[2024-01-24 13:41:20,594] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:20,599] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:20,599] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b86e5f7-9e96-4031-bd61-87ef91bd2d6f/dqc_reference
[2024-01-24 13:41:21,978] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:21,979] [INFO] Task started: Prodigal
[2024-01-24 13:41:21,979] [INFO] Running command: gunzip -c /var/lib/cwl/stg513887f3-1bde-4fa3-b94a-e63edabbe4e6/GCF_007655005.1_ASM765500v1_genomic.fna.gz | prodigal -d GCF_007655005.1_ASM765500v1_genomic.fna/cds.fna -a GCF_007655005.1_ASM765500v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:48,248] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:48,248] [INFO] Task started: HMMsearch
[2024-01-24 13:41:48,249] [INFO] Running command: hmmsearch --tblout GCF_007655005.1_ASM765500v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b86e5f7-9e96-4031-bd61-87ef91bd2d6f/dqc_reference/reference_markers.hmm GCF_007655005.1_ASM765500v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:48,702] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:48,704] [INFO] Found 6/6 markers.
[2024-01-24 13:41:48,784] [INFO] Query marker FASTA was written to GCF_007655005.1_ASM765500v1_genomic.fna/markers.fasta
[2024-01-24 13:41:48,784] [INFO] Task started: Blastn
[2024-01-24 13:41:48,785] [INFO] Running command: blastn -query GCF_007655005.1_ASM765500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b86e5f7-9e96-4031-bd61-87ef91bd2d6f/dqc_reference/reference_markers.fasta -out GCF_007655005.1_ASM765500v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:50,227] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:50,231] [INFO] Selected 13 target genomes.
[2024-01-24 13:41:50,231] [INFO] Target genome list was writen to GCF_007655005.1_ASM765500v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:50,236] [INFO] Task started: fastANI
[2024-01-24 13:41:50,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg513887f3-1bde-4fa3-b94a-e63edabbe4e6/GCF_007655005.1_ASM765500v1_genomic.fna.gz --refList GCF_007655005.1_ASM765500v1_genomic.fna/target_genomes.txt --output GCF_007655005.1_ASM765500v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:21,081] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:21,082] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b86e5f7-9e96-4031-bd61-87ef91bd2d6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:21,082] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b86e5f7-9e96-4031-bd61-87ef91bd2d6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:21,095] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:42:21,095] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:21,095] [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 tibetensis	strain=XZ 46	GCA_005869865.1	2382123	2382123	type	True	100.0	2967	2968	95	conclusive
Streptomyces tibetensis	strain=XZ 46	GCA_007655005.1	2382123	2382123	type	True	100.0	2967	2968	95	conclusive
Streptomyces massasporeus	strain=JCM 4139	GCA_014648995.1	67324	67324	type	True	92.7609	2387	2968	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	92.6366	2024	2968	95	below_threshold
Streptomyces tuirus	strain=JCM 4255	GCA_014701095.1	68278	68278	type	True	92.54	2104	2968	95	below_threshold
Streptomyces hawaiiensis	strain=ATCC 12236	GCA_004803895.1	67305	67305	type	True	92.5101	2291	2968	95	below_threshold
Streptomyces violaceochromogenes	strain=JCM 4530	GCA_014650235.1	67377	67377	type	True	92.4213	2315	2968	95	below_threshold
Streptomyces luteogriseus	strain=DSM 40483	GCA_014205055.1	68233	68233	type	True	92.3878	2300	2968	95	below_threshold
Streptomyces iakyrus	strain=NRRL ISP-5482	GCA_000717055.1	68219	68219	type	True	92.2463	2273	2968	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	91.7118	1828	2968	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	90.5939	2189	2968	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	90.3767	2255	2968	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.2242	1514	2968	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:21,097] [INFO] DFAST Taxonomy check result was written to GCF_007655005.1_ASM765500v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:21,097] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:21,098] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:21,098] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b86e5f7-9e96-4031-bd61-87ef91bd2d6f/dqc_reference/checkm_data
[2024-01-24 13:42:21,099] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:21,179] [INFO] Task started: CheckM
[2024-01-24 13:42:21,180] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007655005.1_ASM765500v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007655005.1_ASM765500v1_genomic.fna/checkm_input GCF_007655005.1_ASM765500v1_genomic.fna/checkm_result
[2024-01-24 13:44:24,193] [INFO] Task succeeded: CheckM
[2024-01-24 13:44:24,195] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.56%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:44:24,221] [INFO] ===== Completeness check finished =====
[2024-01-24 13:44:24,221] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:44:24,222] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007655005.1_ASM765500v1_genomic.fna/markers.fasta)
[2024-01-24 13:44:24,222] [INFO] Task started: Blastn
[2024-01-24 13:44:24,222] [INFO] Running command: blastn -query GCF_007655005.1_ASM765500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b86e5f7-9e96-4031-bd61-87ef91bd2d6f/dqc_reference/reference_markers_gtdb.fasta -out GCF_007655005.1_ASM765500v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:44:26,324] [INFO] Task succeeded: Blastn
[2024-01-24 13:44:26,328] [INFO] Selected 9 target genomes.
[2024-01-24 13:44:26,328] [INFO] Target genome list was writen to GCF_007655005.1_ASM765500v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:44:26,352] [INFO] Task started: fastANI
[2024-01-24 13:44:26,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg513887f3-1bde-4fa3-b94a-e63edabbe4e6/GCF_007655005.1_ASM765500v1_genomic.fna.gz --refList GCF_007655005.1_ASM765500v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007655005.1_ASM765500v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:47,228] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:47,241] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:47,241] [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_007655005.1	s__Streptomyces tibetensis	100.0	2967	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_001280065.1	s__Streptomyces sp001280065	93.9201	2280	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648995.1	s__Streptomyces massasporeus	92.7684	2386	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.09	95.23	0.86	0.83	4	-
GCF_004803895.1	s__Streptomyces hawaiiensis	92.5169	2290	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.39	95.39	0.84	0.84	3	-
GCF_014202475.1	s__Streptomyces paradoxus	92.4741	2277	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205055.1	s__Streptomyces luteogriseus	92.4121	2297	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.10	95.50	0.87	0.84	3	-
GCA_014204745.1	s__Streptomyces collinus	92.401	2354	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	99.36	99.36	0.94	0.94	2	-
GCF_000717055.1	s__Streptomyces iakyrus	92.2601	2271	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	96.00	95.60	0.85	0.85	3	-
GCF_001611795.1	s__Streptomyces qaidamensis	92.1486	2326	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3368	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:44:47,245] [INFO] GTDB search result was written to GCF_007655005.1_ASM765500v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:47,245] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:47,249] [INFO] DFAST_QC result json was written to GCF_007655005.1_ASM765500v1_genomic.fna/dqc_result.json
[2024-01-24 13:44:47,249] [INFO] DFAST_QC completed!
[2024-01-24 13:44:47,250] [INFO] Total running time: 0h3m27s