[2024-01-24 10:57:26,611] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:26,614] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:26,614] [INFO] DQC Reference Directory: /var/lib/cwl/stga100d827-b7e5-4e38-90ae-0873ad5ae474/dqc_reference
[2024-01-24 10:57:28,025] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:28,026] [INFO] Task started: Prodigal
[2024-01-24 10:57:28,027] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8694cd6-4889-4d0c-ba62-d9615b93f76d/GCF_014649835.1_ASM1464983v1_genomic.fna.gz | prodigal -d GCF_014649835.1_ASM1464983v1_genomic.fna/cds.fna -a GCF_014649835.1_ASM1464983v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:49,635] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:49,636] [INFO] Task started: HMMsearch
[2024-01-24 10:57:49,636] [INFO] Running command: hmmsearch --tblout GCF_014649835.1_ASM1464983v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga100d827-b7e5-4e38-90ae-0873ad5ae474/dqc_reference/reference_markers.hmm GCF_014649835.1_ASM1464983v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:50,014] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:50,015] [INFO] Found 6/6 markers.
[2024-01-24 10:57:50,068] [INFO] Query marker FASTA was written to GCF_014649835.1_ASM1464983v1_genomic.fna/markers.fasta
[2024-01-24 10:57:50,068] [INFO] Task started: Blastn
[2024-01-24 10:57:50,069] [INFO] Running command: blastn -query GCF_014649835.1_ASM1464983v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga100d827-b7e5-4e38-90ae-0873ad5ae474/dqc_reference/reference_markers.fasta -out GCF_014649835.1_ASM1464983v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:51,322] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:51,325] [INFO] Selected 16 target genomes.
[2024-01-24 10:57:51,325] [INFO] Target genome list was writen to GCF_014649835.1_ASM1464983v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:51,331] [INFO] Task started: fastANI
[2024-01-24 10:57:51,331] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8694cd6-4889-4d0c-ba62-d9615b93f76d/GCF_014649835.1_ASM1464983v1_genomic.fna.gz --refList GCF_014649835.1_ASM1464983v1_genomic.fna/target_genomes.txt --output GCF_014649835.1_ASM1464983v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:24,962] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:24,963] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga100d827-b7e5-4e38-90ae-0873ad5ae474/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:24,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga100d827-b7e5-4e38-90ae-0873ad5ae474/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:24,977] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:24,977] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:24,977] [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 pilosus	strain=JCM 4403	GCA_014649835.1	28893	28893	type	True	100.0	2515	2518	95	conclusive
Streptomyces griseoflavus	strain=JCM 4479	GCA_014649995.1	35619	35619	type	True	93.5982	2000	2518	95	below_threshold
Streptomyces malachitofuscus	strain=JCM 4493	GCA_014650055.1	67322	67322	type	True	90.0278	1864	2518	95	below_threshold
Streptomyces albaduncus	strain=CECT 3226	GCA_014203495.1	68172	68172	type	True	89.0987	1825	2518	95	below_threshold
Streptomyces capillispiralis	strain=JCM 5075	GCA_014656315.1	68182	68182	type	True	89.0856	1868	2518	95	below_threshold
Streptomyces capillispiralis	strain=DSM 41695	GCA_007829875.1	68182	68182	type	True	89.084	1871	2518	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	88.7747	1863	2518	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	88.6775	1887	2518	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.9368	1667	2518	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.8316	1684	2518	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	85.717	1671	2518	95	below_threshold
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	85.6892	1664	2518	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	85.634	1676	2518	95	below_threshold
Streptomyces tuirus	strain=JCM 4255	GCA_014701095.1	68278	68278	type	True	85.6058	1654	2518	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	85.5003	1542	2518	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.5009	1638	2518	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:24,979] [INFO] DFAST Taxonomy check result was written to GCF_014649835.1_ASM1464983v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:24,980] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:24,980] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:24,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga100d827-b7e5-4e38-90ae-0873ad5ae474/dqc_reference/checkm_data
[2024-01-24 10:58:24,981] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:25,050] [INFO] Task started: CheckM
[2024-01-24 10:58:25,051] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649835.1_ASM1464983v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649835.1_ASM1464983v1_genomic.fna/checkm_input GCF_014649835.1_ASM1464983v1_genomic.fna/checkm_result
[2024-01-24 11:00:10,455] [INFO] Task succeeded: CheckM
[2024-01-24 11:00:10,457] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:00:10,475] [INFO] ===== Completeness check finished =====
[2024-01-24 11:00:10,475] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:00:10,476] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649835.1_ASM1464983v1_genomic.fna/markers.fasta)
[2024-01-24 11:00:10,476] [INFO] Task started: Blastn
[2024-01-24 11:00:10,476] [INFO] Running command: blastn -query GCF_014649835.1_ASM1464983v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga100d827-b7e5-4e38-90ae-0873ad5ae474/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649835.1_ASM1464983v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:00:12,524] [INFO] Task succeeded: Blastn
[2024-01-24 11:00:12,527] [INFO] Selected 14 target genomes.
[2024-01-24 11:00:12,527] [INFO] Target genome list was writen to GCF_014649835.1_ASM1464983v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:00:12,536] [INFO] Task started: fastANI
[2024-01-24 11:00:12,537] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8694cd6-4889-4d0c-ba62-d9615b93f76d/GCF_014649835.1_ASM1464983v1_genomic.fna.gz --refList GCF_014649835.1_ASM1464983v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649835.1_ASM1464983v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:00:40,858] [INFO] Task succeeded: fastANI
[2024-01-24 11:00:40,870] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:00:40,870] [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_014649835.1	s__Streptomyces pilosus	100.0	2515	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.43	99.43	0.94	0.94	2	conclusive
GCF_014649995.1	s__Streptomyces griseoflavus	93.5827	2002	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008312835.1	s__Streptomyces marokkonensis	90.2466	1884	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725125.1	s__Streptomyces toyocaensis	89.8765	1779	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018638295.1	s__Streptomyces sp018638295	89.8235	1819	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905725.1	s__Streptomyces sp001905725	89.7893	1907	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001279005.1	s__Streptomyces caelestis_A	89.6966	1857	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.79	99.58	0.97	0.96	3	-
GCF_000721605.1	s__Streptomyces sp000721605	89.6797	1871	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049255.1	s__Streptomyces sp019049255	89.5848	1917	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003665435.1	s__Streptomyces fungicidicus_A	89.4508	1885	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.86	98.42	0.93	0.90	4	-
GCA_014650015.1	s__Streptomyces griseoloalbus	89.1222	1816	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.17	99.17	0.94	0.94	3	-
GCF_007829875.1	s__Streptomyces capillispiralis	89.0907	1870	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000718785.1	s__Streptomyces sp000718785	88.8012	1806	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002154585.1	s__Streptomyces pseudogriseolus	87.8002	1528	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.58	96.58	0.90	0.87	9	-
--------------------------------------------------------------------------------
[2024-01-24 11:00:40,872] [INFO] GTDB search result was written to GCF_014649835.1_ASM1464983v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:00:40,872] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:00:40,876] [INFO] DFAST_QC result json was written to GCF_014649835.1_ASM1464983v1_genomic.fna/dqc_result.json
[2024-01-24 11:00:40,876] [INFO] DFAST_QC completed!
[2024-01-24 11:00:40,876] [INFO] Total running time: 0h3m14s