[2024-01-24 14:05:31,526] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:31,529] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:31,529] [INFO] DQC Reference Directory: /var/lib/cwl/stg60b57aec-e014-453c-860b-1321263e51a1/dqc_reference
[2024-01-24 14:05:32,719] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:32,720] [INFO] Task started: Prodigal
[2024-01-24 14:05:32,720] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c9298a3-88f6-4717-bb1d-b48f73718f0a/GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna/cds.fna -a GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:45,356] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:45,357] [INFO] Task started: HMMsearch
[2024-01-24 14:05:45,357] [INFO] Running command: hmmsearch --tblout GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60b57aec-e014-453c-860b-1321263e51a1/dqc_reference/reference_markers.hmm GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:45,625] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:45,626] [INFO] Found 6/6 markers.
[2024-01-24 14:05:45,668] [INFO] Query marker FASTA was written to GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:05:45,668] [INFO] Task started: Blastn
[2024-01-24 14:05:45,669] [INFO] Running command: blastn -query GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg60b57aec-e014-453c-860b-1321263e51a1/dqc_reference/reference_markers.fasta -out GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:46,628] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:46,632] [INFO] Selected 30 target genomes.
[2024-01-24 14:05:46,632] [INFO] Target genome list was writen to GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:05:46,643] [INFO] Task started: fastANI
[2024-01-24 14:05:46,643] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c9298a3-88f6-4717-bb1d-b48f73718f0a/GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna.gz --refList GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:09,929] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:09,930] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60b57aec-e014-453c-860b-1321263e51a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:09,930] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60b57aec-e014-453c-860b-1321263e51a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:09,952] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:09,952] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:09,953] [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
Maribius salinus	strain=DSM 26892	GCA_900141995.1	313368	313368	type	True	79.9011	617	1467	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.7922	626	1467	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	79.2802	617	1467	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	79.2622	564	1467	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	79.2585	565	1467	95	below_threshold
Roseivivax marinus	strain=DSM 27511	GCA_900109705.1	1379903	1379903	type	True	79.2505	527	1467	95	below_threshold
Palleronia marisminoris	strain=DSM 26347	GCA_900113405.1	315423	315423	type	True	79.2464	543	1467	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	79.2424	573	1467	95	below_threshold
Palleronia marisminoris	strain=CECT 7066	GCA_900172315.1	315423	315423	type	True	79.21	553	1467	95	below_threshold
Roseivivax halodurans	strain=JCM 10272	GCA_000521785.1	93683	93683	type	True	79.1208	508	1467	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	79.1106	530	1467	95	below_threshold
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	79.0508	537	1467	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	79.0062	558	1467	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	78.9803	547	1467	95	below_threshold
Allosediminivita pacifica	strain=DSM 29329	GCA_003054175.1	1267769	1267769	type	True	78.9207	507	1467	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	78.913	504	1467	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	78.8767	532	1467	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.7047	469	1467	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	78.6407	441	1467	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.5648	487	1467	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	78.4893	465	1467	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.4055	456	1467	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	78.3125	435	1467	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.0967	432	1467	95	below_threshold
Roseivivax halotolerans	strain=JCM 10271	GCA_900115815.1	93684	93684	type	True	78.0677	415	1467	95	below_threshold
Hasllibacter halocynthiae	strain=DSM 29318	GCA_003003095.1	595589	595589	type	True	78.0541	386	1467	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	78.0318	400	1467	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.8426	388	1467	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	77.0765	341	1467	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	77.0246	292	1467	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:09,956] [INFO] DFAST Taxonomy check result was written to GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:06:09,956] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:09,956] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:09,956] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60b57aec-e014-453c-860b-1321263e51a1/dqc_reference/checkm_data
[2024-01-24 14:06:09,957] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:10,017] [INFO] Task started: CheckM
[2024-01-24 14:06:10,017] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna/checkm_input GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:06:53,469] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:53,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:53,510] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:53,510] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:53,511] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:06:53,511] [INFO] Task started: Blastn
[2024-01-24 14:06:53,511] [INFO] Running command: blastn -query GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg60b57aec-e014-453c-860b-1321263e51a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:55,183] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:55,186] [INFO] Selected 23 target genomes.
[2024-01-24 14:06:55,187] [INFO] Target genome list was writen to GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:55,200] [INFO] Task started: fastANI
[2024-01-24 14:06:55,201] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c9298a3-88f6-4717-bb1d-b48f73718f0a/GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna.gz --refList GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:14,856] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:14,876] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:14,876] [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_900115595.1	s__Tranquillimonas alkanivorans	100.0	1462	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900111315.1	s__Tranquillimonas rosea	80.3822	675	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002869745.1	s__Oceaniglobus roseus	80.1776	658	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011175.1	s__Tranquillimonas littorinae	80.0024	611	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102015.1	s__Limimaricola pyoseonensis	79.8091	624	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153305.1	s__Oceanicola granulosus	79.6434	569	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	79.6425	567	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395815.1	s__Roseicyclus sp012395815	79.614	553	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	79.5417	608	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	79.3407	575	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	79.2994	612	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792445.1	s__Rhodobacter_B sp017792445	79.2787	555	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109705.1	s__Roseivivax marinus	79.2545	527	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	97.84	97.84	0.91	0.91	2	-
GCF_900172315.1	s__Palleronia marisminoris	79.2181	552	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_016412875.1	s__Palleronia pontilimi	79.1192	567	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340565.1	s__HLUCCA09 sp003340565	79.053	558	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	78.8855	487	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002166865.1	s__Roseovarius sp002166865	78.8835	420	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	78.7787	491	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004358185.1	s__Antarcticimicrobium luteum	78.5598	487	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	78.529	566	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122205.1	s__QEYE01 sp003122205	78.3673	424	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__QEYE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009830125.1	s__GH1-50 sp009830125	78.313	435	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GH1-50	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:14,878] [INFO] GTDB search result was written to GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:14,878] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:14,883] [INFO] DFAST_QC result json was written to GCF_900115595.1_IMG-taxon_2622736594_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:07:14,883] [INFO] DFAST_QC completed!
[2024-01-24 14:07:14,883] [INFO] Total running time: 0h1m43s