[2024-01-24 15:02:37,084] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:37,087] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:37,087] [INFO] DQC Reference Directory: /var/lib/cwl/stg7152e604-2aa8-47ba-bfa5-2272580de4a1/dqc_reference
[2024-01-24 15:02:38,550] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:38,551] [INFO] Task started: Prodigal
[2024-01-24 15:02:38,552] [INFO] Running command: gunzip -c /var/lib/cwl/stg75c736f4-eb7f-4d04-8001-61d2cfe6445f/GCF_017874495.1_ASM1787449v1_genomic.fna.gz | prodigal -d GCF_017874495.1_ASM1787449v1_genomic.fna/cds.fna -a GCF_017874495.1_ASM1787449v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:21,660] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:21,661] [INFO] Task started: HMMsearch
[2024-01-24 15:03:21,661] [INFO] Running command: hmmsearch --tblout GCF_017874495.1_ASM1787449v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7152e604-2aa8-47ba-bfa5-2272580de4a1/dqc_reference/reference_markers.hmm GCF_017874495.1_ASM1787449v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:22,115] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:22,117] [INFO] Found 6/6 markers.
[2024-01-24 15:03:22,199] [INFO] Query marker FASTA was written to GCF_017874495.1_ASM1787449v1_genomic.fna/markers.fasta
[2024-01-24 15:03:22,199] [INFO] Task started: Blastn
[2024-01-24 15:03:22,200] [INFO] Running command: blastn -query GCF_017874495.1_ASM1787449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7152e604-2aa8-47ba-bfa5-2272580de4a1/dqc_reference/reference_markers.fasta -out GCF_017874495.1_ASM1787449v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:23,603] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:23,607] [INFO] Selected 19 target genomes.
[2024-01-24 15:03:23,607] [INFO] Target genome list was writen to GCF_017874495.1_ASM1787449v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:23,614] [INFO] Task started: fastANI
[2024-01-24 15:03:23,615] [INFO] Running command: fastANI --query /var/lib/cwl/stg75c736f4-eb7f-4d04-8001-61d2cfe6445f/GCF_017874495.1_ASM1787449v1_genomic.fna.gz --refList GCF_017874495.1_ASM1787449v1_genomic.fna/target_genomes.txt --output GCF_017874495.1_ASM1787449v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:04:12,917] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:12,918] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7152e604-2aa8-47ba-bfa5-2272580de4a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:04:12,918] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7152e604-2aa8-47ba-bfa5-2272580de4a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:04:12,933] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:04:12,934] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:04:12,934] [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 griseochromogenes	strain=DSM 40499	GCA_017874495.1	68214	68214	type	True	100.0	3509	3513	95	conclusive
Streptomyces griseochromogenes	strain=ATCC 14511	GCA_001542625.2	68214	68214	type	True	99.9985	3512	3513	95	conclusive
Streptomyces cellostaticus	strain=DSM 40189	GCA_001513965.1	67285	67285	type	True	91.9586	2437	3513	95	below_threshold
Streptomyces bungoensis	strain=DSM 41781	GCA_001514215.1	285568	285568	type	True	87.6495	1972	3513	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	87.6168	2158	3513	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	87.5634	2176	3513	95	below_threshold
Streptomyces filipinensis	strain=JCM 4369	GCA_014649495.1	66887	66887	type	True	87.5243	2205	3513	95	below_threshold
Streptomyces broussonetiae	strain=T44	GCA_009796285.1	2686304	2686304	type	True	87.1821	2159	3513	95	below_threshold
Streptomyces echinatus	strain=JCM4574	GCA_020400685.1	67293	67293	type	True	87.1274	2082	3513	95	below_threshold
Streptomyces canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	87.1185	2039	3513	95	below_threshold
Streptomyces echinatus	strain=CECT 3313	GCA_014203595.1	67293	67293	type	True	87.0761	2134	3513	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	86.9664	1955	3513	95	below_threshold
Streptomyces achromogenes subsp. achromogenes	strain=NRRL B-2120	GCA_000720835.1	67256	67255	type	True	86.6364	1805	3513	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	85.4923	1448	3513	95	below_threshold
Streptomyces fumigatiscleroticus	strain=JCM 3101	GCA_014647975.1	66371	66371	type	True	84.7272	1738	3513	95	below_threshold
Streptomyces davaonensis	strain=JCM 4913	GCA_000349325.1	348043	348043	type	True	84.6887	1861	3513	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	84.6241	1839	3513	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.5171	1421	3513	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.461	1670	3513	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:04:12,940] [INFO] DFAST Taxonomy check result was written to GCF_017874495.1_ASM1787449v1_genomic.fna/tc_result.tsv
[2024-01-24 15:04:12,942] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:04:12,942] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:04:12,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7152e604-2aa8-47ba-bfa5-2272580de4a1/dqc_reference/checkm_data
[2024-01-24 15:04:12,945] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:04:13,051] [INFO] Task started: CheckM
[2024-01-24 15:04:13,051] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874495.1_ASM1787449v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874495.1_ASM1787449v1_genomic.fna/checkm_input GCF_017874495.1_ASM1787449v1_genomic.fna/checkm_result
[2024-01-24 15:07:15,849] [INFO] Task succeeded: CheckM
[2024-01-24 15:07:15,850] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 15:07:15,876] [INFO] ===== Completeness check finished =====
[2024-01-24 15:07:15,877] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:07:15,877] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874495.1_ASM1787449v1_genomic.fna/markers.fasta)
[2024-01-24 15:07:15,877] [INFO] Task started: Blastn
[2024-01-24 15:07:15,878] [INFO] Running command: blastn -query GCF_017874495.1_ASM1787449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7152e604-2aa8-47ba-bfa5-2272580de4a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874495.1_ASM1787449v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:07:17,947] [INFO] Task succeeded: Blastn
[2024-01-24 15:07:17,951] [INFO] Selected 13 target genomes.
[2024-01-24 15:07:17,951] [INFO] Target genome list was writen to GCF_017874495.1_ASM1787449v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:07:17,962] [INFO] Task started: fastANI
[2024-01-24 15:07:17,962] [INFO] Running command: fastANI --query /var/lib/cwl/stg75c736f4-eb7f-4d04-8001-61d2cfe6445f/GCF_017874495.1_ASM1787449v1_genomic.fna.gz --refList GCF_017874495.1_ASM1787449v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874495.1_ASM1787449v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:07:51,480] [INFO] Task succeeded: fastANI
[2024-01-24 15:07:51,497] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:07:51,497] [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_001542625.1	s__Streptomyces griseochromogenes	99.9985	3512	3513	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001513965.1	s__Streptomyces cellostaticus	91.9525	2438	3513	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634225.1	s__Streptomyces sp003634225	91.6585	2530	3513	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.82	99.82	0.97	0.97	3	-
GCF_002242805.1	s__Streptomyces diastatochromogenes	90.0352	2323	3513	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.15	97.09	0.86	0.86	5	-
GCF_007827595.1	s__Streptomyces sp007827595	89.5787	2347	3513	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007176755.1	s__Streptomyces sp007176755	87.7195	1886	3513	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	87.6196	2161	3513	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	87.541	2203	3513	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.80	96.80	0.89	0.89	2	-
GCF_001953885.1	s__Streptomyces sp001953885	87.4459	2200	3513	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720135.1	s__Streptomyces sp000720135	87.202	2002	3513	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.69	98.69	0.94	0.94	2	-
GCF_009796285.1	s__Streptomyces broussonetiae	87.1948	2157	3513	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203595.1	s__Streptomyces echinatus	87.0797	2132	3513	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009865385.1	s__Streptomyces sp009865385	86.8183	1763	3513	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 15:07:51,499] [INFO] GTDB search result was written to GCF_017874495.1_ASM1787449v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:07:51,500] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:07:51,503] [INFO] DFAST_QC result json was written to GCF_017874495.1_ASM1787449v1_genomic.fna/dqc_result.json
[2024-01-24 15:07:51,504] [INFO] DFAST_QC completed!
[2024-01-24 15:07:51,504] [INFO] Total running time: 0h5m14s