[2024-01-24 11:26:12,906] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:12,908] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:12,908] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e952704-66f6-4832-b196-4c88365ee930/dqc_reference
[2024-01-24 11:26:14,240] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:14,241] [INFO] Task started: Prodigal
[2024-01-24 11:26:14,241] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbb624a2-8b25-42f9-a1c6-a59f3adf268b/GCF_014650595.1_ASM1465059v1_genomic.fna.gz | prodigal -d GCF_014650595.1_ASM1465059v1_genomic.fna/cds.fna -a GCF_014650595.1_ASM1465059v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:43,860] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:43,860] [INFO] Task started: HMMsearch
[2024-01-24 11:26:43,861] [INFO] Running command: hmmsearch --tblout GCF_014650595.1_ASM1465059v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e952704-66f6-4832-b196-4c88365ee930/dqc_reference/reference_markers.hmm GCF_014650595.1_ASM1465059v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:44,291] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:44,292] [INFO] Found 6/6 markers.
[2024-01-24 11:26:44,387] [INFO] Query marker FASTA was written to GCF_014650595.1_ASM1465059v1_genomic.fna/markers.fasta
[2024-01-24 11:26:44,388] [INFO] Task started: Blastn
[2024-01-24 11:26:44,388] [INFO] Running command: blastn -query GCF_014650595.1_ASM1465059v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e952704-66f6-4832-b196-4c88365ee930/dqc_reference/reference_markers.fasta -out GCF_014650595.1_ASM1465059v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:46,014] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:46,018] [INFO] Selected 18 target genomes.
[2024-01-24 11:26:46,019] [INFO] Target genome list was writen to GCF_014650595.1_ASM1465059v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:46,032] [INFO] Task started: fastANI
[2024-01-24 11:26:46,032] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbb624a2-8b25-42f9-a1c6-a59f3adf268b/GCF_014650595.1_ASM1465059v1_genomic.fna.gz --refList GCF_014650595.1_ASM1465059v1_genomic.fna/target_genomes.txt --output GCF_014650595.1_ASM1465059v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:30,045] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:30,045] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e952704-66f6-4832-b196-4c88365ee930/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:30,046] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e952704-66f6-4832-b196-4c88365ee930/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:30,064] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:30,064] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:30,064] [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 alanosinicus	strain=JCM 4714	GCA_014650595.1	68171	68171	type	True	100.0	3330	3337	95	conclusive
Streptomyces yokosukanensis	strain=DSM 40224	GCA_001514035.1	67386	67386	type	True	91.0429	2300	3337	95	below_threshold
Streptomyces fodineus	strain=TW1S1	GCA_001735805.1	1904616	1904616	type	True	89.7675	2185	3337	95	below_threshold
Streptomyces puniciscabiei	strain=DSM 41929	GCA_006715785.1	164348	164348	type	True	89.4537	2157	3337	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	89.4333	2149	3337	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	89.4034	2146	3337	95	below_threshold
Streptomyces filipinensis	strain=JCM 4369	GCA_014649495.1	66887	66887	type	True	89.2962	2149	3337	95	below_threshold
Streptomyces broussonetiae	strain=T44	GCA_009796285.1	2686304	2686304	type	True	88.572	2158	3337	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	88.2557	2218	3337	95	below_threshold
Streptomyces cellostaticus	strain=DSM 40189	GCA_001513965.1	67285	67285	type	True	87.4736	2149	3337	95	below_threshold
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	87.473	1938	3337	95	below_threshold
Streptomyces musisoli	strain=CH5-8	GCA_016741855.1	2802280	2802280	type	True	87.4019	1973	3337	95	below_threshold
Streptomyces canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	87.2645	1999	3337	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	87.2585	1873	3337	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	84.989	1429	3337	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	84.8905	1891	3337	95	below_threshold
Streptomyces cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	84.2637	1865	3337	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.0342	1612	3337	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:30,066] [INFO] DFAST Taxonomy check result was written to GCF_014650595.1_ASM1465059v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:30,067] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:30,067] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:30,067] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e952704-66f6-4832-b196-4c88365ee930/dqc_reference/checkm_data
[2024-01-24 11:27:30,068] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:30,160] [INFO] Task started: CheckM
[2024-01-24 11:27:30,160] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650595.1_ASM1465059v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650595.1_ASM1465059v1_genomic.fna/checkm_input GCF_014650595.1_ASM1465059v1_genomic.fna/checkm_result
[2024-01-24 11:29:52,661] [INFO] Task succeeded: CheckM
[2024-01-24 11:29:52,663] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 11:29:52,692] [INFO] ===== Completeness check finished =====
[2024-01-24 11:29:52,693] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:29:52,693] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650595.1_ASM1465059v1_genomic.fna/markers.fasta)
[2024-01-24 11:29:52,694] [INFO] Task started: Blastn
[2024-01-24 11:29:52,694] [INFO] Running command: blastn -query GCF_014650595.1_ASM1465059v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e952704-66f6-4832-b196-4c88365ee930/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650595.1_ASM1465059v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:29:54,795] [INFO] Task succeeded: Blastn
[2024-01-24 11:29:54,798] [INFO] Selected 14 target genomes.
[2024-01-24 11:29:54,798] [INFO] Target genome list was writen to GCF_014650595.1_ASM1465059v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:29:54,807] [INFO] Task started: fastANI
[2024-01-24 11:29:54,808] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbb624a2-8b25-42f9-a1c6-a59f3adf268b/GCF_014650595.1_ASM1465059v1_genomic.fna.gz --refList GCF_014650595.1_ASM1465059v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650595.1_ASM1465059v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:30:29,742] [INFO] Task succeeded: fastANI
[2024-01-24 11:30:29,760] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:30:29,760] [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_014650595.1	s__Streptomyces alanosinicus	100.0	3330	3337	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_001514035.1	s__Streptomyces yokosukanensis	91.0206	2303	3337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953885.1	s__Streptomyces sp001953885	90.8068	2310	3337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000497445.1	s__Streptomyces roseochromogenus	90.6579	2284	3337	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	89.764	2186	3337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009604455.1	s__Streptomyces sp009604455	89.4175	2143	3337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649495.1	s__Streptomyces filipinensis	89.3046	2149	3337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.80	96.80	0.89	0.89	2	-
GCF_001636945.1	s__Streptomyces sp001636945	88.8439	2073	3337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280015.1	s__Streptomyces sp001280015	88.8063	2162	3337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796285.1	s__Streptomyces broussonetiae	88.5696	2159	3337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513965.1	s__Streptomyces cellostaticus	87.517	2142	3337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105245.1	s__Streptomyces sp900105245	87.4652	1951	3337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.80	95.98	0.93	0.89	5	-
GCF_016741775.1	s__Streptomyces actinomycinicus	87.4114	1942	3337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827595.1	s__Streptomyces sp007827595	86.9397	2068	3337	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 11:30:29,762] [INFO] GTDB search result was written to GCF_014650595.1_ASM1465059v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:30:29,762] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:30:29,766] [INFO] DFAST_QC result json was written to GCF_014650595.1_ASM1465059v1_genomic.fna/dqc_result.json
[2024-01-24 11:30:29,766] [INFO] DFAST_QC completed!
[2024-01-24 11:30:29,766] [INFO] Total running time: 0h4m17s