[2024-01-24 13:32:40,745] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:40,747] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:40,747] [INFO] DQC Reference Directory: /var/lib/cwl/stg23e18c72-6c24-45ce-97b7-000a05ffa005/dqc_reference
[2024-01-24 13:32:42,090] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:42,091] [INFO] Task started: Prodigal
[2024-01-24 13:32:42,091] [INFO] Running command: gunzip -c /var/lib/cwl/stg97e91f52-c1f8-48df-a9f9-3a8b7cb78368/GCF_004402605.1_ASM440260v1_genomic.fna.gz | prodigal -d GCF_004402605.1_ASM440260v1_genomic.fna/cds.fna -a GCF_004402605.1_ASM440260v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:49,574] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:49,575] [INFO] Task started: HMMsearch
[2024-01-24 13:32:49,575] [INFO] Running command: hmmsearch --tblout GCF_004402605.1_ASM440260v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23e18c72-6c24-45ce-97b7-000a05ffa005/dqc_reference/reference_markers.hmm GCF_004402605.1_ASM440260v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:49,828] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:49,829] [INFO] Found 6/6 markers.
[2024-01-24 13:32:49,866] [INFO] Query marker FASTA was written to GCF_004402605.1_ASM440260v1_genomic.fna/markers.fasta
[2024-01-24 13:32:49,867] [INFO] Task started: Blastn
[2024-01-24 13:32:49,867] [INFO] Running command: blastn -query GCF_004402605.1_ASM440260v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23e18c72-6c24-45ce-97b7-000a05ffa005/dqc_reference/reference_markers.fasta -out GCF_004402605.1_ASM440260v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:50,958] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:50,961] [INFO] Selected 23 target genomes.
[2024-01-24 13:32:50,962] [INFO] Target genome list was writen to GCF_004402605.1_ASM440260v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:50,981] [INFO] Task started: fastANI
[2024-01-24 13:32:50,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg97e91f52-c1f8-48df-a9f9-3a8b7cb78368/GCF_004402605.1_ASM440260v1_genomic.fna.gz --refList GCF_004402605.1_ASM440260v1_genomic.fna/target_genomes.txt --output GCF_004402605.1_ASM440260v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:03,640] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:03,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23e18c72-6c24-45ce-97b7-000a05ffa005/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:03,642] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23e18c72-6c24-45ce-97b7-000a05ffa005/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:03,663] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:03,664] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:03,664] [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
Terrimesophilobacter mesophilus	strain=DSM 19267	GCA_014200375.1	433647	433647	type	True	99.999	803	803	95	conclusive
Lacisediminihabitans profunda	strain=CHu50b-6-2	GCA_008040105.1	2594790	2594790	type	True	78.8951	304	803	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	78.7562	201	803	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_021952865.1	1401995	1401995	type	True	78.6751	243	803	95	below_threshold
Galbitalea soli	strain=NBRC 108727	GCA_010686725.1	1268042	1268042	type	True	78.5114	259	803	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	78.4922	247	803	95	below_threshold
Clavibacter michiganensis subsp. michiganensis	strain=LMG 7333	GCA_002240575.1	33013	28447	type	True	78.4471	244	803	95	below_threshold
Conyzicola nivalis	strain=CGMCC 1.12813	GCA_014639655.1	1477021	1477021	type	True	78.4339	283	803	95	below_threshold
Clavibacter michiganensis	strain=VKM Ac-1403	GCA_900168345.1	28447	28447	suspected-type	True	78.4179	245	803	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	78.4097	261	803	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	78.3793	242	803	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_014200395.1	424758	424758	type	True	78.3666	260	803	95	below_threshold
Galbitalea soli	strain=DSM 105515	GCA_013410525.1	1268042	1268042	type	True	78.3438	262	803	95	below_threshold
Marisediminicola antarctica	strain=ZS314	GCA_009930795.1	674079	674079	type	True	78.2926	295	803	95	below_threshold
Lacisediminihabitans changchengi	strain=G11-30	GCA_016634425.1	2787634	2787634	type	True	78.26	225	803	95	below_threshold
Frigoribacterium faeni	strain=DSM 10309	GCA_014137965.1	145483	145483	type	True	78.1672	234	803	95	below_threshold
Frigoribacterium faeni	strain=NBRC 103066	GCA_007988805.1	145483	145483	type	True	78.1659	231	803	95	below_threshold
Plantibacter flavus	strain=DSM 14012	GCA_003755125.1	150123	150123	type	True	78.0448	245	803	95	below_threshold
Plantibacter flavus	strain=VKM Ac-2504	GCA_900177615.1	150123	150123	type	True	77.9543	248	803	95	below_threshold
Humibacter albus	strain=DSM 18994	GCA_000421825.1	427754	427754	type	True	77.8976	218	803	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	77.8358	277	803	95	below_threshold
Microbacterium agarici	strain=DSM 21798	GCA_002563955.1	630514	630514	type	True	77.5028	150	803	95	below_threshold
Microbacterium lindanitolerans	strain=DSM 22422	GCA_006788875.1	550448	550448	type	True	77.4968	151	803	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:03,666] [INFO] DFAST Taxonomy check result was written to GCF_004402605.1_ASM440260v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:03,667] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:03,667] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:03,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23e18c72-6c24-45ce-97b7-000a05ffa005/dqc_reference/checkm_data
[2024-01-24 13:33:03,668] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:03,703] [INFO] Task started: CheckM
[2024-01-24 13:33:03,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004402605.1_ASM440260v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004402605.1_ASM440260v1_genomic.fna/checkm_input GCF_004402605.1_ASM440260v1_genomic.fna/checkm_result
[2024-01-24 13:33:42,504] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:42,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:42,525] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:42,526] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:42,526] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004402605.1_ASM440260v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:42,526] [INFO] Task started: Blastn
[2024-01-24 13:33:42,526] [INFO] Running command: blastn -query GCF_004402605.1_ASM440260v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23e18c72-6c24-45ce-97b7-000a05ffa005/dqc_reference/reference_markers_gtdb.fasta -out GCF_004402605.1_ASM440260v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:44,135] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:44,139] [INFO] Selected 20 target genomes.
[2024-01-24 13:33:44,139] [INFO] Target genome list was writen to GCF_004402605.1_ASM440260v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:44,199] [INFO] Task started: fastANI
[2024-01-24 13:33:44,200] [INFO] Running command: fastANI --query /var/lib/cwl/stg97e91f52-c1f8-48df-a9f9-3a8b7cb78368/GCF_004402605.1_ASM440260v1_genomic.fna.gz --refList GCF_004402605.1_ASM440260v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004402605.1_ASM440260v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:56,152] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:56,175] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:56,175] [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_014200375.1	s__Terrimesophilobacter mesophilus	99.999	803	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Terrimesophilobacter	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCA_017306245.1	s__Terrimesophilobacter sp017306245	80.5615	474	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Terrimesophilobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012274275.1	s__Terrimesophilobacter sp012274275	79.3547	324	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Terrimesophilobacter	95.0	98.97	98.97	0.95	0.95	2	-
GCA_001725325.1	s__Rhodoglobus sp001725325	78.9666	328	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001425665.1	s__Yonghaparkia sp001425665	78.679	281	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	99.25	99.25	0.97	0.97	2	-
GCF_001618005.1	s__Clavibacter tessellarius_A	78.6465	233	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008001035.1	s__Homoserinimonas sp008001035	78.6339	259	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Homoserinimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002797715.1	s__Diaminobutyricimonas aerilata	78.5967	285	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Diaminobutyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015234465.1	s__Homoserinimonas sp015234465	78.5536	289	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Homoserinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002150995.1	s__Clavibacter michiganensis_K	78.5172	232	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	98.44	98.42	0.92	0.92	3	-
GCF_016907085.1	s__Clavibacter michiganensis_O	78.4886	247	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000069225.1	s__Clavibacter sepedonicus	78.4772	239	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	99.98	99.98	0.98	0.96	4	-
GCF_900168345.1	s__Clavibacter michiganensis	78.4119	246	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	99.05	95.09	0.97	0.88	49	-
GCA_002325245.1	s__Pseudolysinimonas sp002325245	78.28	268	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	99.78	99.17	0.96	0.89	14	-
GCF_014653215.1	s__Pseudolysinimonas yzui	78.2781	275	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002151125.1	s__Clavibacter michiganensis_C	78.2353	256	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422325.1	s__Leifsonia_A sp001422325	78.2036	252	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia_A	95.0	96.12	96.12	0.77	0.77	2	-
GCA_014378715.1	s__Marisediminicola sp014378715	78.1692	264	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marisediminicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715355.1	s__Agromyces sp006715355	78.0501	292	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421825.1	s__Humibacter albus	77.8832	219	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Humibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:56,177] [INFO] GTDB search result was written to GCF_004402605.1_ASM440260v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:56,178] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:56,183] [INFO] DFAST_QC result json was written to GCF_004402605.1_ASM440260v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:56,183] [INFO] DFAST_QC completed!
[2024-01-24 13:33:56,183] [INFO] Total running time: 0h1m15s