[2024-01-24 14:06:07,033] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:07,035] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:07,036] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b09320f-5018-4538-b10c-47c360c35cae/dqc_reference
[2024-01-24 14:06:08,415] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:08,416] [INFO] Task started: Prodigal
[2024-01-24 14:06:08,417] [INFO] Running command: gunzip -c /var/lib/cwl/stgde2cb9b0-12e0-4e3d-8d66-fd88e8e85119/GCF_008704535.1_ASM870453v1_genomic.fna.gz | prodigal -d GCF_008704535.1_ASM870453v1_genomic.fna/cds.fna -a GCF_008704535.1_ASM870453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:30,095] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:30,096] [INFO] Task started: HMMsearch
[2024-01-24 14:06:30,096] [INFO] Running command: hmmsearch --tblout GCF_008704535.1_ASM870453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b09320f-5018-4538-b10c-47c360c35cae/dqc_reference/reference_markers.hmm GCF_008704535.1_ASM870453v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:30,448] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:30,450] [INFO] Found 6/6 markers.
[2024-01-24 14:06:30,508] [INFO] Query marker FASTA was written to GCF_008704535.1_ASM870453v1_genomic.fna/markers.fasta
[2024-01-24 14:06:30,509] [INFO] Task started: Blastn
[2024-01-24 14:06:30,509] [INFO] Running command: blastn -query GCF_008704535.1_ASM870453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b09320f-5018-4538-b10c-47c360c35cae/dqc_reference/reference_markers.fasta -out GCF_008704535.1_ASM870453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:31,934] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:31,937] [INFO] Selected 15 target genomes.
[2024-01-24 14:06:31,938] [INFO] Target genome list was writen to GCF_008704535.1_ASM870453v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:31,942] [INFO] Task started: fastANI
[2024-01-24 14:06:31,943] [INFO] Running command: fastANI --query /var/lib/cwl/stgde2cb9b0-12e0-4e3d-8d66-fd88e8e85119/GCF_008704535.1_ASM870453v1_genomic.fna.gz --refList GCF_008704535.1_ASM870453v1_genomic.fna/target_genomes.txt --output GCF_008704535.1_ASM870453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:03,285] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:03,286] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b09320f-5018-4538-b10c-47c360c35cae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:03,287] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b09320f-5018-4538-b10c-47c360c35cae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:03,303] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:07:03,303] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:03,303] [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 subrutilus	strain=ATCC 27467	GCA_008704535.1	36818	36818	type	True	100.0	2531	2534	95	conclusive
Streptomyces subrutilus	strain=JCM 4834	GCA_014650935.1	36818	36818	type	True	99.9733	2462	2534	95	conclusive
Streptomyces xanthophaeus	strain=NRRL B-5414	GCA_000725805.1	67385	67385	type	True	87.8773	1776	2534	95	below_threshold
Streptomyces xanthophaeus	strain=NBRC 12829	GCA_016755895.1	67385	67385	type	True	87.8577	1794	2534	95	below_threshold
Streptomyces spororaveus	strain=NBRC 15456	GCA_016755875.1	284039	284039	type	True	87.7508	1748	2534	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_017639205.1	66374	66374	type	True	87.7213	1795	2534	95	below_threshold
Streptomyces avidinii	strain=DSM 40526	GCA_017874515.1	1895	1895	type	True	87.719	1773	2534	95	below_threshold
Streptomyces avidinii	strain=JCM 4726	GCA_014650695.1	1895	1895	type	True	87.711	1763	2534	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_014648615.1	66374	66374	type	True	87.6909	1776	2534	95	below_threshold
Streptomyces virginiae	strain=NRRL ISP-5094	GCA_000720455.1	1961	1961	suspected-type	True	87.47	1725	2534	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	81.8807	1037	2534	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	81.6968	1072	2534	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	81.1261	1307	2534	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	80.9288	1130	2534	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	80.8805	1151	2534	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:03,305] [INFO] DFAST Taxonomy check result was written to GCF_008704535.1_ASM870453v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:03,306] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:03,306] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:03,306] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b09320f-5018-4538-b10c-47c360c35cae/dqc_reference/checkm_data
[2024-01-24 14:07:03,307] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:03,382] [INFO] Task started: CheckM
[2024-01-24 14:07:03,383] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008704535.1_ASM870453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008704535.1_ASM870453v1_genomic.fna/checkm_input GCF_008704535.1_ASM870453v1_genomic.fna/checkm_result
[2024-01-24 14:08:55,643] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:55,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:55,670] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:55,670] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:55,671] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008704535.1_ASM870453v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:55,671] [INFO] Task started: Blastn
[2024-01-24 14:08:55,671] [INFO] Running command: blastn -query GCF_008704535.1_ASM870453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b09320f-5018-4538-b10c-47c360c35cae/dqc_reference/reference_markers_gtdb.fasta -out GCF_008704535.1_ASM870453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:58,003] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:58,006] [INFO] Selected 18 target genomes.
[2024-01-24 14:08:58,007] [INFO] Target genome list was writen to GCF_008704535.1_ASM870453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:58,072] [INFO] Task started: fastANI
[2024-01-24 14:08:58,072] [INFO] Running command: fastANI --query /var/lib/cwl/stgde2cb9b0-12e0-4e3d-8d66-fd88e8e85119/GCF_008704535.1_ASM870453v1_genomic.fna.gz --refList GCF_008704535.1_ASM870453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008704535.1_ASM870453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:09:36,705] [INFO] Task succeeded: fastANI
[2024-01-24 14:09:36,732] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:09:36,732] [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_008704535.1	s__Streptomyces subrutilus	100.0	2531	2534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.97	0.97	2	conclusive
GCF_018614155.1	s__Streptomyces sp018614155	88.2104	1630	2534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018614075.1	s__Streptomyces sp018614075	88.0912	1615	2534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720115.1	s__Streptomyces sp000720115	87.9635	1710	2534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001746425.1	s__Streptomyces subrutilus_A	87.9589	1701	2534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725805.1	s__Streptomyces xanthophaeus	87.8964	1773	2534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.79	99.60	0.97	0.96	3	-
GCF_002080455.1	s__Streptomyces sp002080455	87.8917	1793	2534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.34	98.21	0.92	0.90	7	-
GCF_016755875.1	s__Streptomyces spororaveus	87.793	1744	2534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905445.1	s__Streptomyces sp001905445	87.7785	1712	2534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008642275.1	s__Streptomyces venezuelae_E	87.7603	1702	2534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017639205.1	s__Streptomyces nojiriensis	87.7182	1792	2534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014650695.1	s__Streptomyces avidinii	87.6826	1766	2534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003148825.1	s__Streptomyces sp003148825	87.4927	1734	2534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.84	95.84	0.87	0.86	3	-
GCF_000716685.1	s__Streptomyces virginiae_A	87.4805	1763	2534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.46	95.91	0.89	0.84	3	-
GCF_014648795.1	s__Streptomyces cinnamonensis	87.424	1751	2534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.18	96.61	0.93	0.87	24	-
GCF_014650555.1	s__Streptomyces goshikiensis	87.1896	1709	2534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.27	96.91	0.89	0.81	10	-
GCF_018614195.1	s__Streptomyces sp018614195	87.0224	1668	2534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002803845.1	s__Streptomyces lavendulae_C	86.92	1765	2534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.97	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:09:36,734] [INFO] GTDB search result was written to GCF_008704535.1_ASM870453v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:09:36,734] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:09:36,738] [INFO] DFAST_QC result json was written to GCF_008704535.1_ASM870453v1_genomic.fna/dqc_result.json
[2024-01-24 14:09:36,738] [INFO] DFAST_QC completed!
[2024-01-24 14:09:36,738] [INFO] Total running time: 0h3m30s