[2024-01-24 13:17:59,076] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:59,078] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:59,078] [INFO] DQC Reference Directory: /var/lib/cwl/stge256bd1e-f00d-485b-861f-175ce2e708e7/dqc_reference
[2024-01-24 13:18:00,419] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:00,420] [INFO] Task started: Prodigal
[2024-01-24 13:18:00,420] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b491666-5975-4120-a2d9-36ef7bc68db1/GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna/cds.fna -a GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:14,486] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:14,487] [INFO] Task started: HMMsearch
[2024-01-24 13:18:14,487] [INFO] Running command: hmmsearch --tblout GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge256bd1e-f00d-485b-861f-175ce2e708e7/dqc_reference/reference_markers.hmm GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:14,785] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:14,786] [INFO] Found 6/6 markers.
[2024-01-24 13:18:14,825] [INFO] Query marker FASTA was written to GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:18:14,826] [INFO] Task started: Blastn
[2024-01-24 13:18:14,826] [INFO] Running command: blastn -query GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge256bd1e-f00d-485b-861f-175ce2e708e7/dqc_reference/reference_markers.fasta -out GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:15,695] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:15,700] [INFO] Selected 27 target genomes.
[2024-01-24 13:18:15,701] [INFO] Target genome list was writen to GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:18:15,730] [INFO] Task started: fastANI
[2024-01-24 13:18:15,731] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b491666-5975-4120-a2d9-36ef7bc68db1/GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna.gz --refList GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:35,467] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:35,468] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge256bd1e-f00d-485b-861f-175ce2e708e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:35,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge256bd1e-f00d-485b-861f-175ce2e708e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:35,488] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:18:35,488] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:18:35,488] [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
Shimia sediminis	strain=ZQ172	GCA_003990645.1	2497945	2497945	type	True	79.5802	573	1399	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	78.8796	473	1399	95	below_threshold
Shimia abyssi	strain=DSM 100673	GCA_003014475.1	1662395	1662395	type	True	78.8429	554	1399	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.6357	461	1399	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	78.6246	500	1399	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	78.582	470	1399	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	78.4855	406	1399	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	78.4801	459	1399	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	78.4137	465	1399	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	78.2838	464	1399	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	78.2793	448	1399	95	below_threshold
Shimia isoporae	strain=DSM 26433	GCA_004346865.1	647720	647720	type	True	78.2154	395	1399	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	78.1891	440	1399	95	below_threshold
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	78.1656	369	1399	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	78.106	407	1399	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.0144	411	1399	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.9957	412	1399	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	77.9486	409	1399	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	77.9427	414	1399	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	77.9239	326	1399	95	below_threshold
Ruegeria conchae	strain=TW15	GCA_000192475.2	981384	981384	suspected-type	True	77.8327	272	1399	95	below_threshold
Ruegeria conchae	strain=DSM 29317	GCA_003664205.1	981384	981384	suspected-type	True	77.8145	272	1399	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.6556	294	1399	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.425	281	1399	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.3934	267	1399	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.3772	267	1399	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	77.2127	195	1399	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:35,490] [INFO] DFAST Taxonomy check result was written to GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:18:35,490] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:35,490] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:35,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge256bd1e-f00d-485b-861f-175ce2e708e7/dqc_reference/checkm_data
[2024-01-24 13:18:35,491] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:35,531] [INFO] Task started: CheckM
[2024-01-24 13:18:35,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna/checkm_input GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:19:21,940] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:21,942] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:21,963] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:21,963] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:21,964] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:19:21,964] [INFO] Task started: Blastn
[2024-01-24 13:19:21,964] [INFO] Running command: blastn -query GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge256bd1e-f00d-485b-861f-175ce2e708e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:23,442] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:23,445] [INFO] Selected 18 target genomes.
[2024-01-24 13:19:23,445] [INFO] Target genome list was writen to GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:23,485] [INFO] Task started: fastANI
[2024-01-24 13:19:23,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b491666-5975-4120-a2d9-36ef7bc68db1/GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna.gz --refList GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:38,296] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:38,311] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:38,312] [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_900114635.1	s__Shimia aestuarii	100.0	1396	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016019955.1	s__Shimia sp016019955	81.4426	809	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	99.56	99.56	0.93	0.93	2	-
GCF_003990645.1	s__Shimia sediminis	79.5802	573	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016888515.1	s__Shimia_A biformata	79.5333	589	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018223085.1	s__Shimia sp018223085	79.2278	457	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	78.8703	474	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014475.1	s__Shimia abyssi	78.8429	554	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	78.7763	440	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900114415.1	s__Shimia haliotis	78.6247	500	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	78.6226	463	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129345.1	s__Ruegeria intermedia	78.5732	472	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473325.1	s__Leisingera caerulea	78.5598	460	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743735.1	s__Shimia sp017743735	78.4629	502	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	95.87	95.63	0.93	0.93	3	-
GCF_013032855.1	s__Ruegeria arenilitoris	78.3759	426	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.27	95.93	0.96	0.94	31	-
GCF_001292625.1	s__Shimia sp001292625	78.2117	464	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744095.1	s__Shimia sp017744095	78.1214	432	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	78.0861	394	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003511785.1	s__UBA7951 sp003511785	77.9867	301	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:38,316] [INFO] GTDB search result was written to GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:38,317] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:38,321] [INFO] DFAST_QC result json was written to GCF_900114635.1_IMG-taxon_2616644822_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:19:38,322] [INFO] DFAST_QC completed!
[2024-01-24 13:19:38,322] [INFO] Total running time: 0h1m39s