[2024-01-25 17:35:20,577] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:35:20,579] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:35:20,579] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf44e3ce-b5db-4d11-850e-b220699e5803/dqc_reference
[2024-01-25 17:35:21,733] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:35:21,734] [INFO] Task started: Prodigal
[2024-01-25 17:35:21,734] [INFO] Running command: gunzip -c /var/lib/cwl/stgf30bef5a-b71c-4fbe-bd17-14d5feffd694/GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna.gz | prodigal -d GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna/cds.fna -a GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:35:32,785] [INFO] Task succeeded: Prodigal
[2024-01-25 17:35:32,786] [INFO] Task started: HMMsearch
[2024-01-25 17:35:32,786] [INFO] Running command: hmmsearch --tblout GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf44e3ce-b5db-4d11-850e-b220699e5803/dqc_reference/reference_markers.hmm GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:35:33,002] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:35:33,003] [INFO] Found 6/6 markers.
[2024-01-25 17:35:33,033] [INFO] Query marker FASTA was written to GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta
[2024-01-25 17:35:33,033] [INFO] Task started: Blastn
[2024-01-25 17:35:33,033] [INFO] Running command: blastn -query GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf44e3ce-b5db-4d11-850e-b220699e5803/dqc_reference/reference_markers.fasta -out GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:33,839] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:33,841] [INFO] Selected 28 target genomes.
[2024-01-25 17:35:33,842] [INFO] Target genome list was writen to GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna/target_genomes.txt
[2024-01-25 17:35:33,849] [INFO] Task started: fastANI
[2024-01-25 17:35:33,849] [INFO] Running command: fastANI --query /var/lib/cwl/stgf30bef5a-b71c-4fbe-bd17-14d5feffd694/GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna.gz --refList GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna/target_genomes.txt --output GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:35:55,767] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:55,768] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf44e3ce-b5db-4d11-850e-b220699e5803/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:35:55,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf44e3ce-b5db-4d11-850e-b220699e5803/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:35:55,783] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:35:55,784] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:35:55,784] [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
Actibacterium mucosum	strain=KCTC 23349	GCA_000647975.1	1087332	1087332	type	True	100.0	1224	1226	95	conclusive
Actibacterium atlanticum	strain=22II-S11-z10	GCA_000671395.1	1461693	1461693	type	True	78.6369	369	1226	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	78.4982	386	1226	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.4816	405	1226	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.3621	408	1226	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.0142	332	1226	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.9795	309	1226	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	77.9446	313	1226	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	77.9044	261	1226	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.893	342	1226	95	below_threshold
Aliiroseovarius marinus	strain=A6024	GCA_004360145.1	2500159	2500159	type	True	77.8535	280	1226	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	77.818	283	1226	95	below_threshold
Rhodovulum bhavnagarense	strain=DSM 24766	GCA_004343505.1	992286	992286	type	True	77.8173	271	1226	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	77.8168	342	1226	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	77.7934	306	1226	95	below_threshold
Thalassobius mediterraneus	strain=DSM 16398	GCA_900156595.1	340021	340021	type	True	77.7636	250	1226	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	77.758	335	1226	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	77.7533	308	1226	95	below_threshold
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	77.7234	276	1226	95	below_threshold
Thalassobius mediterraneus	strain=CECT 5383	GCA_001458435.1	340021	340021	type	True	77.6824	256	1226	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	77.6684	343	1226	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	77.6531	306	1226	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	77.6302	299	1226	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	77.6109	312	1226	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.4176	281	1226	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.4071	282	1226	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.347	275	1226	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.2526	255	1226	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:35:55,785] [INFO] DFAST Taxonomy check result was written to GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna/tc_result.tsv
[2024-01-25 17:35:55,786] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:35:55,786] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:35:55,786] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf44e3ce-b5db-4d11-850e-b220699e5803/dqc_reference/checkm_data
[2024-01-25 17:35:55,787] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:35:55,825] [INFO] Task started: CheckM
[2024-01-25 17:35:55,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna/checkm_input GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna/checkm_result
[2024-01-25 17:36:31,441] [INFO] Task succeeded: CheckM
[2024-01-25 17:36:31,442] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:36:31,461] [INFO] ===== Completeness check finished =====
[2024-01-25 17:36:31,461] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:36:31,462] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta)
[2024-01-25 17:36:31,462] [INFO] Task started: Blastn
[2024-01-25 17:36:31,463] [INFO] Running command: blastn -query GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf44e3ce-b5db-4d11-850e-b220699e5803/dqc_reference/reference_markers_gtdb.fasta -out GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:33,008] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:33,011] [INFO] Selected 20 target genomes.
[2024-01-25 17:36:33,011] [INFO] Target genome list was writen to GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:36:33,022] [INFO] Task started: fastANI
[2024-01-25 17:36:33,022] [INFO] Running command: fastANI --query /var/lib/cwl/stgf30bef5a-b71c-4fbe-bd17-14d5feffd694/GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna.gz --refList GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna/target_genomes_gtdb.txt --output GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:36:49,496] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:49,508] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:36:49,508] [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_000647975.1	s__Actibacterium mucosum	100.0	1224	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002285435.1	s__Actibacterium ureilyticum	79.316	525	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744955.1	s__Actibacterium sp000744955	79.0556	472	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196965.1	s__Actibacterium_A naphthalenivorans	79.0252	434	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium_A	95.0	98.28	97.38	0.93	0.89	4	-
GCF_018139985.1	s__JAGSOU01 sp018139985	78.8186	406	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000671395.1	s__Actibacterium atlanticum	78.6256	370	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	78.4821	405	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708925.1	s__Thalassobius sp002708925	78.324	272	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.91	99.91	0.84	0.84	2	-
GCF_019104745.1	s__CAU-1522 sp019104745	78.1215	366	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434965.1	s__Marimonas lutisalis	78.1043	335	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000590925.1	s__Roseicyclus elongatus	77.979	309	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.9264	349	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002073975.1	s__Rhodovulum sp002073975	77.8728	302	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004360145.1	s__Aliiroseovarius marinus	77.8624	280	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019061145.1	s__ASV31 sp019061145	77.7713	321	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002504165.1	s__Pacificitalea manganoxidans	77.7356	275	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pacificitalea	95.0	98.03	97.97	0.89	0.82	4	-
GCF_000429365.1	s__Pseudodonghicola xiamenensis	77.6273	298	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudodonghicola	95.0	99.98	99.98	0.98	0.98	2	-
GCA_001730095.1	s__Leisingera sp001730095	77.6028	250	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002166865.1	s__Roseovarius sp002166865	77.4093	244	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	77.3916	301	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:36:49,516] [INFO] GTDB search result was written to GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna/result_gtdb.tsv
[2024-01-25 17:36:49,518] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:36:49,522] [INFO] DFAST_QC result json was written to GCF_000647975.1_SOAPdenovo_v1.05_genomic.fna/dqc_result.json
[2024-01-25 17:36:49,522] [INFO] DFAST_QC completed!
[2024-01-25 17:36:49,522] [INFO] Total running time: 0h1m29s