[2024-01-25 20:16:05,681] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:16:05,682] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:16:05,683] [INFO] DQC Reference Directory: /var/lib/cwl/stge59a2ba8-ff49-42b7-a8b0-0a2a4d2cd4cf/dqc_reference
[2024-01-25 20:16:06,828] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:16:06,829] [INFO] Task started: Prodigal
[2024-01-25 20:16:06,829] [INFO] Running command: gunzip -c /var/lib/cwl/stg178c0471-02aa-4be6-830c-c57e24f8f9bd/GCF_001939045.1_ASM193904v1_genomic.fna.gz | prodigal -d GCF_001939045.1_ASM193904v1_genomic.fna/cds.fna -a GCF_001939045.1_ASM193904v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:16:22,507] [INFO] Task succeeded: Prodigal
[2024-01-25 20:16:22,507] [INFO] Task started: HMMsearch
[2024-01-25 20:16:22,507] [INFO] Running command: hmmsearch --tblout GCF_001939045.1_ASM193904v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge59a2ba8-ff49-42b7-a8b0-0a2a4d2cd4cf/dqc_reference/reference_markers.hmm GCF_001939045.1_ASM193904v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:16:22,806] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:16:22,807] [INFO] Found 6/6 markers.
[2024-01-25 20:16:22,849] [INFO] Query marker FASTA was written to GCF_001939045.1_ASM193904v1_genomic.fna/markers.fasta
[2024-01-25 20:16:22,849] [INFO] Task started: Blastn
[2024-01-25 20:16:22,849] [INFO] Running command: blastn -query GCF_001939045.1_ASM193904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge59a2ba8-ff49-42b7-a8b0-0a2a4d2cd4cf/dqc_reference/reference_markers.fasta -out GCF_001939045.1_ASM193904v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:23,640] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:23,642] [INFO] Selected 21 target genomes.
[2024-01-25 20:16:23,643] [INFO] Target genome list was writen to GCF_001939045.1_ASM193904v1_genomic.fna/target_genomes.txt
[2024-01-25 20:16:23,666] [INFO] Task started: fastANI
[2024-01-25 20:16:23,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg178c0471-02aa-4be6-830c-c57e24f8f9bd/GCF_001939045.1_ASM193904v1_genomic.fna.gz --refList GCF_001939045.1_ASM193904v1_genomic.fna/target_genomes.txt --output GCF_001939045.1_ASM193904v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:16:40,356] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:40,356] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge59a2ba8-ff49-42b7-a8b0-0a2a4d2cd4cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:16:40,357] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge59a2ba8-ff49-42b7-a8b0-0a2a4d2cd4cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:16:40,369] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:16:40,369] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:16:40,369] [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=DSM 100021	GCA_014196735.1	887144	887144	type	True	78.9745	680	1705	95	below_threshold
Rhizobium taibaishanense	strain=14971	GCA_001938985.1	887144	887144	type	True	78.9533	678	1705	95	below_threshold
Rhizobium rosettiformans	strain=W3	GCA_004912135.1	1368430	1368430	type	True	77.751	306	1705	95	below_threshold
Rhizobium rosettiformans	strain=DSM 26376	GCA_014202175.1	1368430	1368430	type	True	77.6952	306	1705	95	below_threshold
Ciceribacter selenitireducens	strain=ATCC BAA-1503	GCA_000518785.1	448181	448181	type	True	77.6309	334	1705	95	below_threshold
Rhizobium rhizophilum	strain=7209-2	GCA_004912145.1	1850373	1850373	type	True	77.5313	314	1705	95	below_threshold
Rhizobium wuzhouense	strain=W44	GCA_003205195.1	1986026	1986026	type	True	77.4454	343	1705	95	below_threshold
Agrobacterium salinitolerans	strain=YIC 5082	GCA_002008225.1	1183413	1183413	type	True	77.4336	354	1705	95	below_threshold
Rhizobium glycinendophyticum	strain=CL12	GCA_006443685.1	2589807	2589807	type	True	77.4326	307	1705	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	77.3453	368	1705	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	77.1698	256	1705	95	below_threshold
Rhizobium anhuiense	strain=CCBAU 23252	GCA_003985145.1	1184720	1184720	type	True	77.099	298	1705	95	below_threshold
Rhizobium anhuiense	strain=CGMCC 1.12621	GCA_014638185.1	1184720	1184720	type	True	77.0778	293	1705	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	77.018	253	1705	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	77.0154	251	1705	95	below_threshold
Rhizobium pisi	strain=DSM 30132	GCA_003938655.1	574561	574561	type	True	76.9349	278	1705	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	76.8375	268	1705	95	below_threshold
Brucella melitensis	strain=16M	GCA_000007125.1	29459	29459	suspected-type	True	76.5209	149	1705	95	below_threshold
Brucella melitensis	strain=16M	GCA_000160295.1	29459	29459	suspected-type	True	76.5173	152	1705	95	below_threshold
Brucella suis	strain=1330	GCA_000007505.1	29461	29461	suspected-type	True	76.5118	153	1705	95	below_threshold
Brucella melitensis	strain=16M	GCA_000250795.2	29459	29459	suspected-type	True	76.4936	150	1705	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:16:40,371] [INFO] DFAST Taxonomy check result was written to GCF_001939045.1_ASM193904v1_genomic.fna/tc_result.tsv
[2024-01-25 20:16:40,372] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:16:40,372] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:16:40,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge59a2ba8-ff49-42b7-a8b0-0a2a4d2cd4cf/dqc_reference/checkm_data
[2024-01-25 20:16:40,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:16:40,420] [INFO] Task started: CheckM
[2024-01-25 20:16:40,421] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001939045.1_ASM193904v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001939045.1_ASM193904v1_genomic.fna/checkm_input GCF_001939045.1_ASM193904v1_genomic.fna/checkm_result
[2024-01-25 20:17:27,907] [INFO] Task succeeded: CheckM
[2024-01-25 20:17:27,908] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:17:27,925] [INFO] ===== Completeness check finished =====
[2024-01-25 20:17:27,925] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:17:27,925] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001939045.1_ASM193904v1_genomic.fna/markers.fasta)
[2024-01-25 20:17:27,926] [INFO] Task started: Blastn
[2024-01-25 20:17:27,926] [INFO] Running command: blastn -query GCF_001939045.1_ASM193904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge59a2ba8-ff49-42b7-a8b0-0a2a4d2cd4cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_001939045.1_ASM193904v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:29,373] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:29,376] [INFO] Selected 10 target genomes.
[2024-01-25 20:17:29,376] [INFO] Target genome list was writen to GCF_001939045.1_ASM193904v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:17:29,393] [INFO] Task started: fastANI
[2024-01-25 20:17:29,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg178c0471-02aa-4be6-830c-c57e24f8f9bd/GCF_001939045.1_ASM193904v1_genomic.fna.gz --refList GCF_001939045.1_ASM193904v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001939045.1_ASM193904v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:17:40,687] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:40,694] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:17:40,695] [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_001939045.1	s__Allorhizobium oryziradicis	100.0	1702	1705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004801395.1	s__Allorhizobium terrae	89.2155	1300	1705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	98.05	98.05	0.96	0.96	2	-
GCF_014204625.1	s__Allorhizobium vitis_F	83.6689	1073	1705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003501385.1	s__Allorhizobium sp003501385	82.889	955	1705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009744025.1	s__Allorhizobium vitis_A	80.1593	784	1705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.14	95.73	0.87	0.84	24	-
GCF_009744115.1	s__Allorhizobium vitis_E	80.1058	795	1705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013426735.1	s__Allorhizobium vitis_D	80.0794	779	1705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	97.49	97.49	0.89	0.89	2	-
GCF_001541345.2	s__Allorhizobium vitis	79.9919	782	1705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	98.04	96.12	0.92	0.85	14	-
GCF_001938985.1	s__Allorhizobium taibaishanense	78.9867	673	1705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004912145.1	s__Allorhizobium rhizophilum	77.5225	315	1705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	95.70	95.70	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:17:40,697] [INFO] GTDB search result was written to GCF_001939045.1_ASM193904v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:17:40,698] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:17:40,702] [INFO] DFAST_QC result json was written to GCF_001939045.1_ASM193904v1_genomic.fna/dqc_result.json
[2024-01-25 20:17:40,702] [INFO] DFAST_QC completed!
[2024-01-25 20:17:40,702] [INFO] Total running time: 0h1m35s