[2024-01-25 17:34:07,120] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,124] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,124] [INFO] DQC Reference Directory: /var/lib/cwl/stgb92254ff-d23a-4217-8deb-d10c7a9a53ba/dqc_reference
[2024-01-25 17:34:08,951] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:08,952] [INFO] Task started: Prodigal
[2024-01-25 17:34:08,953] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ae797e8-5548-451b-bd0c-1a28a990d47d/GCF_001938985.1_ASM193898v1_genomic.fna.gz | prodigal -d GCF_001938985.1_ASM193898v1_genomic.fna/cds.fna -a GCF_001938985.1_ASM193898v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:23,730] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:23,731] [INFO] Task started: HMMsearch
[2024-01-25 17:34:23,731] [INFO] Running command: hmmsearch --tblout GCF_001938985.1_ASM193898v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb92254ff-d23a-4217-8deb-d10c7a9a53ba/dqc_reference/reference_markers.hmm GCF_001938985.1_ASM193898v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:24,036] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:24,037] [INFO] Found 6/6 markers.
[2024-01-25 17:34:24,079] [INFO] Query marker FASTA was written to GCF_001938985.1_ASM193898v1_genomic.fna/markers.fasta
[2024-01-25 17:34:24,080] [INFO] Task started: Blastn
[2024-01-25 17:34:24,080] [INFO] Running command: blastn -query GCF_001938985.1_ASM193898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb92254ff-d23a-4217-8deb-d10c7a9a53ba/dqc_reference/reference_markers.fasta -out GCF_001938985.1_ASM193898v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:25,024] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:25,027] [INFO] Selected 22 target genomes.
[2024-01-25 17:34:25,027] [INFO] Target genome list was writen to GCF_001938985.1_ASM193898v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:25,038] [INFO] Task started: fastANI
[2024-01-25 17:34:25,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ae797e8-5548-451b-bd0c-1a28a990d47d/GCF_001938985.1_ASM193898v1_genomic.fna.gz --refList GCF_001938985.1_ASM193898v1_genomic.fna/target_genomes.txt --output GCF_001938985.1_ASM193898v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:48,195] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:48,195] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb92254ff-d23a-4217-8deb-d10c7a9a53ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:48,195] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb92254ff-d23a-4217-8deb-d10c7a9a53ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:48,208] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:34:48,208] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:34:48,209] [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
Rhizobium taibaishanense	strain=14971	GCA_001938985.1	887144	887144	type	True	100.0	1793	1793	95	conclusive
Rhizobium taibaishanense	strain=DSM 100021	GCA_014196735.1	887144	887144	type	True	99.9982	1793	1793	95	conclusive
Ciceribacter selenitireducens	strain=ATCC BAA-1503	GCA_000518785.1	448181	448181	type	True	79.429	677	1793	95	below_threshold
Rhizobium wuzhouense	strain=W44	GCA_003205195.1	1986026	1986026	type	True	79.3671	635	1793	95	below_threshold
Rhizobium halophytocola	strain=DSM 21600	GCA_017873095.1	735519	735519	type	True	79.3221	642	1793	95	below_threshold
Rhizobium glycinendophyticum	strain=CL12	GCA_006443685.1	2589807	2589807	type	True	79.2435	609	1793	95	below_threshold
Rhizobium rosettiformans	strain=DSM 26376	GCA_014202175.1	1368430	1368430	type	True	79.1294	615	1793	95	below_threshold
Rhizobium rhizophilum	strain=7209-2	GCA_004912145.1	1850373	1850373	type	True	79.1285	586	1793	95	below_threshold
Rhizobium rosettiformans	strain=W3	GCA_004912135.1	1368430	1368430	type	True	79.0947	614	1793	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	78.9112	597	1793	95	below_threshold
Neorhizobium galegae	strain=HAMBI 540	GCA_000731315.1	399	399	suspected-type	True	78.7327	577	1793	95	below_threshold
Ciceribacter lividus	strain=DSM 25528	GCA_003337715.1	1197950	1197950	type	True	78.6584	533	1793	95	below_threshold
Rhizobium phaseoli	strain=ATCC 14482	GCA_003985125.1	396	396	type	True	78.6581	625	1793	95	below_threshold
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	78.6357	516	1793	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	78.6352	520	1793	95	below_threshold
Rhizobium binae	strain=BLR195	GCA_017357225.1	1138190	1138190	type	True	78.6231	616	1793	95	below_threshold
Ciceribacter naphthalenivorans	strain=NBRC 107585	GCA_007992095.1	1118451	1118451	type	True	78.5758	522	1793	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	78.5607	539	1793	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	78.5568	543	1793	95	below_threshold
Rhizobium sophorae	strain=CCBAU 03386	GCA_013087515.1	1535242	1535242	type	True	78.507	637	1793	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.4422	483	1793	95	below_threshold
Neorhizobium lilium	strain=24NR	GCA_004053875.1	2503024	2503024	type	True	78.2643	513	1793	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:48,210] [INFO] DFAST Taxonomy check result was written to GCF_001938985.1_ASM193898v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:48,211] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:48,211] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:48,211] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb92254ff-d23a-4217-8deb-d10c7a9a53ba/dqc_reference/checkm_data
[2024-01-25 17:34:48,212] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:48,264] [INFO] Task started: CheckM
[2024-01-25 17:34:48,264] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001938985.1_ASM193898v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001938985.1_ASM193898v1_genomic.fna/checkm_input GCF_001938985.1_ASM193898v1_genomic.fna/checkm_result
[2024-01-25 17:35:31,949] [INFO] Task succeeded: CheckM
[2024-01-25 17:35:31,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:35:31,968] [INFO] ===== Completeness check finished =====
[2024-01-25 17:35:31,968] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:35:31,969] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001938985.1_ASM193898v1_genomic.fna/markers.fasta)
[2024-01-25 17:35:31,969] [INFO] Task started: Blastn
[2024-01-25 17:35:31,969] [INFO] Running command: blastn -query GCF_001938985.1_ASM193898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb92254ff-d23a-4217-8deb-d10c7a9a53ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_001938985.1_ASM193898v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:33,994] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:33,996] [INFO] Selected 16 target genomes.
[2024-01-25 17:35:33,997] [INFO] Target genome list was writen to GCF_001938985.1_ASM193898v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:35:34,007] [INFO] Task started: fastANI
[2024-01-25 17:35:34,007] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ae797e8-5548-451b-bd0c-1a28a990d47d/GCF_001938985.1_ASM193898v1_genomic.fna.gz --refList GCF_001938985.1_ASM193898v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001938985.1_ASM193898v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:35:52,914] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:52,924] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:35:52,924] [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_001938985.1	s__Allorhizobium taibaishanense	100.0	1793	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_009744115.1	s__Allorhizobium vitis_E	82.3544	1153	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001541345.2	s__Allorhizobium vitis	82.2989	1172	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	98.04	96.12	0.92	0.85	14	-
GCF_001758275.2	s__Allorhizobium vitis_B	82.287	1187	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	98.87	95.34	0.94	0.85	14	-
GCF_013426735.1	s__Allorhizobium vitis_D	82.2765	1179	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	97.49	97.49	0.89	0.89	2	-
GCF_009744025.1	s__Allorhizobium vitis_A	82.2032	1194	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.14	95.73	0.87	0.84	24	-
GCF_000621665.1	s__Allorhizobium undicola	79.5022	680	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300855.1	s__Allorhizobium albertimagni	79.2882	605	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014237835.1	s__Allorhizobium sp014237835	79.1998	592	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004912135.1	s__Allorhizobium rosettiformans	79.0906	614	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.40	95.42	0.87	0.84	7	-
GCA_900466945.1	s__Allorhizobium sp900466945	79.0242	583	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002855515.1	s__Allorhizobium sp002855515	79.0162	616	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005860795.2	s__Allorhizobium desertarenae	78.7329	458	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001657485.1	s__Rhizobium sp001657485	78.6746	623	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.95	97.95	0.90	0.90	2	-
GCF_003985125.1	s__Rhizobium phaseoli	78.6443	627	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.51	96.92	0.91	0.87	41	-
GCF_000009265.1	s__Rhizobium leguminosarum_L	78.5629	640	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.59	95.46	0.90	0.82	60	-
--------------------------------------------------------------------------------
[2024-01-25 17:35:52,926] [INFO] GTDB search result was written to GCF_001938985.1_ASM193898v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:35:52,927] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:35:52,930] [INFO] DFAST_QC result json was written to GCF_001938985.1_ASM193898v1_genomic.fna/dqc_result.json
[2024-01-25 17:35:52,930] [INFO] DFAST_QC completed!
[2024-01-25 17:35:52,930] [INFO] Total running time: 0h1m46s