[2024-01-24 13:58:41,232] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:41,234] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:41,234] [INFO] DQC Reference Directory: /var/lib/cwl/stg0dc85687-2636-469c-ac4c-7b06e23b004c/dqc_reference
[2024-01-24 13:58:42,534] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:42,535] [INFO] Task started: Prodigal
[2024-01-24 13:58:42,535] [INFO] Running command: gunzip -c /var/lib/cwl/stg81e08538-ece4-4842-bb44-8d2e385adf78/GCF_014654675.1_ASM1465467v1_genomic.fna.gz | prodigal -d GCF_014654675.1_ASM1465467v1_genomic.fna/cds.fna -a GCF_014654675.1_ASM1465467v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:59:11,405] [INFO] Task succeeded: Prodigal
[2024-01-24 13:59:11,405] [INFO] Task started: HMMsearch
[2024-01-24 13:59:11,406] [INFO] Running command: hmmsearch --tblout GCF_014654675.1_ASM1465467v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0dc85687-2636-469c-ac4c-7b06e23b004c/dqc_reference/reference_markers.hmm GCF_014654675.1_ASM1465467v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:59:11,789] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:59:11,791] [INFO] Found 6/6 markers.
[2024-01-24 13:59:11,871] [INFO] Query marker FASTA was written to GCF_014654675.1_ASM1465467v1_genomic.fna/markers.fasta
[2024-01-24 13:59:11,872] [INFO] Task started: Blastn
[2024-01-24 13:59:11,872] [INFO] Running command: blastn -query GCF_014654675.1_ASM1465467v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dc85687-2636-469c-ac4c-7b06e23b004c/dqc_reference/reference_markers.fasta -out GCF_014654675.1_ASM1465467v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:13,216] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:13,221] [INFO] Selected 20 target genomes.
[2024-01-24 13:59:13,222] [INFO] Target genome list was writen to GCF_014654675.1_ASM1465467v1_genomic.fna/target_genomes.txt
[2024-01-24 13:59:13,234] [INFO] Task started: fastANI
[2024-01-24 13:59:13,234] [INFO] Running command: fastANI --query /var/lib/cwl/stg81e08538-ece4-4842-bb44-8d2e385adf78/GCF_014654675.1_ASM1465467v1_genomic.fna.gz --refList GCF_014654675.1_ASM1465467v1_genomic.fna/target_genomes.txt --output GCF_014654675.1_ASM1465467v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:49,375] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:49,376] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0dc85687-2636-469c-ac4c-7b06e23b004c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:49,376] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0dc85687-2636-469c-ac4c-7b06e23b004c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:49,394] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:49,394] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:49,394] [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 spiralis	strain=JCM 3302	GCA_014654675.1	66376	66376	type	True	100.0	3187	3194	95	conclusive
Streptomyces carpinensis	strain=NRRL B-16921	GCA_002154505.1	66369	66369	type	True	91.0395	2087	3194	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	87.7866	1693	3194	95	below_threshold
Streptomyces anandii	strain=JCM 4720	GCA_014650655.1	285454	285454	type	True	87.7732	1834	3194	95	below_threshold
Streptomyces naganishii	strain=JCM 4654	GCA_014650575.1	285447	285447	type	True	87.7011	1843	3194	95	below_threshold
Streptomyces triticisoli	strain=NEAU-DSCPA1-4-4	GCA_003270085.1	2182797	2182797	type	True	87.587	1519	3194	95	below_threshold
Streptomyces kebangsaanensis	strain=SUK12	GCA_001906585.1	864058	864058	type	True	87.5528	1706	3194	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	86.2523	1596	3194	95	below_threshold
Streptomyces bungoensis	strain=DSM 41781	GCA_001514215.1	285568	285568	type	True	85.5533	1777	3194	95	below_threshold
Streptomyces puniciscabiei	strain=DSM 41929	GCA_006715785.1	164348	164348	type	True	85.5209	1871	3194	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	85.4437	1832	3194	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.0489	1427	3194	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.0379	1752	3194	95	below_threshold
Streptomyces eurythermus	strain=JCM 4206	GCA_014649115.1	42237	42237	type	True	84.9418	1754	3194	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.4295	1568	3194	95	below_threshold
Parenemella sanctibonifatiensis	strain=NML 150081	GCA_002250565.1	2016505	2016505	type	True	76.223	215	3194	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	76.204	489	3194	95	below_threshold
Glycomyces paridis	strain=CPCC 204357	GCA_004912155.1	2126555	2126555	type	True	76.151	521	3194	95	below_threshold
Actinopolyspora righensis	strain=DSM 45501	GCA_900116555.1	995060	995060	type	True	75.9825	267	3194	95	below_threshold
Rhodoblastus sphagnicola	strain=DSM 16996	GCA_002937075.1	333368	333368	type	True	74.7296	110	3194	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:49,396] [INFO] DFAST Taxonomy check result was written to GCF_014654675.1_ASM1465467v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:49,396] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:49,397] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:49,397] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0dc85687-2636-469c-ac4c-7b06e23b004c/dqc_reference/checkm_data
[2024-01-24 13:59:49,398] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:49,495] [INFO] Task started: CheckM
[2024-01-24 13:59:49,495] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014654675.1_ASM1465467v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014654675.1_ASM1465467v1_genomic.fna/checkm_input GCF_014654675.1_ASM1465467v1_genomic.fna/checkm_result
[2024-01-24 14:02:02,837] [INFO] Task succeeded: CheckM
[2024-01-24 14:02:02,839] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:02:02,862] [INFO] ===== Completeness check finished =====
[2024-01-24 14:02:02,863] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:02:02,863] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014654675.1_ASM1465467v1_genomic.fna/markers.fasta)
[2024-01-24 14:02:02,863] [INFO] Task started: Blastn
[2024-01-24 14:02:02,864] [INFO] Running command: blastn -query GCF_014654675.1_ASM1465467v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dc85687-2636-469c-ac4c-7b06e23b004c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014654675.1_ASM1465467v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:02:04,992] [INFO] Task succeeded: Blastn
[2024-01-24 14:02:04,997] [INFO] Selected 16 target genomes.
[2024-01-24 14:02:04,997] [INFO] Target genome list was writen to GCF_014654675.1_ASM1465467v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:02:05,062] [INFO] Task started: fastANI
[2024-01-24 14:02:05,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg81e08538-ece4-4842-bb44-8d2e385adf78/GCF_014654675.1_ASM1465467v1_genomic.fna.gz --refList GCF_014654675.1_ASM1465467v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014654675.1_ASM1465467v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:02:41,339] [INFO] Task succeeded: fastANI
[2024-01-24 14:02:41,364] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:02:41,365] [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_014654675.1	s__Streptomyces spiralis	100.0	3187	3194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.07	98.07	0.87	0.87	2	conclusive
GCF_002154505.1	s__Streptomyces carpinensis	91.0587	2083	3194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506575.1	s__Streptomyces mexicanus	88.086	1876	3194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.95	96.19	0.87	0.78	3	-
GCF_014650655.1	s__Streptomyces anandii	87.773	1834	3194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650575.1	s__Streptomyces naganishii	87.6886	1845	3194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383935.1	s__Streptomyces sp000383935	87.5924	1829	3194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.62	97.70	0.92	0.84	4	-
GCF_001906585.1	s__Streptomyces kebangsaanensis	87.5359	1709	3194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364255.1	s__Streptomyces seoulensis_A	87.3403	1832	3194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514215.1	s__Streptomyces bungoensis	85.5795	1773	3194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715785.1	s__Streptomyces puniciscabiei	85.5042	1874	3194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.70	95.42	0.91	0.82	3	-
GCF_009604455.1	s__Streptomyces sp009604455	85.4815	1966	3194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905845.1	s__Streptomyces sp001905845	85.0707	1742	3194	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	84.9025	1754	3194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003671715.1	s__Streptomyces sp003671715	84.894	1692	3194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.92	95.92	0.81	0.81	2	-
GCF_000761215.1	s__Streptomyces glaucescens	84.7971	1645	3194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143855.1	s__Streptomyces sp003143855	84.1221	1623	3194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:02:41,370] [INFO] GTDB search result was written to GCF_014654675.1_ASM1465467v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:02:41,370] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:02:41,376] [INFO] DFAST_QC result json was written to GCF_014654675.1_ASM1465467v1_genomic.fna/dqc_result.json
[2024-01-24 14:02:41,376] [INFO] DFAST_QC completed!
[2024-01-24 14:02:41,376] [INFO] Total running time: 0h4m0s