[2024-01-24 11:44:22,863] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:22,874] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:22,875] [INFO] DQC Reference Directory: /var/lib/cwl/stgd14f763f-598d-41ec-ac36-ae47ba567cba/dqc_reference
[2024-01-24 11:44:26,339] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,340] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,341] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9ddde90-dcc4-4a06-b442-60f98eca778a/GCF_021440105.1_ASM2144010v1_genomic.fna.gz | prodigal -d GCF_021440105.1_ASM2144010v1_genomic.fna/cds.fna -a GCF_021440105.1_ASM2144010v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:51,201] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:51,202] [INFO] Task started: HMMsearch
[2024-01-24 11:44:51,202] [INFO] Running command: hmmsearch --tblout GCF_021440105.1_ASM2144010v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd14f763f-598d-41ec-ac36-ae47ba567cba/dqc_reference/reference_markers.hmm GCF_021440105.1_ASM2144010v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:51,569] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:51,571] [INFO] Found 6/6 markers.
[2024-01-24 11:44:51,639] [INFO] Query marker FASTA was written to GCF_021440105.1_ASM2144010v1_genomic.fna/markers.fasta
[2024-01-24 11:44:51,640] [INFO] Task started: Blastn
[2024-01-24 11:44:51,640] [INFO] Running command: blastn -query GCF_021440105.1_ASM2144010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd14f763f-598d-41ec-ac36-ae47ba567cba/dqc_reference/reference_markers.fasta -out GCF_021440105.1_ASM2144010v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:52,967] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:52,972] [INFO] Selected 19 target genomes.
[2024-01-24 11:44:52,973] [INFO] Target genome list was writen to GCF_021440105.1_ASM2144010v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:53,000] [INFO] Task started: fastANI
[2024-01-24 11:44:53,001] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9ddde90-dcc4-4a06-b442-60f98eca778a/GCF_021440105.1_ASM2144010v1_genomic.fna.gz --refList GCF_021440105.1_ASM2144010v1_genomic.fna/target_genomes.txt --output GCF_021440105.1_ASM2144010v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:35,807] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:35,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd14f763f-598d-41ec-ac36-ae47ba567cba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:35,808] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd14f763f-598d-41ec-ac36-ae47ba567cba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:35,826] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:45:35,826] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:45:35,827] [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 lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	100.0	2893	2894	95	conclusive
Streptomyces lomondensis	strain=JCM 4866	GCA_014651035.1	68229	68229	type	True	99.9959	2880	2894	95	conclusive
Streptomyces coeruleorubidus	strain=JCM 4359	GCA_014649455.1	116188	116188	suspected-type	True	91.8248	2282	2894	95	below_threshold
Streptomyces coeruleorubidus	strain=ATCC 13740	GCA_008705135.1	116188	116188	suspected-type	True	91.7768	2312	2894	95	below_threshold
Streptomyces azureus	strain=ATCC 14921	GCA_001270025.1	146537	146537	type	True	91.7327	2150	2894	95	below_threshold
Streptomyces caelestis	strain=JCM 4566	GCA_014650295.1	36816	36816	type	True	91.6316	2235	2894	95	below_threshold
Streptomyces caelestis	strain=DSM 40084	GCA_014205255.1	36816	36816	type	True	91.5819	2264	2894	95	below_threshold
Streptomyces africanus	strain=NRRL B-24243	GCA_002150735.1	231024	231024	type	True	91.554	1915	2894	95	below_threshold
Streptomyces purpurascens	strain=JCM 4509	GCA_014650155.1	1924	1924	type	True	91.4675	2277	2894	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	91.4111	2257	2894	95	below_threshold
Streptomyces massasporeus	strain=JCM 4139	GCA_014648995.1	67324	67324	type	True	91.0564	2238	2894	95	below_threshold
Streptomyces violaceochromogenes	strain=JCM 4530	GCA_014650235.1	67377	67377	type	True	91.0008	2200	2894	95	below_threshold
Streptomyces iakyrus	strain=NRRL ISP-5482	GCA_000717055.1	68219	68219	type	True	90.973	2150	2894	95	below_threshold
Streptomyces tuirus	strain=JCM 4255	GCA_014701095.1	68278	68278	type	True	90.911	2020	2894	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	90.6954	1787	2894	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	90.4035	1887	2894	95	below_threshold
Streptomyces calvus	strain=JCM 4326	GCA_014649315.1	67282	67282	type	True	86.4167	1819	2894	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	86.3744	1815	2894	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.9011	1524	2894	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:35,829] [INFO] DFAST Taxonomy check result was written to GCF_021440105.1_ASM2144010v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:35,830] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:35,830] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:35,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd14f763f-598d-41ec-ac36-ae47ba567cba/dqc_reference/checkm_data
[2024-01-24 11:45:35,831] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:35,913] [INFO] Task started: CheckM
[2024-01-24 11:45:35,913] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021440105.1_ASM2144010v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021440105.1_ASM2144010v1_genomic.fna/checkm_input GCF_021440105.1_ASM2144010v1_genomic.fna/checkm_result
[2024-01-24 11:47:35,668] [INFO] Task succeeded: CheckM
[2024-01-24 11:47:35,669] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:47:35,699] [INFO] ===== Completeness check finished =====
[2024-01-24 11:47:35,700] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:47:35,701] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021440105.1_ASM2144010v1_genomic.fna/markers.fasta)
[2024-01-24 11:47:35,702] [INFO] Task started: Blastn
[2024-01-24 11:47:35,702] [INFO] Running command: blastn -query GCF_021440105.1_ASM2144010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd14f763f-598d-41ec-ac36-ae47ba567cba/dqc_reference/reference_markers_gtdb.fasta -out GCF_021440105.1_ASM2144010v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:47:37,795] [INFO] Task succeeded: Blastn
[2024-01-24 11:47:37,800] [INFO] Selected 16 target genomes.
[2024-01-24 11:47:37,800] [INFO] Target genome list was writen to GCF_021440105.1_ASM2144010v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:47:37,814] [INFO] Task started: fastANI
[2024-01-24 11:47:37,814] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9ddde90-dcc4-4a06-b442-60f98eca778a/GCF_021440105.1_ASM2144010v1_genomic.fna.gz --refList GCF_021440105.1_ASM2144010v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021440105.1_ASM2144010v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:48:15,112] [INFO] Task succeeded: fastANI
[2024-01-24 11:48:15,139] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:48:15,140] [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_014651035.1	s__Streptomyces lomondensis	99.9959	2880	2894	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_003330845.1	s__Streptomyces sp003330845	93.556	2348	2894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000696115.1	s__Streptomyces olindensis	93.3412	2294	2894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008705135.1	s__Streptomyces coeruleorubidus	91.7771	2312	2894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.68	95.03	0.91	0.83	4	-
GCF_900236475.1	s__Streptomyces chartreusis_D	91.7719	2297	2894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	4	-
GCA_000415505.1	s__Streptomyces afghaniensis	91.721	2095	2894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205255.1	s__Streptomyces caelestis	91.6038	2261	2894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002150735.1	s__Streptomyces africanus	91.5578	1913	2894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018195615.1	s__Streptomyces tuirus_A	91.3518	2183	2894	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	91.0713	2236	2894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.09	95.23	0.86	0.83	4	-
GCF_014202475.1	s__Streptomyces paradoxus	91.0359	2193	2894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237655.1	s__Streptomyces sp002237655	90.9842	2095	2894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014204745.1	s__Streptomyces collinus	90.9826	2224	2894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	99.36	99.36	0.94	0.94	2	-
GCF_001611795.1	s__Streptomyces qaidamensis	90.9289	2222	2894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3368	N/A	N/A	N/A	N/A	1	-
GCF_000158955.1	s__Streptomyces viridochromogenes_B	90.7559	2125	2894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280065.1	s__Streptomyces sp001280065	90.2976	2064	2894	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 11:48:15,141] [INFO] GTDB search result was written to GCF_021440105.1_ASM2144010v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:48:15,142] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:48:15,146] [INFO] DFAST_QC result json was written to GCF_021440105.1_ASM2144010v1_genomic.fna/dqc_result.json
[2024-01-24 11:48:15,147] [INFO] DFAST_QC completed!
[2024-01-24 11:48:15,147] [INFO] Total running time: 0h3m52s