[2024-01-24 11:05:03,926] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,927] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,928] [INFO] DQC Reference Directory: /var/lib/cwl/stge00e508a-e053-4eb3-b6d3-47cb3391a9ff/dqc_reference
[2024-01-24 11:05:05,766] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,767] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,767] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d04b732-6fb0-49f0-895c-61ef3a8ec7a0/GCF_014201615.1_ASM1420161v1_genomic.fna.gz | prodigal -d GCF_014201615.1_ASM1420161v1_genomic.fna/cds.fna -a GCF_014201615.1_ASM1420161v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:18,304] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:18,304] [INFO] Task started: HMMsearch
[2024-01-24 11:05:18,304] [INFO] Running command: hmmsearch --tblout GCF_014201615.1_ASM1420161v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge00e508a-e053-4eb3-b6d3-47cb3391a9ff/dqc_reference/reference_markers.hmm GCF_014201615.1_ASM1420161v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:18,668] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:18,669] [INFO] Found 6/6 markers.
[2024-01-24 11:05:18,707] [INFO] Query marker FASTA was written to GCF_014201615.1_ASM1420161v1_genomic.fna/markers.fasta
[2024-01-24 11:05:18,708] [INFO] Task started: Blastn
[2024-01-24 11:05:18,708] [INFO] Running command: blastn -query GCF_014201615.1_ASM1420161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge00e508a-e053-4eb3-b6d3-47cb3391a9ff/dqc_reference/reference_markers.fasta -out GCF_014201615.1_ASM1420161v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:19,725] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:19,728] [INFO] Selected 22 target genomes.
[2024-01-24 11:05:19,729] [INFO] Target genome list was writen to GCF_014201615.1_ASM1420161v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:19,735] [INFO] Task started: fastANI
[2024-01-24 11:05:19,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d04b732-6fb0-49f0-895c-61ef3a8ec7a0/GCF_014201615.1_ASM1420161v1_genomic.fna.gz --refList GCF_014201615.1_ASM1420161v1_genomic.fna/target_genomes.txt --output GCF_014201615.1_ASM1420161v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:44,836] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:44,836] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge00e508a-e053-4eb3-b6d3-47cb3391a9ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:44,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge00e508a-e053-4eb3-b6d3-47cb3391a9ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:44,849] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:44,849] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:44,849] [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
Aquamicrobium lusatiense	strain=DSM 11099	GCA_014201615.1	89772	89772	type	True	100.0	1455	1456	95	conclusive
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	85.5951	941	1456	95	below_threshold
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	80.0354	645	1456	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	80.0077	593	1456	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	80.003	629	1456	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	79.9313	615	1456	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	79.8888	624	1456	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	79.7987	627	1456	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	79.7969	651	1456	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	79.7938	622	1456	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	79.7298	566	1456	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	79.6874	600	1456	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	79.6821	625	1456	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	79.6816	585	1456	95	below_threshold
Mesorhizobium sangaii	strain=DSM 100039	GCA_014207355.1	505389	505389	type	True	79.6409	606	1456	95	below_threshold
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	79.5728	630	1456	95	below_threshold
Aminobacter aminovorans	strain=DSM 7048	GCA_004341645.1	83263	83263	type	True	79.5545	605	1456	95	below_threshold
Aminobacter aminovorans	strain=NCTC10684	GCA_900445235.1	83263	83263	type	True	79.5527	621	1456	95	below_threshold
Aminobacter ciceronei	strain=DSM 17455	GCA_014138635.1	150723	150723	type	True	79.5285	637	1456	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.4156	453	1456	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	78.4028	453	1456	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	78.3899	463	1456	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:44,854] [INFO] DFAST Taxonomy check result was written to GCF_014201615.1_ASM1420161v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:44,855] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:44,855] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:44,855] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge00e508a-e053-4eb3-b6d3-47cb3391a9ff/dqc_reference/checkm_data
[2024-01-24 11:05:44,856] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:44,896] [INFO] Task started: CheckM
[2024-01-24 11:05:44,896] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201615.1_ASM1420161v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201615.1_ASM1420161v1_genomic.fna/checkm_input GCF_014201615.1_ASM1420161v1_genomic.fna/checkm_result
[2024-01-24 11:06:26,958] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:26,959] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:26,973] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:26,973] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:26,973] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201615.1_ASM1420161v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:26,974] [INFO] Task started: Blastn
[2024-01-24 11:06:26,974] [INFO] Running command: blastn -query GCF_014201615.1_ASM1420161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge00e508a-e053-4eb3-b6d3-47cb3391a9ff/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201615.1_ASM1420161v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:28,949] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:28,953] [INFO] Selected 21 target genomes.
[2024-01-24 11:06:28,954] [INFO] Target genome list was writen to GCF_014201615.1_ASM1420161v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:28,967] [INFO] Task started: fastANI
[2024-01-24 11:06:28,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d04b732-6fb0-49f0-895c-61ef3a8ec7a0/GCF_014201615.1_ASM1420161v1_genomic.fna.gz --refList GCF_014201615.1_ASM1420161v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201615.1_ASM1420161v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:51,771] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:51,783] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:51,784] [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_014201615.1	s__Mesorhizobium lusatiense	100.0	1455	1456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004363725.1	s__Mesorhizobium defluvii	85.586	942	1456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.28	99.28	0.87	0.87	2	-
GCF_001427385.1	s__Mesorhizobium sp001427385	80.3446	640	1456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427285.1	s__Mesorhizobium sp001427285	80.155	637	1456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727715.1	s__Mesorhizobium terrae	80.0983	662	1456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.80	99.17	0.95	0.89	9	-
GCF_003952485.1	s__Mesorhizobium sp003952485	80.0928	630	1456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.38	98.21	0.91	0.89	5	-
GCF_003148475.1	s__Pseudaminobacter salicylatoxidans	80.0837	618	1456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	97.95	97.95	0.90	0.90	2	-
GCF_006442815.1	s__Mesorhizobium sp006442815	79.9888	617	1456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_006440735.1	s__Mesorhizobium sp006440735	79.9575	616	1456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004791255.1	s__Mesorhizobium sp004791255	79.9206	623	1456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.78	99.47	0.95	0.87	5	-
GCA_004020545.1	s__Mesorhizobium sp004020545	79.8569	630	1456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	97.54	0.89	0.86	9	-
GCF_000472705.1	s__Mesorhizobium erdmanii	79.802	621	1456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.40	97.39	0.90	0.90	3	-
GCF_003590645.1	s__Pseudaminobacter sp900116595	79.7428	586	1456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	98.40	97.54	0.93	0.88	4	-
GCA_004017275.1	s__Mesorhizobium sp004017275	79.7116	610	1456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.13	97.50	0.90	0.85	4	-
GCF_016836705.1	s__Mesorhizobium caraganae	79.6742	625	1456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.40	96.20	0.88	0.86	3	-
GCF_011045115.1	s__Pseudaminobacter zhangyensis	79.6653	602	1456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014138625.1	s__Aminobacter ciceronei	79.5689	631	1456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.84	97.89	0.89	0.85	7	-
GCF_900445235.1	s__Aminobacter aminovorans	79.5532	621	1456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001303895.1	s__Mesorhizobium sp001303895	79.3899	599	1456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002075885.1	s__Mesorhizobium manganicum	79.3446	549	1456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002858745.1	s__Mesorhizobium loti_F	79.2014	573	1456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:51,785] [INFO] GTDB search result was written to GCF_014201615.1_ASM1420161v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:51,785] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:51,789] [INFO] DFAST_QC result json was written to GCF_014201615.1_ASM1420161v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:51,789] [INFO] DFAST_QC completed!
[2024-01-24 11:06:51,789] [INFO] Total running time: 0h1m48s