[2024-01-24 12:14:35,533] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:35,535] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:35,535] [INFO] DQC Reference Directory: /var/lib/cwl/stg77913716-8401-4068-adf3-b98a0345aacd/dqc_reference
[2024-01-24 12:14:36,898] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:36,899] [INFO] Task started: Prodigal
[2024-01-24 12:14:36,899] [INFO] Running command: gunzip -c /var/lib/cwl/stgc97dfd80-39a2-4b6a-985c-04b9cae233d0/GCF_021441825.1_ASM2144182v1_genomic.fna.gz | prodigal -d GCF_021441825.1_ASM2144182v1_genomic.fna/cds.fna -a GCF_021441825.1_ASM2144182v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:01,969] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:01,969] [INFO] Task started: HMMsearch
[2024-01-24 12:15:01,969] [INFO] Running command: hmmsearch --tblout GCF_021441825.1_ASM2144182v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77913716-8401-4068-adf3-b98a0345aacd/dqc_reference/reference_markers.hmm GCF_021441825.1_ASM2144182v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:02,373] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:02,374] [INFO] Found 6/6 markers.
[2024-01-24 12:15:02,445] [INFO] Query marker FASTA was written to GCF_021441825.1_ASM2144182v1_genomic.fna/markers.fasta
[2024-01-24 12:15:02,445] [INFO] Task started: Blastn
[2024-01-24 12:15:02,445] [INFO] Running command: blastn -query GCF_021441825.1_ASM2144182v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77913716-8401-4068-adf3-b98a0345aacd/dqc_reference/reference_markers.fasta -out GCF_021441825.1_ASM2144182v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:03,788] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:03,795] [INFO] Selected 26 target genomes.
[2024-01-24 12:15:03,795] [INFO] Target genome list was writen to GCF_021441825.1_ASM2144182v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:03,804] [INFO] Task started: fastANI
[2024-01-24 12:15:03,804] [INFO] Running command: fastANI --query /var/lib/cwl/stgc97dfd80-39a2-4b6a-985c-04b9cae233d0/GCF_021441825.1_ASM2144182v1_genomic.fna.gz --refList GCF_021441825.1_ASM2144182v1_genomic.fna/target_genomes.txt --output GCF_021441825.1_ASM2144182v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:57,985] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:57,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77913716-8401-4068-adf3-b98a0345aacd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:57,986] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77913716-8401-4068-adf3-b98a0345aacd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:58,009] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:58,009] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:58,009] [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 plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	99.8559	2745	2874	95	conclusive
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	87.1671	1940	2874	95	below_threshold
Streptomyces antibioticus	strain=DSM 40234	GCA_001514065.1	1890	1890	suspected-type	True	85.9239	1960	2874	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	85.8876	2007	2874	95	below_threshold
Streptomyces pseudovenezuelae	strain=DSM 40212	GCA_001513955.1	67350	67350	type	True	85.7438	1964	2874	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.6287	1812	2874	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	85.5774	1912	2874	95	below_threshold
Streptomyces lomondensis	strain=JCM 4866	GCA_014651035.1	68229	68229	type	True	85.5649	1832	2874	95	below_threshold
Streptomyces griseorubiginosus	strain=DSM 40469	GCA_001514195.1	67304	67304	type	True	85.5306	1922	2874	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.4547	1670	2874	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	85.2907	1786	2874	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.2767	1727	2874	95	below_threshold
Streptomyces gossypiisoli	strain=TRM 44567	GCA_013433285.1	2748864	2748864	type	True	85.26	1764	2874	95	below_threshold
Streptomyces cellostaticus	strain=DSM 40189	GCA_001513965.1	67285	67285	type	True	85.249	1863	2874	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	85.0712	1678	2874	95	below_threshold
Streptomyces hyaluromycini	strain=NBRC 110483	GCA_002217755.1	1377993	1377993	type	True	85.059	1957	2874	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	85.0263	1672	2874	95	below_threshold
Streptomyces griseochromogenes	strain=DSM 40499	GCA_017874495.1	68214	68214	type	True	85.0006	1866	2874	95	below_threshold
Streptomyces griseochromogenes	strain=ATCC 14511	GCA_001542625.2	68214	68214	type	True	84.9241	1904	2874	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	84.8807	1546	2874	95	below_threshold
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	84.8696	1723	2874	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	84.8209	1731	2874	95	below_threshold
Streptomyces humi	strain=MUSC 119	GCA_001005085.2	1428620	1428620	type	True	84.8192	1905	2874	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	84.7999	1820	2874	95	below_threshold
Streptomyces hirsutus	strain=NRRL B-2713	GCA_001418415.1	35620	35620	type	True	84.0707	1374	2874	95	below_threshold
Streptomyces ossamyceticus	strain=NRRL B-3822	GCA_001418475.1	249581	249581	type	True	83.8433	1422	2874	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:58,011] [INFO] DFAST Taxonomy check result was written to GCF_021441825.1_ASM2144182v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:58,012] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:58,012] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:58,012] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77913716-8401-4068-adf3-b98a0345aacd/dqc_reference/checkm_data
[2024-01-24 12:15:58,014] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:58,090] [INFO] Task started: CheckM
[2024-01-24 12:15:58,090] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021441825.1_ASM2144182v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021441825.1_ASM2144182v1_genomic.fna/checkm_input GCF_021441825.1_ASM2144182v1_genomic.fna/checkm_result
[2024-01-24 12:18:11,038] [INFO] Task succeeded: CheckM
[2024-01-24 12:18:11,040] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 12:18:11,066] [INFO] ===== Completeness check finished =====
[2024-01-24 12:18:11,066] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:18:11,067] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021441825.1_ASM2144182v1_genomic.fna/markers.fasta)
[2024-01-24 12:18:11,067] [INFO] Task started: Blastn
[2024-01-24 12:18:11,067] [INFO] Running command: blastn -query GCF_021441825.1_ASM2144182v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77913716-8401-4068-adf3-b98a0345aacd/dqc_reference/reference_markers_gtdb.fasta -out GCF_021441825.1_ASM2144182v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:18:13,020] [INFO] Task succeeded: Blastn
[2024-01-24 12:18:13,024] [INFO] Selected 15 target genomes.
[2024-01-24 12:18:13,024] [INFO] Target genome list was writen to GCF_021441825.1_ASM2144182v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:18:13,031] [INFO] Task started: fastANI
[2024-01-24 12:18:13,032] [INFO] Running command: fastANI --query /var/lib/cwl/stgc97dfd80-39a2-4b6a-985c-04b9cae233d0/GCF_021441825.1_ASM2144182v1_genomic.fna.gz --refList GCF_021441825.1_ASM2144182v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021441825.1_ASM2144182v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:18:45,655] [INFO] Task succeeded: fastANI
[2024-01-24 12:18:45,666] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:18:45,667] [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_004104505.1	s__Streptomyces sp003046555	99.4508	2815	2874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.74	99.48	0.99	0.97	3	conclusive
GCF_000411315.1	s__Streptomyces sp000411315	94.1522	2554	2874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720765.1	s__Streptomyces sp000720765	88.1194	2124	2874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.07	96.07	0.83	0.83	2	-
GCF_003384795.1	s__Streptomyces sp003384795	88.061	2010	2874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754715.1	s__Streptomyces sp002754715	87.994	2100	2874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001484565.1	s__Streptomyces sp001484565	87.1588	2097	2874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715395.1	s__Streptomyces sp006715395	87.1319	2067	2874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.35	95.35	0.79	0.79	2	-
GCF_001282115.1	s__Streptomyces sp001282115	85.8952	1707	2874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.95	0.95	0.95	2	-
GCF_003443735.1	s__Streptomyces sviceus	85.7823	1961	2874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0589	99.86	99.86	0.99	0.99	3	-
GCF_004187715.1	s__Streptomyces sp004187715	85.4036	1761	2874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014534645.1	s__Streptomyces sp014534645	85.2826	1726	2874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342105.1	s__Streptomyces sp004342105	84.8513	1817	2874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001005085.2	s__Streptomyces humi	84.7996	1908	2874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.38	96.38	0.85	0.85	2	-
GCF_001418415.1	s__Streptomyces hirsutus	84.0438	1379	2874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.60	97.60	0.78	0.78	2	-
GCF_009857135.1	s__Streptomyces sp009857135	84.0081	1614	2874	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 12:18:45,668] [INFO] GTDB search result was written to GCF_021441825.1_ASM2144182v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:18:45,669] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:18:45,673] [INFO] DFAST_QC result json was written to GCF_021441825.1_ASM2144182v1_genomic.fna/dqc_result.json
[2024-01-24 12:18:45,673] [INFO] DFAST_QC completed!
[2024-01-24 12:18:45,673] [INFO] Total running time: 0h4m10s