[2024-01-25 19:43:50,361] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:43:50,363] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:43:50,363] [INFO] DQC Reference Directory: /var/lib/cwl/stg9828f116-60c3-4f1c-9dff-81d90047790a/dqc_reference
[2024-01-25 19:43:51,460] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:43:51,461] [INFO] Task started: Prodigal
[2024-01-25 19:43:51,461] [INFO] Running command: gunzip -c /var/lib/cwl/stg089cb70d-ca8b-4d18-a33c-ea2b1aaec807/GCF_027944115.1_ASM2794411v1_genomic.fna.gz | prodigal -d GCF_027944115.1_ASM2794411v1_genomic.fna/cds.fna -a GCF_027944115.1_ASM2794411v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:44:05,600] [INFO] Task succeeded: Prodigal
[2024-01-25 19:44:05,601] [INFO] Task started: HMMsearch
[2024-01-25 19:44:05,601] [INFO] Running command: hmmsearch --tblout GCF_027944115.1_ASM2794411v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9828f116-60c3-4f1c-9dff-81d90047790a/dqc_reference/reference_markers.hmm GCF_027944115.1_ASM2794411v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:44:05,900] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:44:05,902] [INFO] Found 6/6 markers.
[2024-01-25 19:44:05,944] [INFO] Query marker FASTA was written to GCF_027944115.1_ASM2794411v1_genomic.fna/markers.fasta
[2024-01-25 19:44:05,944] [INFO] Task started: Blastn
[2024-01-25 19:44:05,944] [INFO] Running command: blastn -query GCF_027944115.1_ASM2794411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9828f116-60c3-4f1c-9dff-81d90047790a/dqc_reference/reference_markers.fasta -out GCF_027944115.1_ASM2794411v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:06,820] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:06,824] [INFO] Selected 30 target genomes.
[2024-01-25 19:44:06,824] [INFO] Target genome list was writen to GCF_027944115.1_ASM2794411v1_genomic.fna/target_genomes.txt
[2024-01-25 19:44:06,857] [INFO] Task started: fastANI
[2024-01-25 19:44:06,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg089cb70d-ca8b-4d18-a33c-ea2b1aaec807/GCF_027944115.1_ASM2794411v1_genomic.fna.gz --refList GCF_027944115.1_ASM2794411v1_genomic.fna/target_genomes.txt --output GCF_027944115.1_ASM2794411v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:34,551] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:34,552] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9828f116-60c3-4f1c-9dff-81d90047790a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:34,552] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9828f116-60c3-4f1c-9dff-81d90047790a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:34,569] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:44:34,569] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:44:34,569] [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
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	77.3824	167	1678	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	77.1523	241	1678	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	77.0648	249	1678	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.0595	223	1678	95	below_threshold
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	77.0592	241	1678	95	below_threshold
Hoeflea halophila	strain=KCTC 23107	GCA_900220985.1	714899	714899	type	True	76.9849	209	1678	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	76.9835	194	1678	95	below_threshold
Ensifer sojae	strain=CCBAU 05684	GCA_002288525.1	716925	716925	type	True	76.9435	191	1678	95	below_threshold
Sinorhizobium fredii	strain=USDA205	GCA_009601405.1	380	380	type	True	76.9434	216	1678	95	below_threshold
Ciceribacter lividus	strain=DSM 25528	GCA_003337715.1	1197950	1197950	type	True	76.904	189	1678	95	below_threshold
Mesorhizobium japonicum	strain=MAFF 303099	GCA_000009625.1	2066070	2066070	type	True	76.9026	229	1678	95	below_threshold
Sinorhizobium fredii	strain=USDA 205	GCA_001461695.1	380	380	type	True	76.8925	208	1678	95	below_threshold
Ensifer sojae	strain=CCBAU 05684	GCA_000261485.1	716925	716925	type	True	76.8912	187	1678	95	below_threshold
Sinorhizobium fredii	strain=NBRC 14780	GCA_006539605.1	380	380	type	True	76.8879	209	1678	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	76.8736	196	1678	95	below_threshold
Rhizobium anhuiense	strain=CGMCC 1.12621	GCA_014638185.1	1184720	1184720	type	True	76.8733	207	1678	95	below_threshold
Rhizobium ruizarguesonis	strain=UPM1133	GCA_012349115.1	2081791	2081791	type	True	76.8582	212	1678	95	below_threshold
Rhizobium giardinii	strain=H152	GCA_000379605.1	56731	56731	type	True	76.8486	210	1678	95	below_threshold
Ensifer sesbaniae	strain=CCBAU 65729	GCA_013283665.1	1214071	1214071	type	True	76.8469	230	1678	95	below_threshold
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	76.7978	184	1678	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	76.7727	222	1678	95	below_threshold
Mesorhizobium albiziae	strain=DSM 21822	GCA_900114255.1	335020	335020	type	True	76.7632	199	1678	95	below_threshold
Mesorhizobium wenxiniae	strain=WYCCWR 10195	GCA_002284535.1	2014805	2014805	type	True	76.7608	190	1678	95	below_threshold
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	76.7458	172	1678	95	below_threshold
Aquamicrobium lusatiense	strain=DSM 11099	GCA_014201615.1	89772	89772	type	True	76.7404	165	1678	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	76.7079	179	1678	95	below_threshold
Rhizobium indicum	strain=JKLM 12A2	GCA_005862305.2	2583231	2583231	type	True	76.6963	207	1678	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	76.6527	169	1678	95	below_threshold
Rhizobium hainanense	strain=CCBAU 57015	GCA_900094555.1	52131	52131	type	True	76.6164	201	1678	95	below_threshold
Phyllobacterium phragmitis	strain=1N-3	GCA_002980495.1	2670329	2670329	type	True	76.5204	222	1678	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:34,571] [INFO] DFAST Taxonomy check result was written to GCF_027944115.1_ASM2794411v1_genomic.fna/tc_result.tsv
[2024-01-25 19:44:34,572] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:34,572] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:34,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9828f116-60c3-4f1c-9dff-81d90047790a/dqc_reference/checkm_data
[2024-01-25 19:44:34,573] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:34,641] [INFO] Task started: CheckM
[2024-01-25 19:44:34,641] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027944115.1_ASM2794411v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027944115.1_ASM2794411v1_genomic.fna/checkm_input GCF_027944115.1_ASM2794411v1_genomic.fna/checkm_result
[2024-01-25 19:45:18,005] [INFO] Task succeeded: CheckM
[2024-01-25 19:45:18,006] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:45:18,024] [INFO] ===== Completeness check finished =====
[2024-01-25 19:45:18,024] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:45:18,025] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027944115.1_ASM2794411v1_genomic.fna/markers.fasta)
[2024-01-25 19:45:18,025] [INFO] Task started: Blastn
[2024-01-25 19:45:18,025] [INFO] Running command: blastn -query GCF_027944115.1_ASM2794411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9828f116-60c3-4f1c-9dff-81d90047790a/dqc_reference/reference_markers_gtdb.fasta -out GCF_027944115.1_ASM2794411v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:19,692] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:19,695] [INFO] Selected 22 target genomes.
[2024-01-25 19:45:19,695] [INFO] Target genome list was writen to GCF_027944115.1_ASM2794411v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:45:19,720] [INFO] Task started: fastANI
[2024-01-25 19:45:19,721] [INFO] Running command: fastANI --query /var/lib/cwl/stg089cb70d-ca8b-4d18-a33c-ea2b1aaec807/GCF_027944115.1_ASM2794411v1_genomic.fna.gz --refList GCF_027944115.1_ASM2794411v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027944115.1_ASM2794411v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:39,021] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:39,033] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:45:39,034] [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_004959855.1	s__SPNT01 sp004959855	78.8339	720	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__SPNT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017794825.1	s__SPNT01 sp017794825	77.4729	308	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__SPNT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001938945.1	s__Pararhizobium rhizosphaerae	77.1569	193	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	97.96	97.96	0.94	0.94	2	-
GCF_000759435.1	s__Hoeflea sp000759435	77.1257	255	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018545.1	s__Sinorhizobium fredii_A	77.0116	223	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427285.1	s__Mesorhizobium sp001427285	77.0083	170	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900220985.1	s__Hoeflea halophila	76.9849	209	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018829385.1	s__Hoeflea sp018829385	76.9779	167	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002288525.1	s__Sinorhizobium sojae	76.9553	190	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.99	99.99	1.00	1.00	2	-
GCA_000961635.1	s__Hoeflea sp000961635	76.9086	173	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000421085.1	s__Sinorhizobium sp000421085	76.8936	209	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733955.1	s__Hoeflea sp002733955	76.8841	235	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012349115.1	s__Rhizobium ruizarguesonis	76.8582	212	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.01	96.15	0.89	0.84	170	-
GCA_900472575.1	s__Neorhizobium cellulosilyticum	76.8403	153	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.58	97.10	0.87	0.85	7	-
GCF_003148475.1	s__Pseudaminobacter salicylatoxidans	76.8296	218	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	97.95	97.95	0.90	0.90	2	-
GCF_017874015.1	s__Pseudaminobacter sp017874015	76.7712	203	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001652265.1	s__Rhizobium leguminosarum_D	76.7092	209	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.67	97.67	0.88	0.88	3	-
GCA_002709005.1	s__Pseudohoeflea sp002709005	76.6867	176	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudohoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197615.1	s__Rhizobium esperanzae_A	76.6583	209	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001704765.1	s__Sinorhizobium shofinae	76.6284	150	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006440735.1	s__Mesorhizobium sp006440735	76.4513	231	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:45:39,035] [INFO] GTDB search result was written to GCF_027944115.1_ASM2794411v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:39,036] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:39,040] [INFO] DFAST_QC result json was written to GCF_027944115.1_ASM2794411v1_genomic.fna/dqc_result.json
[2024-01-25 19:45:39,040] [INFO] DFAST_QC completed!
[2024-01-25 19:45:39,040] [INFO] Total running time: 0h1m49s