[2024-01-24 11:12:28,315] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:28,317] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:28,317] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b66392f-8a6c-467b-b87e-eceac52d882d/dqc_reference
[2024-01-24 11:12:29,634] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:29,635] [INFO] Task started: Prodigal
[2024-01-24 11:12:29,635] [INFO] Running command: gunzip -c /var/lib/cwl/stg47659cb3-6754-4ca1-a62c-8228962f428f/GCF_900289045.1_MPGL2_genomic.fna.gz | prodigal -d GCF_900289045.1_MPGL2_genomic.fna/cds.fna -a GCF_900289045.1_MPGL2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:42,312] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:42,312] [INFO] Task started: HMMsearch
[2024-01-24 11:12:42,312] [INFO] Running command: hmmsearch --tblout GCF_900289045.1_MPGL2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b66392f-8a6c-467b-b87e-eceac52d882d/dqc_reference/reference_markers.hmm GCF_900289045.1_MPGL2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:42,571] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:42,572] [INFO] Found 6/6 markers.
[2024-01-24 11:12:42,607] [INFO] Query marker FASTA was written to GCF_900289045.1_MPGL2_genomic.fna/markers.fasta
[2024-01-24 11:12:42,607] [INFO] Task started: Blastn
[2024-01-24 11:12:42,607] [INFO] Running command: blastn -query GCF_900289045.1_MPGL2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b66392f-8a6c-467b-b87e-eceac52d882d/dqc_reference/reference_markers.fasta -out GCF_900289045.1_MPGL2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:43,698] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:43,701] [INFO] Selected 18 target genomes.
[2024-01-24 11:12:43,702] [INFO] Target genome list was writen to GCF_900289045.1_MPGL2_genomic.fna/target_genomes.txt
[2024-01-24 11:12:43,708] [INFO] Task started: fastANI
[2024-01-24 11:12:43,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg47659cb3-6754-4ca1-a62c-8228962f428f/GCF_900289045.1_MPGL2_genomic.fna.gz --refList GCF_900289045.1_MPGL2_genomic.fna/target_genomes.txt --output GCF_900289045.1_MPGL2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:58,312] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:58,313] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b66392f-8a6c-467b-b87e-eceac52d882d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:58,313] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b66392f-8a6c-467b-b87e-eceac52d882d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:58,329] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:12:58,329] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:12:58,329] [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
Micropruina glycogenica		GCA_900289045.1	75385	75385	type	True	100.0	1281	1281	95	conclusive
Propionicimonas paludicola	strain=DSM 15597	GCA_002563675.1	185243	185243	type	True	78.4126	326	1281	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	78.2513	376	1281	95	below_threshold
Aestuariimicrobium ganziense	strain=YIM S02566	GCA_015352975.1	2773677	2773677	type	True	78.1993	331	1281	95	below_threshold
Propioniciclava soli	strain=YIM S02567	GCA_014858005.1	2775081	2775081	type	True	78.1581	344	1281	95	below_threshold
Propioniciclava sinopodophylli	strain=KCTC 33808	GCA_004324755.1	1837344	1837344	type	True	78.0546	343	1281	95	below_threshold
Propioniciclava tarda	strain=DSM 22130	GCA_004324765.1	433330	433330	type	True	77.9415	284	1281	95	below_threshold
Propioniciclava tarda	strain=DSM 22130	GCA_900182665.1	433330	433330	type	True	77.9132	289	1281	95	below_threshold
Auraticoccus cholistanensis	strain=F435	GCA_009742705.1	2656650	2656650	type	True	77.7573	331	1281	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	77.6663	328	1281	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	77.5787	305	1281	95	below_threshold
Microlunatus sagamiharensis	strain=DSM 21743	GCA_900105785.1	546874	546874	type	True	77.4778	298	1281	95	below_threshold
Microlunatus flavus	strain=CGMCC 4.6856	GCA_900110855.1	1036181	1036181	type	True	77.3392	313	1281	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	77.2965	206	1281	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	76.92	263	1281	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	76.8867	213	1281	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	76.6603	211	1281	95	below_threshold
Streptomyces mimosae	strain=3MP-10	GCA_006334995.2	2586635	2586635	type	True	75.6978	246	1281	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:58,331] [INFO] DFAST Taxonomy check result was written to GCF_900289045.1_MPGL2_genomic.fna/tc_result.tsv
[2024-01-24 11:12:58,331] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:58,332] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:58,332] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b66392f-8a6c-467b-b87e-eceac52d882d/dqc_reference/checkm_data
[2024-01-24 11:12:58,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:58,372] [INFO] Task started: CheckM
[2024-01-24 11:12:58,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900289045.1_MPGL2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900289045.1_MPGL2_genomic.fna/checkm_input GCF_900289045.1_MPGL2_genomic.fna/checkm_result
[2024-01-24 11:13:48,742] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:48,743] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:48,765] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:48,766] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:48,766] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900289045.1_MPGL2_genomic.fna/markers.fasta)
[2024-01-24 11:13:48,766] [INFO] Task started: Blastn
[2024-01-24 11:13:48,767] [INFO] Running command: blastn -query GCF_900289045.1_MPGL2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b66392f-8a6c-467b-b87e-eceac52d882d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900289045.1_MPGL2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:50,438] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:50,442] [INFO] Selected 11 target genomes.
[2024-01-24 11:13:50,442] [INFO] Target genome list was writen to GCF_900289045.1_MPGL2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:50,451] [INFO] Task started: fastANI
[2024-01-24 11:13:50,451] [INFO] Running command: fastANI --query /var/lib/cwl/stg47659cb3-6754-4ca1-a62c-8228962f428f/GCF_900289045.1_MPGL2_genomic.fna.gz --refList GCF_900289045.1_MPGL2_genomic.fna/target_genomes_gtdb.txt --output GCF_900289045.1_MPGL2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:00,300] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:00,315] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:00,315] [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_900289045.1	s__Micropruina glycogenica	100.0	1281	1281	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016711205.1	s__Micropruina sp016711205	83.1608	830	1281	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018055925.1	s__Micropruina sp018055925	81.1823	566	1281	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013693855.1	s__Micropruina sp013693855	79.0903	481	1281	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002843035.1	s__Propionicimonas sp002843035	78.5463	360	1281	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838755.1	s__Brevilactibacter sp012838755	78.2503	305	1281	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306015.1	s__Propionicimonas sp017306015	78.2363	417	1281	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015352975.1	s__Aestuariimicrobium ganziense	78.1888	332	1281	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Aestuariimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017569205.1	s__Brevilactibacter sp014164685	78.0792	386	1281	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	99.00	98.00	0.92	0.83	3	-
GCA_001603275.1	s__Propionicimonas sp001603275	78.0666	311	1281	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344635.1	s__Desertihabitans aurantiacus	77.5616	307	1281	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:00,319] [INFO] GTDB search result was written to GCF_900289045.1_MPGL2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:00,320] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:00,324] [INFO] DFAST_QC result json was written to GCF_900289045.1_MPGL2_genomic.fna/dqc_result.json
[2024-01-24 11:14:00,324] [INFO] DFAST_QC completed!
[2024-01-24 11:14:00,325] [INFO] Total running time: 0h1m32s