[2024-01-24 13:40:34,917] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,919] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,919] [INFO] DQC Reference Directory: /var/lib/cwl/stge98ec11b-8f1c-4e95-95d6-a0ac5377d9a5/dqc_reference
[2024-01-24 13:40:36,269] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,270] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,271] [INFO] Running command: gunzip -c /var/lib/cwl/stge836b75f-7a1d-4ab4-a2c0-0f7efc841196/GCF_003067705.1_ASM306770v1_genomic.fna.gz | prodigal -d GCF_003067705.1_ASM306770v1_genomic.fna/cds.fna -a GCF_003067705.1_ASM306770v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:47,044] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:47,045] [INFO] Task started: HMMsearch
[2024-01-24 13:40:47,045] [INFO] Running command: hmmsearch --tblout GCF_003067705.1_ASM306770v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge98ec11b-8f1c-4e95-95d6-a0ac5377d9a5/dqc_reference/reference_markers.hmm GCF_003067705.1_ASM306770v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:47,334] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:47,335] [INFO] Found 6/6 markers.
[2024-01-24 13:40:47,368] [INFO] Query marker FASTA was written to GCF_003067705.1_ASM306770v1_genomic.fna/markers.fasta
[2024-01-24 13:40:47,369] [INFO] Task started: Blastn
[2024-01-24 13:40:47,369] [INFO] Running command: blastn -query GCF_003067705.1_ASM306770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge98ec11b-8f1c-4e95-95d6-a0ac5377d9a5/dqc_reference/reference_markers.fasta -out GCF_003067705.1_ASM306770v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:48,675] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:48,680] [INFO] Selected 18 target genomes.
[2024-01-24 13:40:48,680] [INFO] Target genome list was writen to GCF_003067705.1_ASM306770v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:48,685] [INFO] Task started: fastANI
[2024-01-24 13:40:48,685] [INFO] Running command: fastANI --query /var/lib/cwl/stge836b75f-7a1d-4ab4-a2c0-0f7efc841196/GCF_003067705.1_ASM306770v1_genomic.fna.gz --refList GCF_003067705.1_ASM306770v1_genomic.fna/target_genomes.txt --output GCF_003067705.1_ASM306770v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:01,951] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:01,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge98ec11b-8f1c-4e95-95d6-a0ac5377d9a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:01,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge98ec11b-8f1c-4e95-95d6-a0ac5377d9a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:01,967] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:01,967] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:01,967] [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
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	80.6494	409	1230	95	below_threshold
Clavibacter zhangzhiyongii	strain=DM1	GCA_014775655.1	2768071	2768071	type	True	80.4346	536	1230	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	80.4119	537	1230	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	80.3532	532	1230	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	80.3345	547	1230	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	80.2977	543	1230	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=LMG 3663	GCA_002240565.1	33014	28447	type	True	80.2891	525	1230	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_021952865.1	1401995	1401995	type	True	80.2686	534	1230	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=CFBP 2404	GCA_003693415.1	33014	28447	type	True	80.2535	528	1230	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	80.1539	555	1230	95	below_threshold
Herbiconiux flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	79.5374	495	1230	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	79.3389	443	1230	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	79.1708	438	1230	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.1147	495	1230	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	79.0306	465	1230	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	79.0137	420	1230	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	78.9218	488	1230	95	below_threshold
Agromyces salentinus	strain=JCM 14323	GCA_009749395.1	269421	269421	type	True	78.7971	461	1230	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:01,969] [INFO] DFAST Taxonomy check result was written to GCF_003067705.1_ASM306770v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:01,969] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:01,970] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:01,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge98ec11b-8f1c-4e95-95d6-a0ac5377d9a5/dqc_reference/checkm_data
[2024-01-24 13:41:01,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:02,011] [INFO] Task started: CheckM
[2024-01-24 13:41:02,012] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003067705.1_ASM306770v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003067705.1_ASM306770v1_genomic.fna/checkm_input GCF_003067705.1_ASM306770v1_genomic.fna/checkm_result
[2024-01-24 13:41:39,523] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:39,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.43%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:39,557] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:39,557] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:39,558] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003067705.1_ASM306770v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:39,558] [INFO] Task started: Blastn
[2024-01-24 13:41:39,559] [INFO] Running command: blastn -query GCF_003067705.1_ASM306770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge98ec11b-8f1c-4e95-95d6-a0ac5377d9a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003067705.1_ASM306770v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:41,677] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:41,682] [INFO] Selected 19 target genomes.
[2024-01-24 13:41:41,682] [INFO] Target genome list was writen to GCF_003067705.1_ASM306770v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:41,716] [INFO] Task started: fastANI
[2024-01-24 13:41:41,717] [INFO] Running command: fastANI --query /var/lib/cwl/stge836b75f-7a1d-4ab4-a2c0-0f7efc841196/GCF_003067705.1_ASM306770v1_genomic.fna.gz --refList GCF_003067705.1_ASM306770v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003067705.1_ASM306770v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:56,410] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:56,425] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:56,425] [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_003067705.1	s__Planctomonas deserti	100.0	1229	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Planctomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_008642235.1	s__Planctomonas sp008642235	81.1118	608	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Planctomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576185.1	s__Clavibacter phaseoli	80.8237	404	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	96.97	95.69	0.87	0.85	4	-
GCF_003576405.1	s__Clavibacter sp003576405	80.6243	460	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	99.88	99.88	0.93	0.93	2	-
GCF_001280205.1	s__Clavibacter capsici	80.4403	550	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	98.16	95.31	0.96	0.91	6	-
GCF_002240635.1	s__Clavibacter tessellarius	80.4024	542	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	96.95	95.37	0.96	0.94	3	-
GCF_001618005.1	s__Clavibacter tessellarius_A	80.4002	526	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384945.1	s__Clavibacter sp003384945	80.3891	540	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002151125.1	s__Clavibacter michiganensis_C	80.3305	550	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002240565.1	s__Clavibacter insidiosus	80.2832	526	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.1408	99.26	95.88	0.97	0.89	7	-
GCF_015351105.1	s__Clavibacter sp015351105	80.1869	524	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355965.1	s__JAFIQW01 sp017355965	79.8532	499	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__JAFIQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797855.1	s__Compostimonas suwonensis	79.5499	455	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Compostimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409865.1	s__Herbiconiux flava	79.4964	500	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	95.35	95.35	0.90	0.90	2	-
GCF_012317045.1	s__Leifsonia sp002105485	79.1676	458	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.03	98.03	0.91	0.91	2	-
GCF_013408745.1	s__Leifsonia soli	79.1598	438	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.25	98.25	0.89	0.89	2	-
GCF_008122505.1	s__Agromyces sp008122505	79.0774	499	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216665.1	s__Agromyces ramosus	79.0221	466	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648575.1	s__Agromyces mediolanus	78.9287	485	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:56,427] [INFO] GTDB search result was written to GCF_003067705.1_ASM306770v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:56,428] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:56,432] [INFO] DFAST_QC result json was written to GCF_003067705.1_ASM306770v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:56,432] [INFO] DFAST_QC completed!
[2024-01-24 13:41:56,432] [INFO] Total running time: 0h1m22s