[2024-01-24 13:57:56,139] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:56,142] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:56,142] [INFO] DQC Reference Directory: /var/lib/cwl/stgc61a00ff-b764-46a3-b66f-11c178000f57/dqc_reference
[2024-01-24 13:57:57,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:57,683] [INFO] Task started: Prodigal
[2024-01-24 13:57:57,683] [INFO] Running command: gunzip -c /var/lib/cwl/stg13717371-eb4d-454e-810a-e3d07b2fde8c/GCF_015482775.1_ASM1548277v1_genomic.fna.gz | prodigal -d GCF_015482775.1_ASM1548277v1_genomic.fna/cds.fna -a GCF_015482775.1_ASM1548277v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:11,987] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:11,988] [INFO] Task started: HMMsearch
[2024-01-24 13:58:11,988] [INFO] Running command: hmmsearch --tblout GCF_015482775.1_ASM1548277v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc61a00ff-b764-46a3-b66f-11c178000f57/dqc_reference/reference_markers.hmm GCF_015482775.1_ASM1548277v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:12,290] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:12,292] [INFO] Found 6/6 markers.
[2024-01-24 13:58:12,330] [INFO] Query marker FASTA was written to GCF_015482775.1_ASM1548277v1_genomic.fna/markers.fasta
[2024-01-24 13:58:12,331] [INFO] Task started: Blastn
[2024-01-24 13:58:12,331] [INFO] Running command: blastn -query GCF_015482775.1_ASM1548277v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc61a00ff-b764-46a3-b66f-11c178000f57/dqc_reference/reference_markers.fasta -out GCF_015482775.1_ASM1548277v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:13,453] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:13,457] [INFO] Selected 23 target genomes.
[2024-01-24 13:58:13,458] [INFO] Target genome list was writen to GCF_015482775.1_ASM1548277v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:13,470] [INFO] Task started: fastANI
[2024-01-24 13:58:13,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg13717371-eb4d-454e-810a-e3d07b2fde8c/GCF_015482775.1_ASM1548277v1_genomic.fna.gz --refList GCF_015482775.1_ASM1548277v1_genomic.fna/target_genomes.txt --output GCF_015482775.1_ASM1548277v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:33,122] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:33,122] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc61a00ff-b764-46a3-b66f-11c178000f57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:33,123] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc61a00ff-b764-46a3-b66f-11c178000f57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:33,140] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:33,140] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:33,140] [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
Kaustia mangrovi	strain=R1DC25	GCA_015482775.1	2593653	2593653	type	True	100.0	1543	1543	95	conclusive
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	77.6212	372	1543	95	below_threshold
Afifella pfennigii	strain=DSM 17143	GCA_000688515.1	209897	209897	type	True	77.5279	342	1543	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.5248	360	1543	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	77.4083	282	1543	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	77.3972	309	1543	95	below_threshold
Breoghania corrubedonensis	strain=DSM 23382	GCA_003053845.1	665038	665038	type	True	77.3637	289	1543	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	77.1664	337	1543	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	77.1246	306	1543	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	77.1081	290	1543	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	77.1058	304	1543	95	below_threshold
Xanthobacter tagetidis	strain=DSM 11105	GCA_014206845.1	60216	60216	type	True	77.1012	363	1543	95	below_threshold
Rhodoligotrophos appendicifer	strain=120-1	GCA_007474605.1	987056	987056	type	True	77.0529	241	1543	95	below_threshold
Chelatococcus composti	strain=CGMCC 1.15283	GCA_014641535.1	1743235	1743235	type	True	77.0475	304	1543	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.0443	374	1543	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	77.0055	318	1543	95	below_threshold
Ancylobacter oerskovii	strain=CCM 7435	GCA_018390555.1	459519	459519	type	True	76.9536	368	1543	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	76.9412	310	1543	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	76.8761	371	1543	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	76.8723	288	1543	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	76.858	302	1543	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.7716	220	1543	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	76.7482	366	1543	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:33,142] [INFO] DFAST Taxonomy check result was written to GCF_015482775.1_ASM1548277v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:33,142] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:33,143] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:33,143] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc61a00ff-b764-46a3-b66f-11c178000f57/dqc_reference/checkm_data
[2024-01-24 13:58:33,144] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:33,188] [INFO] Task started: CheckM
[2024-01-24 13:58:33,188] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015482775.1_ASM1548277v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015482775.1_ASM1548277v1_genomic.fna/checkm_input GCF_015482775.1_ASM1548277v1_genomic.fna/checkm_result
[2024-01-24 13:59:21,340] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:21,342] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:21,358] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:21,358] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:21,359] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015482775.1_ASM1548277v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:21,359] [INFO] Task started: Blastn
[2024-01-24 13:59:21,359] [INFO] Running command: blastn -query GCF_015482775.1_ASM1548277v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc61a00ff-b764-46a3-b66f-11c178000f57/dqc_reference/reference_markers_gtdb.fasta -out GCF_015482775.1_ASM1548277v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:23,614] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:23,619] [INFO] Selected 20 target genomes.
[2024-01-24 13:59:23,619] [INFO] Target genome list was writen to GCF_015482775.1_ASM1548277v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:24,147] [INFO] Task started: fastANI
[2024-01-24 13:59:24,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg13717371-eb4d-454e-810a-e3d07b2fde8c/GCF_015482775.1_ASM1548277v1_genomic.fna.gz --refList GCF_015482775.1_ASM1548277v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015482775.1_ASM1548277v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:43,353] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:43,374] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:43,374] [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_015482775.1	s__Kaustia mangrovi	100.0	1543	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Im1;g__Kaustia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005281615.1	s__Rhodoligotrophos sp005281615	77.6382	370	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Im1;g__Rhodoligotrophos	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688515.1	s__Afifella pfennigii	77.5127	343	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Afifella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576695.1	s__Nordella sp003576695	77.4919	372	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900185725.1	s__Stappia sp900185725	77.4912	408	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	97.99	0.94	0.94	3	-
GCF_013341275.1	s__Methyloligella sp013341275	77.4132	240	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloligella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196925.1	s__Chelatococcus_A caeni	77.3917	405	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	98.75	98.72	0.96	0.95	3	-
GCA_003574785.1	s__Nordella sp003574785	77.3444	400	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011046735.1	s__Nordella sp011046735	77.2742	340	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702305.1	s__GCF-000702305 sp000702305	77.2618	355	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__GCF-000702305	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000496075.1	s__Lutibaculum baratangense	77.2099	337	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Tepidamorphaceae;g__Lutibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018729455.1	s__Prosthecomicrobium_A sp018729455	77.1302	384	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Prosthecomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201415.1	s__Chelatococcus_A composti	77.0919	302	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	99.84	99.53	0.99	0.98	4	-
GCF_007474605.1	s__Rhodoligotrophos appendicifer	77.0628	240	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Im1;g__Rhodoligotrophos	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305515.1	s__Prosthecomicrobium_A hirschii	77.0416	409	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Prosthecomicrobium_A	95.0	97.89	97.89	0.95	0.95	2	-
GCA_017307955.1	s__Kaistia sp017307955	77.0158	330	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196455.1	s__Kaistia hirudinis	76.9805	305	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	96.80	96.80	0.96	0.96	2	-
GCF_016629525.1	s__Kaistia sp016629525	76.9353	321	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390555.1	s__Ancylobacter_B oerskovii	76.9329	370	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823325.1	s__Bosea sp013823325	76.6274	338	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	97.82	97.82	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:43,376] [INFO] GTDB search result was written to GCF_015482775.1_ASM1548277v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:43,377] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:43,382] [INFO] DFAST_QC result json was written to GCF_015482775.1_ASM1548277v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:43,382] [INFO] DFAST_QC completed!
[2024-01-24 13:59:43,382] [INFO] Total running time: 0h1m47s