[2024-01-24 14:28:15,809] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:15,816] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:15,816] [INFO] DQC Reference Directory: /var/lib/cwl/stg620efdf0-baf5-43cc-85e0-97bdc46f5912/dqc_reference
[2024-01-24 14:28:17,941] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:17,941] [INFO] Task started: Prodigal
[2024-01-24 14:28:17,942] [INFO] Running command: gunzip -c /var/lib/cwl/stg737d36e6-3d70-494f-bd54-500e12ab9a50/GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna/cds.fna -a GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:33,009] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:33,010] [INFO] Task started: HMMsearch
[2024-01-24 14:28:33,010] [INFO] Running command: hmmsearch --tblout GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg620efdf0-baf5-43cc-85e0-97bdc46f5912/dqc_reference/reference_markers.hmm GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:33,282] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:33,283] [INFO] Found 6/6 markers.
[2024-01-24 14:28:33,331] [INFO] Query marker FASTA was written to GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:28:33,332] [INFO] Task started: Blastn
[2024-01-24 14:28:33,332] [INFO] Running command: blastn -query GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg620efdf0-baf5-43cc-85e0-97bdc46f5912/dqc_reference/reference_markers.fasta -out GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:34,378] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:34,390] [INFO] Selected 22 target genomes.
[2024-01-24 14:28:34,391] [INFO] Target genome list was writen to GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:28:34,424] [INFO] Task started: fastANI
[2024-01-24 14:28:34,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg737d36e6-3d70-494f-bd54-500e12ab9a50/GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna.gz --refList GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:56,630] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:56,630] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg620efdf0-baf5-43cc-85e0-97bdc46f5912/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:56,631] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg620efdf0-baf5-43cc-85e0-97bdc46f5912/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:56,647] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:28:56,647] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:28:56,647] [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
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	80.7525	931	1763	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	78.6054	498	1763	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	78.4311	447	1763	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	78.0755	407	1763	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	77.9273	370	1763	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	77.6582	440	1763	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	77.4827	559	1763	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	77.4694	558	1763	95	below_threshold
Nisaea denitrificans	strain=DSM 18348	GCA_000426505.1	390877	390877	type	True	77.4672	359	1763	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	77.4349	375	1763	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	77.2066	435	1763	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	77.1671	392	1763	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	77.0112	394	1763	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	77.0035	438	1763	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.8885	372	1763	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.8168	403	1763	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	76.7891	217	1763	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	76.7844	303	1763	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.7592	345	1763	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.4197	304	1763	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	76.409	159	1763	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	76.323	379	1763	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:56,649] [INFO] DFAST Taxonomy check result was written to GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:28:56,649] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:56,649] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:56,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg620efdf0-baf5-43cc-85e0-97bdc46f5912/dqc_reference/checkm_data
[2024-01-24 14:28:56,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:56,700] [INFO] Task started: CheckM
[2024-01-24 14:28:56,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna/checkm_input GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:29:41,748] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:41,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:41,775] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:41,775] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:41,775] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:29:41,776] [INFO] Task started: Blastn
[2024-01-24 14:29:41,776] [INFO] Running command: blastn -query GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg620efdf0-baf5-43cc-85e0-97bdc46f5912/dqc_reference/reference_markers_gtdb.fasta -out GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:43,850] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:43,854] [INFO] Selected 12 target genomes.
[2024-01-24 14:29:43,854] [INFO] Target genome list was writen to GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:43,870] [INFO] Task started: fastANI
[2024-01-24 14:29:43,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg737d36e6-3d70-494f-bd54-500e12ab9a50/GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna.gz --refList GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:58,059] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:58,069] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:58,070] [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_900102465.1	s__Thalassobaculum litoreum	100.0	1756	1763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	conclusive
GCF_014652915.1	s__Thalassobaculum_A fulvum	80.7629	930	1763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401495.1	s__Thalassobaculum_A sp018401495	80.0404	815	1763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000171835.1	s__Thalassobaculum_A sp000171835	79.2322	710	1763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203465.1	s__JABMNR01 sp013203465	79.1075	636	1763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__JABMNR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904705.1	s__Nisaea sp014904705	78.5977	499	1763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640745.1	s__Nisaea sp017640745	78.3309	498	1763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336875.1	s__Oleisolibacter albus	77.3653	280	1763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Oleisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230255.1	s__Caenispirillum bisanense	77.0447	435	1763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000576635.1	s__Skermanella stibiiresistens	77.0357	392	1763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013423485.1	s__Azospirillum oleiclasticum	76.9357	450	1763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	0.99	0.99	2	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	76.7113	296	1763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:58,074] [INFO] GTDB search result was written to GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:58,075] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:58,079] [INFO] DFAST_QC result json was written to GCF_900102465.1_IMG-taxon_2599185271_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:29:58,079] [INFO] DFAST_QC completed!
[2024-01-24 14:29:58,079] [INFO] Total running time: 0h1m42s