[2024-01-24 10:47:06,547] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,553] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,554] [INFO] DQC Reference Directory: /var/lib/cwl/stg956f9bb6-afb1-42bd-94af-bc6d30941d4e/dqc_reference
[2024-01-24 10:47:12,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,102] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,102] [INFO] Running command: gunzip -c /var/lib/cwl/stg7890c580-690e-4789-944a-34cd45a276be/GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna/cds.fna -a GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:24,994] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:24,994] [INFO] Task started: HMMsearch
[2024-01-24 10:47:24,994] [INFO] Running command: hmmsearch --tblout GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg956f9bb6-afb1-42bd-94af-bc6d30941d4e/dqc_reference/reference_markers.hmm GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:25,243] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:25,244] [INFO] Found 6/6 markers.
[2024-01-24 10:47:25,312] [INFO] Query marker FASTA was written to GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 10:47:25,312] [INFO] Task started: Blastn
[2024-01-24 10:47:25,313] [INFO] Running command: blastn -query GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg956f9bb6-afb1-42bd-94af-bc6d30941d4e/dqc_reference/reference_markers.fasta -out GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:26,257] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:26,260] [INFO] Selected 23 target genomes.
[2024-01-24 10:47:26,261] [INFO] Target genome list was writen to GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 10:47:26,287] [INFO] Task started: fastANI
[2024-01-24 10:47:26,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg7890c580-690e-4789-944a-34cd45a276be/GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna.gz --refList GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:46,566] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:46,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg956f9bb6-afb1-42bd-94af-bc6d30941d4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:46,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg956f9bb6-afb1-42bd-94af-bc6d30941d4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:46,585] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:46,586] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:46,586] [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
Halomonas muralis	strain=DSM 14789	GCA_900102945.1	119000	119000	type	True	100.0	1368	1370	95	conclusive
Halomonas zincidurans	strain=B6	GCA_000731955.1	1178777	1178777	type	True	81.3648	680	1370	95	below_threshold
Halomonas ilicicola	strain=DSM 19980	GCA_900128925.1	480814	480814	type	True	80.3451	669	1370	95	below_threshold
Halomonas xianhensis	strain=CGMCC 1.6848	GCA_900113605.1	442341	442341	type	True	80.2207	615	1370	95	below_threshold
Halomonas salipaludis	strain=WRN001	GCA_002286975.1	2032625	2032625	type	True	80.1631	588	1370	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	80.0836	575	1370	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	80.0384	561	1370	95	below_threshold
Halomonas pantelleriensis	strain=AAP	GCA_900102875.1	48727	48727	type	True	79.9919	562	1370	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	79.9888	574	1370	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	79.9419	617	1370	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	79.847	531	1370	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	79.8143	582	1370	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	79.6474	514	1370	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	79.5482	547	1370	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	79.4632	569	1370	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	79.4549	503	1370	95	below_threshold
Halomonas lutea	strain=KCTC 12847	GCA_014651575.1	453962	453962	type	True	79.4309	539	1370	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_013697085.1	321266	321266	type	True	79.4162	490	1370	95	below_threshold
Halomonas lutea	strain=DSM 23508	GCA_000378505.1	453962	453962	type	True	79.3965	526	1370	95	below_threshold
Halomonas alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	79.3962	503	1370	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	79.3275	490	1370	95	below_threshold
Salinicola peritrichatus	strain=JCM 18795	GCA_003206715.1	1267424	1267424	type	True	79.2774	465	1370	95	below_threshold
Salinicola salarius	strain=DSM 18044	GCA_003206135.1	430457	430457	type	True	78.9512	433	1370	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:46,588] [INFO] DFAST Taxonomy check result was written to GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 10:47:46,589] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:46,589] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:46,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg956f9bb6-afb1-42bd-94af-bc6d30941d4e/dqc_reference/checkm_data
[2024-01-24 10:47:46,591] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:46,633] [INFO] Task started: CheckM
[2024-01-24 10:47:46,633] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna/checkm_input GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 10:48:23,820] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:23,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:23,841] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:23,841] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:23,842] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 10:48:23,842] [INFO] Task started: Blastn
[2024-01-24 10:48:23,842] [INFO] Running command: blastn -query GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg956f9bb6-afb1-42bd-94af-bc6d30941d4e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:25,562] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:25,567] [INFO] Selected 16 target genomes.
[2024-01-24 10:48:25,568] [INFO] Target genome list was writen to GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:25,579] [INFO] Task started: fastANI
[2024-01-24 10:48:25,579] [INFO] Running command: fastANI --query /var/lib/cwl/stg7890c580-690e-4789-944a-34cd45a276be/GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna.gz --refList GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:39,261] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:39,273] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:39,274] [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_900102945.1	s__Halomonas_C muralis	100.0	1368	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000731955.1	s__Halomonas_C zincidurans	81.3584	681	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993675.1	s__Halomonas_C sp010993675	81.1138	633	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900961225.1	s__Halomonas_C sp900961225	81.0308	709	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001577635.1	s__Halomonas_C sp001577635	81.0244	631	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004117855.1	s__Halomonas_C coralii	80.9824	715	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971685.1	s__Halomonas_B sp001971685	80.6021	581	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128925.1	s__Halomonas_C ilicicola	80.3452	669	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010977575.1	s__Halomonas_B socia	80.3149	593	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113605.1	s__Halomonas_C xianhensis	80.1993	616	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	96.25	96.25	0.87	0.87	2	-
GCF_002286975.1	s__Halomonas_B sp002286975	80.1259	592	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265245.1	s__Halomonas smyrnensis	80.0646	561	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_007989465.1	s__Halomonas halophila	79.9663	576	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
GCF_005780185.1	s__Halomonas urmiana	79.8321	532	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378505.1	s__Halomonas_C lutea	79.3875	527	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013697085.1	s__Halomonas kenyensis	79.3763	494	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:39,275] [INFO] GTDB search result was written to GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:39,276] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:39,281] [INFO] DFAST_QC result json was written to GCF_900102945.1_IMG-taxon_2599185144_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 10:48:39,282] [INFO] DFAST_QC completed!
[2024-01-24 10:48:39,282] [INFO] Total running time: 0h1m33s