[2024-01-24 12:22:48,496] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,497] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,497] [INFO] DQC Reference Directory: /var/lib/cwl/stg12b59ff0-f4c0-4949-80c9-4d851b785e7e/dqc_reference
[2024-01-24 12:22:49,731] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:49,731] [INFO] Task started: Prodigal
[2024-01-24 12:22:49,732] [INFO] Running command: gunzip -c /var/lib/cwl/stg5355ce48-8ee0-4521-9420-a45754b5c102/GCF_001050155.1_ASM105015v1_genomic.fna.gz | prodigal -d GCF_001050155.1_ASM105015v1_genomic.fna/cds.fna -a GCF_001050155.1_ASM105015v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:05,997] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:05,997] [INFO] Task started: HMMsearch
[2024-01-24 12:23:05,997] [INFO] Running command: hmmsearch --tblout GCF_001050155.1_ASM105015v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12b59ff0-f4c0-4949-80c9-4d851b785e7e/dqc_reference/reference_markers.hmm GCF_001050155.1_ASM105015v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:06,261] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:06,262] [INFO] Found 6/6 markers.
[2024-01-24 12:23:06,306] [INFO] Query marker FASTA was written to GCF_001050155.1_ASM105015v1_genomic.fna/markers.fasta
[2024-01-24 12:23:06,306] [INFO] Task started: Blastn
[2024-01-24 12:23:06,307] [INFO] Running command: blastn -query GCF_001050155.1_ASM105015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12b59ff0-f4c0-4949-80c9-4d851b785e7e/dqc_reference/reference_markers.fasta -out GCF_001050155.1_ASM105015v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:07,367] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:07,371] [INFO] Selected 14 target genomes.
[2024-01-24 12:23:07,371] [INFO] Target genome list was writen to GCF_001050155.1_ASM105015v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:07,378] [INFO] Task started: fastANI
[2024-01-24 12:23:07,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg5355ce48-8ee0-4521-9420-a45754b5c102/GCF_001050155.1_ASM105015v1_genomic.fna.gz --refList GCF_001050155.1_ASM105015v1_genomic.fna/target_genomes.txt --output GCF_001050155.1_ASM105015v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:24,090] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:24,090] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12b59ff0-f4c0-4949-80c9-4d851b785e7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:24,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12b59ff0-f4c0-4949-80c9-4d851b785e7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:24,103] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:24,103] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:24,104] [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
Nitratireductor soli	strain=ZZ-1	GCA_001050155.1	1670619	1670619	type	True	100.0	1682	1682	95	conclusive
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	86.2686	1110	1682	95	below_threshold
Nitratireductor aquibiodomus	strain=JCM 21793	GCA_000615975.1	204799	204799	type	True	81.1083	828	1682	95	below_threshold
Nitratireductor indicus	strain=C115	GCA_000300515.1	721133	721133	type	True	80.522	780	1682	95	below_threshold
Chelativorans xinjiangense	strain=lm93	GCA_009812055.1	2681485	2681485	type	True	80.3783	738	1682	95	below_threshold
Nitratireductor kimnyeongensis	strain=KACC 11904	GCA_019891395.1	430679	430679	type	True	80.3019	758	1682	95	below_threshold
Chelativorans alearense	strain=UJN715	GCA_010993735.1	2681495	2681495	type	True	80.1423	738	1682	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	79.6153	662	1682	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	79.4225	609	1682	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	79.3455	635	1682	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	79.3193	679	1682	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	79.187	609	1682	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.3802	486	1682	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	78.3586	489	1682	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:24,106] [INFO] DFAST Taxonomy check result was written to GCF_001050155.1_ASM105015v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:24,113] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:24,114] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:24,114] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12b59ff0-f4c0-4949-80c9-4d851b785e7e/dqc_reference/checkm_data
[2024-01-24 12:23:24,115] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:24,161] [INFO] Task started: CheckM
[2024-01-24 12:23:24,161] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001050155.1_ASM105015v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001050155.1_ASM105015v1_genomic.fna/checkm_input GCF_001050155.1_ASM105015v1_genomic.fna/checkm_result
[2024-01-24 12:24:13,011] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:13,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:13,030] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:13,030] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:13,031] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001050155.1_ASM105015v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:13,031] [INFO] Task started: Blastn
[2024-01-24 12:24:13,031] [INFO] Running command: blastn -query GCF_001050155.1_ASM105015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12b59ff0-f4c0-4949-80c9-4d851b785e7e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001050155.1_ASM105015v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:15,109] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:15,113] [INFO] Selected 14 target genomes.
[2024-01-24 12:24:15,113] [INFO] Target genome list was writen to GCF_001050155.1_ASM105015v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:15,121] [INFO] Task started: fastANI
[2024-01-24 12:24:15,121] [INFO] Running command: fastANI --query /var/lib/cwl/stg5355ce48-8ee0-4521-9420-a45754b5c102/GCF_001050155.1_ASM105015v1_genomic.fna.gz --refList GCF_001050155.1_ASM105015v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001050155.1_ASM105015v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:29,528] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:29,540] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:29,540] [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_001050155.1	s__Nitratireductor soli	100.0	1682	1682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000300335.1	s__Nitratireductor pacificus	86.2686	1110	1682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255295.1	s__Nitratireductor aquimarinus	81.535	891	1682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	98.42	98.07	0.93	0.92	7	-
GCF_000615975.1	s__Nitratireductor aquibiodomus	81.1144	826	1682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	97.24	95.23	0.87	0.84	4	-
GCA_017794765.1	s__Nitratireductor sp017794765	80.5436	726	1682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300515.1	s__Nitratireductor indicus	80.5368	777	1682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002697745.1	s__Nitratireductor sp002697745	80.52	755	1682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009812055.1	s__Chelativorans xinjiangense	80.4039	735	1682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009749525.1	s__Im94 sp009749525	79.8216	666	1682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Im94	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590645.1	s__Pseudaminobacter sp900116595	79.4337	620	1682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	98.40	97.54	0.93	0.88	4	-
GCF_018588885.1	s__Mesorhizobium sp018588885	79.127	637	1682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015500075.1	s__Mesorhizobium sp015500075	78.7819	603	1682	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	78.3826	471	1682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001603335.1	s__Alpha-05 sp001603335	76.5483	92	1682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Alpha-05	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:29,542] [INFO] GTDB search result was written to GCF_001050155.1_ASM105015v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:29,543] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:29,546] [INFO] DFAST_QC result json was written to GCF_001050155.1_ASM105015v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:29,546] [INFO] DFAST_QC completed!
[2024-01-24 12:24:29,546] [INFO] Total running time: 0h1m41s