[2024-01-24 13:31:35,651] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:35,653] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:35,653] [INFO] DQC Reference Directory: /var/lib/cwl/stg29626dbe-bf02-46c1-aeb8-446be31c53b0/dqc_reference
[2024-01-24 13:31:37,072] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:37,073] [INFO] Task started: Prodigal
[2024-01-24 13:31:37,073] [INFO] Running command: gunzip -c /var/lib/cwl/stg032fa58e-427c-421e-a64a-b7ef4799ef08/GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna/cds.fna -a GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:59,660] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:59,660] [INFO] Task started: HMMsearch
[2024-01-24 13:31:59,661] [INFO] Running command: hmmsearch --tblout GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29626dbe-bf02-46c1-aeb8-446be31c53b0/dqc_reference/reference_markers.hmm GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:00,058] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:00,061] [INFO] Found 6/6 markers.
[2024-01-24 13:32:00,126] [INFO] Query marker FASTA was written to GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:32:00,126] [INFO] Task started: Blastn
[2024-01-24 13:32:00,127] [INFO] Running command: blastn -query GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg29626dbe-bf02-46c1-aeb8-446be31c53b0/dqc_reference/reference_markers.fasta -out GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:01,447] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:01,450] [INFO] Selected 16 target genomes.
[2024-01-24 13:32:01,450] [INFO] Target genome list was writen to GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:32:01,461] [INFO] Task started: fastANI
[2024-01-24 13:32:01,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg032fa58e-427c-421e-a64a-b7ef4799ef08/GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna.gz --refList GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:31,890] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:31,891] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29626dbe-bf02-46c1-aeb8-446be31c53b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:31,891] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29626dbe-bf02-46c1-aeb8-446be31c53b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:31,903] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:31,903] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:31,904] [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
Streptomyces wuyuanensis	strain=CGMCC 4.7042	GCA_900103455.1	1196353	1196353	type	True	100.0	2654	2655	95	conclusive
Streptomyces marianii	strain=ICN19	GCA_005795905.1	1817406	1817406	type	True	91.1228	1981	2655	95	below_threshold
Streptomyces tirandamycinicus	strain=HNM0039	GCA_003097515.1	2174846	2174846	type	True	90.2993	1846	2655	95	below_threshold
Streptomyces spongiicola	strain=HNM0071	GCA_003122365.1	1690221	1690221	type	True	88.9841	1745	2655	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	85.3149	1757	2655	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	82.6906	1458	2655	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.6013	1471	2655	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	82.5147	1110	2655	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	82.4524	1071	2655	95	below_threshold
Streptomyces microflavus	strain=JCM 4496	GCA_014650075.1	1919	1919	type	True	82.1244	1443	2655	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	81.3629	1378	2655	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	81.2735	1372	2655	95	below_threshold
Streptomyces sioyaensis	strain=DSM 40032	GCA_004122735.1	67364	67364	type	True	80.972	1182	2655	95	below_threshold
Streptomyces physcomitrii	strain=LD120	GCA_012273655.1	2724184	2724184	type	True	80.9307	1244	2655	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	80.4389	1037	2655	95	below_threshold
Actinacidiphila alni	strain=CGMCC 4.3510	GCA_900112845.1	380248	380248	type	True	79.9839	1137	2655	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:31,905] [INFO] DFAST Taxonomy check result was written to GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:32:31,906] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:31,906] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:31,906] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29626dbe-bf02-46c1-aeb8-446be31c53b0/dqc_reference/checkm_data
[2024-01-24 13:32:31,907] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:31,978] [INFO] Task started: CheckM
[2024-01-24 13:32:31,978] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna/checkm_input GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:34:25,007] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:25,009] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:25,035] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:25,035] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:25,036] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:34:25,036] [INFO] Task started: Blastn
[2024-01-24 13:34:25,036] [INFO] Running command: blastn -query GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg29626dbe-bf02-46c1-aeb8-446be31c53b0/dqc_reference/reference_markers_gtdb.fasta -out GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:27,113] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:27,118] [INFO] Selected 10 target genomes.
[2024-01-24 13:34:27,118] [INFO] Target genome list was writen to GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:27,142] [INFO] Task started: fastANI
[2024-01-24 13:34:27,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg032fa58e-427c-421e-a64a-b7ef4799ef08/GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna.gz --refList GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:46,259] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:46,273] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:46,273] [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_900103455.1	s__Streptomyces wuyuanensis	100.0	2654	2655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005795905.1	s__Streptomyces marianii	91.1417	1978	2655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097515.1	s__Streptomyces tirandamycinicus	90.2628	1850	2655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.65	98.27	0.90	0.88	6	-
GCA_003725745.1	s__Streptomyces sp003725745	89.8038	1825	2655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122365.1	s__Streptomyces spongiicola	88.9744	1746	2655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.39	99.39	0.96	0.96	2	-
GCF_011766325.1	s__Streptomyces sp011766325	88.3497	1583	2655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013387495.1	s__Streptomyces sp013387495	83.2326	1482	2655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704425.1	s__Streptomyces fradiae	82.4112	1320	2655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.82	99.37	0.98	0.97	5	-
GCF_001279725.1	s__Streptomyces sp001279725	81.4637	1208	2655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007595705.1	s__Streptomyces sp007595705	81.1842	1254	2655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:46,275] [INFO] GTDB search result was written to GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:46,275] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:46,279] [INFO] DFAST_QC result json was written to GCF_900103455.1_IMG-taxon_2675903062_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:34:46,279] [INFO] DFAST_QC completed!
[2024-01-24 13:34:46,279] [INFO] Total running time: 0h3m11s