[2024-01-24 12:22:28,021] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:28,023] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:28,023] [INFO] DQC Reference Directory: /var/lib/cwl/stg63efbe5e-018b-4a85-a1e7-b46e163e0fbf/dqc_reference
[2024-01-24 12:22:29,588] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:29,589] [INFO] Task started: Prodigal
[2024-01-24 12:22:29,589] [INFO] Running command: gunzip -c /var/lib/cwl/stg0451f80d-87d0-45aa-b61e-7d9eed9c6a0d/GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna.gz | prodigal -d GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna/cds.fna -a GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:41,007] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:41,008] [INFO] Task started: HMMsearch
[2024-01-24 12:22:41,008] [INFO] Running command: hmmsearch --tblout GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63efbe5e-018b-4a85-a1e7-b46e163e0fbf/dqc_reference/reference_markers.hmm GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:41,301] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:41,302] [INFO] Found 6/6 markers.
[2024-01-24 12:22:41,350] [INFO] Query marker FASTA was written to GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna/markers.fasta
[2024-01-24 12:22:41,351] [INFO] Task started: Blastn
[2024-01-24 12:22:41,351] [INFO] Running command: blastn -query GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg63efbe5e-018b-4a85-a1e7-b46e163e0fbf/dqc_reference/reference_markers.fasta -out GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:42,166] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:42,170] [INFO] Selected 13 target genomes.
[2024-01-24 12:22:42,171] [INFO] Target genome list was writen to GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 12:22:42,178] [INFO] Task started: fastANI
[2024-01-24 12:22:42,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg0451f80d-87d0-45aa-b61e-7d9eed9c6a0d/GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna.gz --refList GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna/target_genomes.txt --output GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:52,388] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:52,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63efbe5e-018b-4a85-a1e7-b46e163e0fbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:52,389] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63efbe5e-018b-4a85-a1e7-b46e163e0fbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:52,402] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:22:52,402] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:52,402] [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
Thalassobius mediterraneus	strain=CECT 5383	GCA_001458435.1	340021	340021	type	True	100.0	1133	1134	95	conclusive
Thalassobius mediterraneus	strain=DSM 16398	GCA_900156595.1	340021	340021	type	True	99.9936	1112	1134	95	conclusive
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	82.3088	785	1134	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	79.0069	528	1134	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	78.9517	478	1134	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	78.5892	309	1134	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	78.5342	362	1134	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.9594	260	1134	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	77.5227	294	1134	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.4306	195	1134	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	77.3929	216	1134	95	below_threshold
Ruegeria conchae	strain=TW15	GCA_000192475.2	981384	981384	suspected-type	True	77.3808	234	1134	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	77.149	263	1134	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:52,406] [INFO] DFAST Taxonomy check result was written to GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 12:22:52,409] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:52,410] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:52,410] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63efbe5e-018b-4a85-a1e7-b46e163e0fbf/dqc_reference/checkm_data
[2024-01-24 12:22:52,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:52,459] [INFO] Task started: CheckM
[2024-01-24 12:22:52,460] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna/checkm_input GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna/checkm_result
[2024-01-24 12:23:29,408] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:29,409] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:29,429] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:29,430] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:29,430] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna/markers.fasta)
[2024-01-24 12:23:29,431] [INFO] Task started: Blastn
[2024-01-24 12:23:29,431] [INFO] Running command: blastn -query GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg63efbe5e-018b-4a85-a1e7-b46e163e0fbf/dqc_reference/reference_markers_gtdb.fasta -out GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:30,619] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:30,623] [INFO] Selected 13 target genomes.
[2024-01-24 12:23:30,623] [INFO] Target genome list was writen to GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:30,635] [INFO] Task started: fastANI
[2024-01-24 12:23:30,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg0451f80d-87d0-45aa-b61e-7d9eed9c6a0d/GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna.gz --refList GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:40,316] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:40,327] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:40,327] [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_001458435.1	s__Thalassobius mediterraneus	100.0	1133	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001458255.1	s__Thalassobius autumnalis	82.3187	784	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.93	99.93	0.99	0.99	2	-
GCF_009857745.1	s__Thalassobius mangrovi	79.0064	528	1134	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	78.9517	478	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799325.1	s__Thalassobius vesicularis	78.7925	421	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511385.1	s__Phaeobacter gallaeciensis	78.7852	313	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.42	98.01	0.98	0.96	8	-
GCA_002708925.1	s__Thalassobius sp002708925	78.5062	364	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.91	99.91	0.84	0.84	2	-
GCF_001678945.1	s__Pseudophaeobacter_A gallaeciensis_A	78.4045	375	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter_A	95.0	100.00	100.00	0.99	0.99	2	-
GCA_017792425.1	s__Thalassobius sp017792425	78.3807	367	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458355.1	s__Thalassobius gelatinovorus	78.2176	413	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	100.00	99.99	0.99	0.99	3	-
GCF_013112245.1	s__Ruegeria sp013112245	78.1229	262	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.18	96.94	0.93	0.89	11	-
GCF_017743735.1	s__Shimia sp017743735	78.0793	362	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	95.87	95.63	0.93	0.93	3	-
GCF_000743705.1	s__Ruegeria halocynthiae_B	77.9578	300	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:40,330] [INFO] GTDB search result was written to GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:40,332] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:40,335] [INFO] DFAST_QC result json was written to GCF_001458435.1_T.mediterraneus_CECT5383_Seqman_Prokka_genomic.fna/dqc_result.json
[2024-01-24 12:23:40,336] [INFO] DFAST_QC completed!
[2024-01-24 12:23:40,336] [INFO] Total running time: 0h1m12s