[2024-01-24 10:47:06,642] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,645] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,645] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6a88805-b860-40e8-8746-ab0ea17cced1/dqc_reference
[2024-01-24 10:47:19,018] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:19,027] [INFO] Task started: Prodigal
[2024-01-24 10:47:19,027] [INFO] Running command: gunzip -c /var/lib/cwl/stgcdf846a3-4b84-4a8b-ae51-f002b7b500d4/GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna/cds.fna -a GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:31,544] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:31,545] [INFO] Task started: HMMsearch
[2024-01-24 10:47:31,545] [INFO] Running command: hmmsearch --tblout GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6a88805-b860-40e8-8746-ab0ea17cced1/dqc_reference/reference_markers.hmm GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:32,011] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:32,012] [INFO] Found 6/6 markers.
[2024-01-24 10:47:32,054] [INFO] Query marker FASTA was written to GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 10:47:32,167] [INFO] Task started: Blastn
[2024-01-24 10:47:32,168] [INFO] Running command: blastn -query GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6a88805-b860-40e8-8746-ab0ea17cced1/dqc_reference/reference_markers.fasta -out GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:36,678] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:36,682] [INFO] Selected 31 target genomes.
[2024-01-24 10:47:36,682] [INFO] Target genome list was writen to GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 10:47:39,116] [INFO] Task started: fastANI
[2024-01-24 10:47:39,117] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdf846a3-4b84-4a8b-ae51-f002b7b500d4/GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna.gz --refList GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:01,585] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:01,586] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd6a88805-b860-40e8-8746-ab0ea17cced1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:01,587] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd6a88805-b860-40e8-8746-ab0ea17cced1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:01,732] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:48:01,733] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:48:01,733] [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
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.1077	535	1364	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.984	589	1364	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	78.939	573	1364	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	78.9134	577	1364	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	78.9008	577	1364	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	78.7754	516	1364	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	78.7495	550	1364	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	78.7479	532	1364	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	78.7041	526	1364	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	78.6769	492	1364	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	78.5991	491	1364	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	78.5916	486	1364	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	78.5731	500	1364	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	78.5397	506	1364	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	78.5147	504	1364	95	below_threshold
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	78.3957	466	1364	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	78.3817	498	1364	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	78.3714	401	1364	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.3442	499	1364	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	78.3104	409	1364	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.2775	416	1364	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.259	404	1364	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.2352	445	1364	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	78.0937	436	1364	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	77.9965	393	1364	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.9299	374	1364	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	77.7656	369	1364	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	77.7395	353	1364	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.7229	345	1364	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	77.6944	359	1364	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	77.2373	249	1364	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:01,735] [INFO] DFAST Taxonomy check result was written to GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 10:48:01,735] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:01,736] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:01,736] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6a88805-b860-40e8-8746-ab0ea17cced1/dqc_reference/checkm_data
[2024-01-24 10:48:01,741] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:01,794] [INFO] Task started: CheckM
[2024-01-24 10:48:01,795] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna/checkm_input GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 10:48:55,978] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:55,980] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:56,001] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:56,001] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:56,002] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 10:48:56,003] [INFO] Task started: Blastn
[2024-01-24 10:48:56,003] [INFO] Running command: blastn -query GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6a88805-b860-40e8-8746-ab0ea17cced1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:58,952] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:58,957] [INFO] Selected 11 target genomes.
[2024-01-24 10:48:58,957] [INFO] Target genome list was writen to GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:59,019] [INFO] Task started: fastANI
[2024-01-24 10:48:59,020] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdf846a3-4b84-4a8b-ae51-f002b7b500d4/GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna.gz --refList GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:09,415] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:09,441] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:09,442] [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_900142295.1	s__Vannielia litorea	100.0	1362	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Vannielia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017792405.1	s__Vannielia sp017792405	85.6994	1059	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Vannielia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018424695.1	s__Vannielia litorea_A	84.6731	966	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Vannielia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006351965.1	s__Vannielia sp006351965	83.9092	998	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Vannielia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188335.1	s__Tropicimonas sediminicola	79.1504	556	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153725.1	s__Salipiger bermudensis	78.9035	577	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_012395815.1	s__Roseicyclus sp012395815	78.8927	572	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	78.7117	533	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	78.5553	518	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003789055.1	s__Oceanicola lentulus	78.4251	461	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	78.3069	499	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:09,444] [INFO] GTDB search result was written to GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:09,445] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:09,449] [INFO] DFAST_QC result json was written to GCF_900142295.1_IMG-taxon_2698536701_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 10:49:09,450] [INFO] DFAST_QC completed!
[2024-01-24 10:49:09,450] [INFO] Total running time: 0h2m3s