[2024-01-25 20:19:06,230] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:19:06,234] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:19:06,234] [INFO] DQC Reference Directory: /var/lib/cwl/stg088bf9a1-f270-4e8d-bb22-4bb1712c1469/dqc_reference
[2024-01-25 20:19:07,377] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:19:07,378] [INFO] Task started: Prodigal
[2024-01-25 20:19:07,378] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f2479d6-4a0d-4447-829f-f9f87a69deaf/GCF_017876255.1_ASM1787625v1_genomic.fna.gz | prodigal -d GCF_017876255.1_ASM1787625v1_genomic.fna/cds.fna -a GCF_017876255.1_ASM1787625v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:19:27,777] [INFO] Task succeeded: Prodigal
[2024-01-25 20:19:27,777] [INFO] Task started: HMMsearch
[2024-01-25 20:19:27,777] [INFO] Running command: hmmsearch --tblout GCF_017876255.1_ASM1787625v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg088bf9a1-f270-4e8d-bb22-4bb1712c1469/dqc_reference/reference_markers.hmm GCF_017876255.1_ASM1787625v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:19:28,076] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:19:28,077] [INFO] Found 6/6 markers.
[2024-01-25 20:19:28,134] [INFO] Query marker FASTA was written to GCF_017876255.1_ASM1787625v1_genomic.fna/markers.fasta
[2024-01-25 20:19:28,135] [INFO] Task started: Blastn
[2024-01-25 20:19:28,135] [INFO] Running command: blastn -query GCF_017876255.1_ASM1787625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg088bf9a1-f270-4e8d-bb22-4bb1712c1469/dqc_reference/reference_markers.fasta -out GCF_017876255.1_ASM1787625v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:29,352] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:29,356] [INFO] Selected 16 target genomes.
[2024-01-25 20:19:29,356] [INFO] Target genome list was writen to GCF_017876255.1_ASM1787625v1_genomic.fna/target_genomes.txt
[2024-01-25 20:19:29,370] [INFO] Task started: fastANI
[2024-01-25 20:19:29,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f2479d6-4a0d-4447-829f-f9f87a69deaf/GCF_017876255.1_ASM1787625v1_genomic.fna.gz --refList GCF_017876255.1_ASM1787625v1_genomic.fna/target_genomes.txt --output GCF_017876255.1_ASM1787625v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:20:00,145] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:00,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg088bf9a1-f270-4e8d-bb22-4bb1712c1469/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:20:00,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg088bf9a1-f270-4e8d-bb22-4bb1712c1469/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:20:00,155] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:20:00,156] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:20:00,156] [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 clavifer	strain=DSM 40843	GCA_017876255.1	68188	68188	type	True	100.0	2563	2566	95	conclusive
Streptomyces clavifer	strain=JCM 5059	GCA_014651175.1	68188	68188	type	True	99.9858	2539	2566	95	conclusive
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	87.3497	1854	2566	95	below_threshold
Streptomyces griseolus	strain=NRRL B-2925	GCA_000721185.1	1909	1909	type	True	86.7049	1648	2566	95	below_threshold
Streptomyces nitrosporeus	strain=ATCC 12769	GCA_008704555.1	28894	28894	type	True	86.0713	1697	2566	95	below_threshold
Streptomyces nitrosporeus	strain=JCM 4598	GCA_014650375.1	28894	28894	type	True	85.9972	1683	2566	95	below_threshold
Streptomyces fulvorobeus	strain=DSM 41455	GCA_013409565.1	284028	284028	type	True	85.7233	1479	2566	95	below_threshold
Streptomyces fulvorobeus	strain=NBRC 15897	GCA_013167895.1	284028	284028	type	True	85.6828	1487	2566	95	below_threshold
Streptomyces microflavus	strain=JCM 4496	GCA_014650075.1	1919	1919	type	True	85.1798	1670	2566	95	below_threshold
Streptomyces brevispora	strain=DSM 42059	GCA_007829885.1	887462	887462	type	True	85.1434	1595	2566	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	85.0846	1684	2566	95	below_threshold
Streptomyces poriferorum	strain=P01-B04	GCA_019399235.1	2798799	2798799	type	True	84.967	1510	2566	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	84.8841	1345	2566	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	81.6707	1281	2566	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	81.5114	1372	2566	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	80.8439	1210	2566	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:20:00,157] [INFO] DFAST Taxonomy check result was written to GCF_017876255.1_ASM1787625v1_genomic.fna/tc_result.tsv
[2024-01-25 20:20:00,157] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:20:00,158] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:20:00,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg088bf9a1-f270-4e8d-bb22-4bb1712c1469/dqc_reference/checkm_data
[2024-01-25 20:20:00,159] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:20:00,229] [INFO] Task started: CheckM
[2024-01-25 20:20:00,229] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017876255.1_ASM1787625v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017876255.1_ASM1787625v1_genomic.fna/checkm_input GCF_017876255.1_ASM1787625v1_genomic.fna/checkm_result
[2024-01-25 20:22:14,379] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:14,380] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:14,402] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:14,402] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:14,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017876255.1_ASM1787625v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:14,403] [INFO] Task started: Blastn
[2024-01-25 20:22:14,403] [INFO] Running command: blastn -query GCF_017876255.1_ASM1787625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg088bf9a1-f270-4e8d-bb22-4bb1712c1469/dqc_reference/reference_markers_gtdb.fasta -out GCF_017876255.1_ASM1787625v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:16,428] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:16,431] [INFO] Selected 16 target genomes.
[2024-01-25 20:22:16,431] [INFO] Target genome list was writen to GCF_017876255.1_ASM1787625v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:16,442] [INFO] Task started: fastANI
[2024-01-25 20:22:16,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f2479d6-4a0d-4447-829f-f9f87a69deaf/GCF_017876255.1_ASM1787625v1_genomic.fna.gz --refList GCF_017876255.1_ASM1787625v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017876255.1_ASM1787625v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:46,816] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:46,826] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:22:46,827] [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
GCA_014651175.1	s__Streptomyces clavifer	99.9858	2539	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.53	99.32	0.96	0.94	5	conclusive
GCF_001700505.1	s__Streptomyces mutomycini	88.0048	1610	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.53	99.53	0.96	0.96	2	-
GCF_002941025.1	s__Streptomyces sp002941025	87.9398	1820	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002910915.1	s__Streptomyces sp002910915	87.9295	1672	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905505.1	s__Streptomyces sp001905505	87.8853	1839	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016804005.1	s__Streptomyces pratensis_A	87.8408	1820	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002711365.1	s__Streptomyces sp002711365	87.8359	1810	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	96.67	0.92	0.87	7	-
GCF_000717025.1	s__Streptomyces atroolivaceus	87.7412	1890	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016909575.1	s__Streptomyces sp016909575	87.7115	1793	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042155.1	s__Streptomyces sp008042155	87.5558	1871	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001715295.1	s__Streptomyces griseus_G	87.3228	1648	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000177195.2	s__Streptomyces sp000177195	87.1287	1725	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.71	97.52	0.98	0.91	17	-
GCF_008704555.1	s__Streptomyces nitrosporeus	86.0456	1698	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.98	0.98	2	-
GCF_007829885.1	s__Streptomyces brevispora	85.1544	1593	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018619185.1	s__Streptomyces sp018619185	85.1357	1498	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377965.1	s__Streptomyces sp000377965	85.0393	1606	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:22:46,828] [INFO] GTDB search result was written to GCF_017876255.1_ASM1787625v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:22:46,828] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:22:46,831] [INFO] DFAST_QC result json was written to GCF_017876255.1_ASM1787625v1_genomic.fna/dqc_result.json
[2024-01-25 20:22:46,831] [INFO] DFAST_QC completed!
[2024-01-25 20:22:46,832] [INFO] Total running time: 0h3m41s