[2024-01-24 13:27:45,402] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:45,404] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:45,404] [INFO] DQC Reference Directory: /var/lib/cwl/stg2dd9d919-2122-4ed7-9cce-a809b13eaa04/dqc_reference
[2024-01-24 13:27:46,811] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:46,812] [INFO] Task started: Prodigal
[2024-01-24 13:27:46,812] [INFO] Running command: gunzip -c /var/lib/cwl/stg158daec3-a04b-4ae4-ba74-f44836cd68b8/GCF_014651035.1_ASM1465103v1_genomic.fna.gz | prodigal -d GCF_014651035.1_ASM1465103v1_genomic.fna/cds.fna -a GCF_014651035.1_ASM1465103v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:12,589] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:12,589] [INFO] Task started: HMMsearch
[2024-01-24 13:28:12,589] [INFO] Running command: hmmsearch --tblout GCF_014651035.1_ASM1465103v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2dd9d919-2122-4ed7-9cce-a809b13eaa04/dqc_reference/reference_markers.hmm GCF_014651035.1_ASM1465103v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:13,056] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:13,057] [INFO] Found 6/6 markers.
[2024-01-24 13:28:13,128] [INFO] Query marker FASTA was written to GCF_014651035.1_ASM1465103v1_genomic.fna/markers.fasta
[2024-01-24 13:28:13,128] [INFO] Task started: Blastn
[2024-01-24 13:28:13,128] [INFO] Running command: blastn -query GCF_014651035.1_ASM1465103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dd9d919-2122-4ed7-9cce-a809b13eaa04/dqc_reference/reference_markers.fasta -out GCF_014651035.1_ASM1465103v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:14,570] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:14,574] [INFO] Selected 19 target genomes.
[2024-01-24 13:28:14,574] [INFO] Target genome list was writen to GCF_014651035.1_ASM1465103v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:14,587] [INFO] Task started: fastANI
[2024-01-24 13:28:14,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg158daec3-a04b-4ae4-ba74-f44836cd68b8/GCF_014651035.1_ASM1465103v1_genomic.fna.gz --refList GCF_014651035.1_ASM1465103v1_genomic.fna/target_genomes.txt --output GCF_014651035.1_ASM1465103v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:02,837] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:02,838] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2dd9d919-2122-4ed7-9cce-a809b13eaa04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:02,838] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2dd9d919-2122-4ed7-9cce-a809b13eaa04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:02,859] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:29:02,859] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:02,859] [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=JCM 4866	GCA_014651035.1	68229	68229	type	True	100.0	2896	2899	95	conclusive
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	99.9887	2874	2899	95	conclusive
Streptomyces coeruleorubidus	strain=ATCC 13740	GCA_008705135.1	116188	116188	suspected-type	True	91.8512	2303	2899	95	below_threshold
Streptomyces coeruleorubidus	strain=JCM 4359	GCA_014649455.1	116188	116188	suspected-type	True	91.8472	2289	2899	95	below_threshold
Streptomyces azureus	strain=ATCC 14921	GCA_001270025.1	146537	146537	type	True	91.7925	2151	2899	95	below_threshold
Streptomyces caelestis	strain=JCM 4566	GCA_014650295.1	36816	36816	type	True	91.6368	2228	2899	95	below_threshold
Streptomyces caelestis	strain=DSM 40084	GCA_014205255.1	36816	36816	type	True	91.5611	2258	2899	95	below_threshold
Streptomyces africanus	strain=NRRL B-24243	GCA_002150735.1	231024	231024	type	True	91.5347	1911	2899	95	below_threshold
Streptomyces purpurascens	strain=JCM 4509	GCA_014650155.1	1924	1924	type	True	91.402	2257	2899	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	91.39	2239	2899	95	below_threshold
Streptomyces tuirus	strain=JCM 4255	GCA_014701095.1	68278	68278	type	True	90.991	2017	2899	95	below_threshold
Streptomyces massasporeus	strain=JCM 4139	GCA_014648995.1	67324	67324	type	True	90.9843	2241	2899	95	below_threshold
Streptomyces iakyrus	strain=NRRL ISP-5482	GCA_000717055.1	68219	68219	type	True	90.9621	2163	2899	95	below_threshold
Streptomyces violaceochromogenes	strain=JCM 4530	GCA_014650235.1	67377	67377	type	True	90.9259	2225	2899	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	90.6031	1791	2899	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	90.4037	1895	2899	95	below_threshold
Streptomyces calvus	strain=JCM 4326	GCA_014649315.1	67282	67282	type	True	86.4069	1835	2899	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	86.3338	1817	2899	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.8447	1530	2899	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:02,861] [INFO] DFAST Taxonomy check result was written to GCF_014651035.1_ASM1465103v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:02,862] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:02,862] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:02,862] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2dd9d919-2122-4ed7-9cce-a809b13eaa04/dqc_reference/checkm_data
[2024-01-24 13:29:02,863] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:02,947] [INFO] Task started: CheckM
[2024-01-24 13:29:02,948] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651035.1_ASM1465103v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651035.1_ASM1465103v1_genomic.fna/checkm_input GCF_014651035.1_ASM1465103v1_genomic.fna/checkm_result
[2024-01-24 13:30:32,888] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:32,890] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:32,927] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:32,928] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:32,928] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651035.1_ASM1465103v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:32,929] [INFO] Task started: Blastn
[2024-01-24 13:30:32,929] [INFO] Running command: blastn -query GCF_014651035.1_ASM1465103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dd9d919-2122-4ed7-9cce-a809b13eaa04/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651035.1_ASM1465103v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:35,054] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:35,058] [INFO] Selected 16 target genomes.
[2024-01-24 13:30:35,058] [INFO] Target genome list was writen to GCF_014651035.1_ASM1465103v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:35,078] [INFO] Task started: fastANI
[2024-01-24 13:30:35,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg158daec3-a04b-4ae4-ba74-f44836cd68b8/GCF_014651035.1_ASM1465103v1_genomic.fna.gz --refList GCF_014651035.1_ASM1465103v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651035.1_ASM1465103v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:12,692] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:12,712] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:31:12,712] [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	100.0	2896	2899	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	93.5826	2352	2899	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	93.3578	2292	2899	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	91.8514	2303	2899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.68	95.03	0.91	0.83	4	-
GCA_000415505.1	s__Streptomyces afghaniensis	91.7767	2093	2899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900236475.1	s__Streptomyces chartreusis_D	91.7677	2284	2899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	4	-
GCF_014205255.1	s__Streptomyces caelestis	91.5659	2257	2899	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	91.5526	1909	2899	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	91.3402	2192	2899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202475.1	s__Streptomyces paradoxus	91.08	2193	2899	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	91.0178	2106	2899	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	90.976	2242	2899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.09	95.23	0.86	0.83	4	-
GCA_014204745.1	s__Streptomyces collinus	90.9673	2220	2899	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	90.95	2218	2899	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	90.7286	2151	2899	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	90.3095	2064	2899	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 13:31:12,714] [INFO] GTDB search result was written to GCF_014651035.1_ASM1465103v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:12,714] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:12,718] [INFO] DFAST_QC result json was written to GCF_014651035.1_ASM1465103v1_genomic.fna/dqc_result.json
[2024-01-24 13:31:12,718] [INFO] DFAST_QC completed!
[2024-01-24 13:31:12,718] [INFO] Total running time: 0h3m27s