[2024-01-24 15:02:46,317] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:46,321] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:46,322] [INFO] DQC Reference Directory: /var/lib/cwl/stg87e79f68-d860-42ab-800a-a0a9cbc30048/dqc_reference
[2024-01-24 15:02:47,704] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:47,705] [INFO] Task started: Prodigal
[2024-01-24 15:02:47,705] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf6a5595-24d0-4dfa-a214-66d7b140e0fd/GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna/cds.fna -a GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:39,394] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:39,395] [INFO] Task started: HMMsearch
[2024-01-24 15:03:39,395] [INFO] Running command: hmmsearch --tblout GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87e79f68-d860-42ab-800a-a0a9cbc30048/dqc_reference/reference_markers.hmm GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:39,855] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:39,857] [INFO] Found 6/6 markers.
[2024-01-24 15:03:39,945] [INFO] Query marker FASTA was written to GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:03:39,946] [INFO] Task started: Blastn
[2024-01-24 15:03:39,946] [INFO] Running command: blastn -query GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg87e79f68-d860-42ab-800a-a0a9cbc30048/dqc_reference/reference_markers.fasta -out GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:41,333] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:41,337] [INFO] Selected 15 target genomes.
[2024-01-24 15:03:41,337] [INFO] Target genome list was writen to GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:03:41,343] [INFO] Task started: fastANI
[2024-01-24 15:03:41,343] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf6a5595-24d0-4dfa-a214-66d7b140e0fd/GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna.gz --refList GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:04:33,104] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:33,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87e79f68-d860-42ab-800a-a0a9cbc30048/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:04:33,105] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87e79f68-d860-42ab-800a-a0a9cbc30048/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:04:33,120] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:04:33,121] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 15:04:33,121] [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 antimycoticus	strain=NBRC 12839	GCA_005405925.1	68175	68175	type	True	96.8868	3122	3589	95	inconclusive
Streptomyces yatensis	strain=DSM 41771	GCA_018069625.1	155177	155177	type	True	96.1335	3002	3589	95	inconclusive
Streptomyces iranensis	strain=DSM 41954	GCA_017874715.1	576784	576784	type	True	92.3108	2864	3589	95	below_threshold
Streptomyces sabulosicollis	strain=PRKS01-29	GCA_016103465.1	2715963	2715963	type	True	92.2959	2303	3589	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_003675955.1	1226757	1226757	type	True	92.2496	2967	3589	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	92.2477	2953	3589	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_000418455.1	1226757	1226757	type	True	92.2061	2960	3589	95	below_threshold
Streptomyces javensis	strain=DSM 41764	GCA_016103505.1	114698	114698	type	True	92.0756	2138	3589	95	below_threshold
Streptomyces hygroscopicus subsp. hygroscopicus	strain=NBRC 13472	GCA_001553455.1	68042	1912	type	True	90.602	2096	3589	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	82.2845	1248	3589	95	below_threshold
Streptomyces pactum	strain=ATCC 27456	GCA_016031615.1	68249	68249	type	True	81.6149	1505	3589	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	81.1057	1518	3589	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	81.0651	1402	3589	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	80.9459	1457	3589	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	80.3091	1458	3589	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:04:33,123] [INFO] DFAST Taxonomy check result was written to GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:04:33,123] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:04:33,124] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:04:33,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87e79f68-d860-42ab-800a-a0a9cbc30048/dqc_reference/checkm_data
[2024-01-24 15:04:33,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:04:33,229] [INFO] Task started: CheckM
[2024-01-24 15:04:33,229] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna/checkm_input GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:08:25,036] [INFO] Task succeeded: CheckM
[2024-01-24 15:08:25,037] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:08:25,068] [INFO] ===== Completeness check finished =====
[2024-01-24 15:08:25,069] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:08:25,069] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:08:25,069] [INFO] Task started: Blastn
[2024-01-24 15:08:25,070] [INFO] Running command: blastn -query GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg87e79f68-d860-42ab-800a-a0a9cbc30048/dqc_reference/reference_markers_gtdb.fasta -out GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:08:27,172] [INFO] Task succeeded: Blastn
[2024-01-24 15:08:27,177] [INFO] Selected 10 target genomes.
[2024-01-24 15:08:27,177] [INFO] Target genome list was writen to GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:08:27,251] [INFO] Task started: fastANI
[2024-01-24 15:08:27,251] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf6a5595-24d0-4dfa-a214-66d7b140e0fd/GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna.gz --refList GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:09:11,060] [INFO] Task succeeded: fastANI
[2024-01-24 15:09:11,088] [INFO] Found 10 fastANI hits (3 hits with ANI > circumscription radius)
[2024-01-24 15:09:11,088] [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_005405925.1	s__Streptomyces antimycoticus	96.8775	3123	3589	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.0185	97.28	96.80	0.85	0.81	7	inconclusive
GCF_018069625.1	s__Streptomyces yatensis	96.1126	3005	3589	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.0185	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000147815.2	s__Streptomyces violaceusniger_A	95.4587	2905	3589	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3301	95.69	95.54	0.80	0.80	4	inconclusive
GCF_016741935.1	s__Streptomyces sp016741935	92.3547	2847	3589	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0488	N/A	N/A	N/A	N/A	1	-
GCF_017874715.1	s__Streptomyces iranensis	92.3326	2861	3589	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.67	99.98	99.98	1.00	1.00	2	-
GCF_018138715.1	s__Streptomyces asiaticus	92.2735	2836	3589	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	95.36	0.90	0.81	10	-
GCF_003675955.1	s__Streptomyces rapamycinicus	92.2345	2970	3589	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.67	99.95	99.91	0.99	0.99	3	-
GCA_005405945.1	s__Streptomyces violaceusniger	92.1519	2762	3589	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.67	97.67	0.85	0.85	2	-
GCF_015689475.1	s__Streptomyces solisilvae	92.0879	2725	3589	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.71	97.94	0.94	0.86	10	-
GCF_001553455.1	s__Streptomyces hygroscopicus	90.5818	2101	3589	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.24	98.00	0.92	0.90	7	-
--------------------------------------------------------------------------------
[2024-01-24 15:09:11,090] [INFO] GTDB search result was written to GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:09:11,091] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:09:11,101] [INFO] DFAST_QC result json was written to GCF_900105695.1_IMG-taxon_2634166371_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:09:11,101] [INFO] DFAST_QC completed!
[2024-01-24 15:09:11,102] [INFO] Total running time: 0h6m25s