[2024-01-24 13:42:14,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg60e44490-ab05-4424-a25a-72153fce1cff/GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna.gz --refList GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:26,271] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:26,287] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:26,287] [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_900112335.1	s__Tropicimonas isoalkanivorans	100.0	1631	1632	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900188335.1	s__Tropicimonas sediminicola	80.2332	749	1632	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001509585.1	s__Tropicimonas marinistellae	79.269	667	1632	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345735.1	s__Rhodovulum adriaticum	79.2537	315	1632	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004146235.1	s__Tropicimonas sp004146235	79.1964	606	1632	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001558155.1	s__Tropicimonas sabulilitoris	79.1239	559	1632	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900099935.1	s__Tropicimonas lutimaris	78.8873	553	1632	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390845.1	s__Tropicimonas sp003390845	78.7478	492	1632	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003255.1	s__Tropicimonas haliotis	78.7084	500	1632	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	78.2175	425	1632	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102075.1	s__Salipiger thiooxidans	78.0291	441	1632	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_009857745.1	s__Thalassobius mangrovi	77.5585	333	1632	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018219815.1	s__Thalassobius aquimarinus	77.3447	310	1632	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:26,289] [INFO] GTDB search result was written to GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:26,290] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:26,294] [INFO] DFAST_QC result json was written to GCF_900112335.1_IMG-taxon_2615840715_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:42:26,294] [INFO] DFAST_QC completed!
[2024-01-24 13:42:26,294] [INFO] Total running time: 0h1m42s