[2024-01-24 13:55:25,495] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:25,497] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:25,497] [INFO] DQC Reference Directory: /var/lib/cwl/stga1b92678-e354-4c4d-9887-781d512142ee/dqc_reference
[2024-01-24 13:55:26,751] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:26,752] [INFO] Task started: Prodigal
[2024-01-24 13:55:26,752] [INFO] Running command: gunzip -c /var/lib/cwl/stg28f5e468-c61b-4f7c-bbbb-a8ddf4e56e5a/GCF_014650315.1_ASM1465031v1_genomic.fna.gz | prodigal -d GCF_014650315.1_ASM1465031v1_genomic.fna/cds.fna -a GCF_014650315.1_ASM1465031v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:59,279] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:59,280] [INFO] Task started: HMMsearch
[2024-01-24 13:55:59,280] [INFO] Running command: hmmsearch --tblout GCF_014650315.1_ASM1465031v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1b92678-e354-4c4d-9887-781d512142ee/dqc_reference/reference_markers.hmm GCF_014650315.1_ASM1465031v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:59,678] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:59,680] [INFO] Found 6/6 markers.
[2024-01-24 13:55:59,762] [INFO] Query marker FASTA was written to GCF_014650315.1_ASM1465031v1_genomic.fna/markers.fasta
[2024-01-24 13:55:59,762] [INFO] Task started: Blastn
[2024-01-24 13:55:59,762] [INFO] Running command: blastn -query GCF_014650315.1_ASM1465031v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1b92678-e354-4c4d-9887-781d512142ee/dqc_reference/reference_markers.fasta -out GCF_014650315.1_ASM1465031v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:01,061] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:01,066] [INFO] Selected 17 target genomes.
[2024-01-24 13:56:01,066] [INFO] Target genome list was writen to GCF_014650315.1_ASM1465031v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:01,138] [INFO] Task started: fastANI
[2024-01-24 13:56:01,138] [INFO] Running command: fastANI --query /var/lib/cwl/stg28f5e468-c61b-4f7c-bbbb-a8ddf4e56e5a/GCF_014650315.1_ASM1465031v1_genomic.fna.gz --refList GCF_014650315.1_ASM1465031v1_genomic.fna/target_genomes.txt --output GCF_014650315.1_ASM1465031v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:45,267] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:45,268] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1b92678-e354-4c4d-9887-781d512142ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:45,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1b92678-e354-4c4d-9887-781d512142ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:45,286] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:56:45,286] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:45,287] [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 chartreusis	strain=JCM 4570	GCA_014650315.1	1969	1969	suspected-type	True	100.0	3341	3341	95	conclusive
Streptomyces chartreusis	strain=ATCC 14922	GCA_008704715.1	1969	1969	suspected-type	True	99.9983	3276	3341	95	conclusive
Streptomyces lanatus	strain=JCM 4588	GCA_014655715.1	66900	66900	type	True	90.3781	2508	3341	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	90.0122	2368	3341	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	89.2846	2467	3341	95	below_threshold
Streptomyces cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	89.215	2390	3341	95	below_threshold
Streptomyces curacoi	strain=DSM 40107	GCA_001513975.1	146536	146536	type	True	89.203	2160	3341	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	89.1993	2330	3341	95	below_threshold
Streptomyces zinciresistens	strain=K42	GCA_000225525.2	1073330	1073330	type	True	87.3276	1759	3341	95	below_threshold
Streptomyces davaonensis	strain=JCM 4913	GCA_000349325.1	348043	348043	type	True	86.1563	2090	3341	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	86.0989	2191	3341	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	85.8277	2086	3341	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.7985	1813	3341	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	85.6236	1977	3341	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	85.6065	1982	3341	95	below_threshold
Streptomyces hyaluromycini	strain=NBRC 110483	GCA_002217755.1	1377993	1377993	type	True	84.7206	2083	3341	95	below_threshold
Streptomyces fodineus	strain=TW1S1	GCA_001735805.1	1904616	1904616	type	True	84.3298	1937	3341	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:45,288] [INFO] DFAST Taxonomy check result was written to GCF_014650315.1_ASM1465031v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:45,289] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:45,289] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:45,289] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1b92678-e354-4c4d-9887-781d512142ee/dqc_reference/checkm_data
[2024-01-24 13:56:45,290] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:45,380] [INFO] Task started: CheckM
[2024-01-24 13:56:45,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650315.1_ASM1465031v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650315.1_ASM1465031v1_genomic.fna/checkm_input GCF_014650315.1_ASM1465031v1_genomic.fna/checkm_result
[2024-01-24 13:58:41,907] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:41,909] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:41,942] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:41,942] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:41,942] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650315.1_ASM1465031v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:41,943] [INFO] Task started: Blastn
[2024-01-24 13:58:41,943] [INFO] Running command: blastn -query GCF_014650315.1_ASM1465031v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1b92678-e354-4c4d-9887-781d512142ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650315.1_ASM1465031v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:44,248] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:44,251] [INFO] Selected 15 target genomes.
[2024-01-24 13:58:44,251] [INFO] Target genome list was writen to GCF_014650315.1_ASM1465031v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:44,428] [INFO] Task started: fastANI
[2024-01-24 13:58:44,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg28f5e468-c61b-4f7c-bbbb-a8ddf4e56e5a/GCF_014650315.1_ASM1465031v1_genomic.fna.gz --refList GCF_014650315.1_ASM1465031v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650315.1_ASM1465031v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:23,098] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:23,111] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:23,112] [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_008704715.1	s__Streptomyces chartreusis	99.9983	3276	3341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.83	96.55	0.93	0.86	10	conclusive
GCF_008042075.1	s__Streptomyces sp008042075	91.7995	2651	3341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014655715.1	s__Streptomyces lanatus	90.3989	2505	3341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015160855.1	s__Streptomyces ferrugineus	90.0166	2368	3341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103585.1	s__Streptomyces sp900103585	89.3232	2460	3341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003963535.1	s__Streptomyces cyaneochromogenes	89.2798	2468	3341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514235.1	s__Streptomyces caeruleatus	89.2148	2328	3341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004028635.1	s__Streptomyces cyaneus	89.213	2390	3341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513975.1	s__Streptomyces curacoi	89.1841	2162	3341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.35	97.22	0.89	0.84	4	-
GCA_013362785.1	s__Streptomyces sp013362785	89.1656	1778	3341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049285.1	s__Streptomyces sp019049285	88.9987	2251	3341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000225525.1	s__Streptomyces zinciresistens	87.3185	1759	3341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000349325.1	s__Streptomyces davaonensis	86.168	2088	3341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000411315.1	s__Streptomyces sp000411315	85.7772	2087	3341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001735805.1	s__Streptomyces fodineus	84.3733	1928	3341	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 13:59:23,114] [INFO] GTDB search result was written to GCF_014650315.1_ASM1465031v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:23,115] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:23,121] [INFO] DFAST_QC result json was written to GCF_014650315.1_ASM1465031v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:23,121] [INFO] DFAST_QC completed!
[2024-01-24 13:59:23,121] [INFO] Total running time: 0h3m58s