[2024-01-24 13:31:44,332] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,334] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,334] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a09b669-8e19-41bb-ab82-2ccf0c569916/dqc_reference
[2024-01-24 13:31:45,675] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,676] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,677] [INFO] Running command: gunzip -c /var/lib/cwl/stg91ead76a-505c-464a-8160-1446cefe2ca2/GCF_018070025.1_ASM1807002v1_genomic.fna.gz | prodigal -d GCF_018070025.1_ASM1807002v1_genomic.fna/cds.fna -a GCF_018070025.1_ASM1807002v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:39,253] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:39,254] [INFO] Task started: HMMsearch
[2024-01-24 13:32:39,254] [INFO] Running command: hmmsearch --tblout GCF_018070025.1_ASM1807002v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a09b669-8e19-41bb-ab82-2ccf0c569916/dqc_reference/reference_markers.hmm GCF_018070025.1_ASM1807002v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:39,873] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:39,875] [INFO] Found 6/6 markers.
[2024-01-24 13:32:39,961] [INFO] Query marker FASTA was written to GCF_018070025.1_ASM1807002v1_genomic.fna/markers.fasta
[2024-01-24 13:32:39,962] [INFO] Task started: Blastn
[2024-01-24 13:32:39,962] [INFO] Running command: blastn -query GCF_018070025.1_ASM1807002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a09b669-8e19-41bb-ab82-2ccf0c569916/dqc_reference/reference_markers.fasta -out GCF_018070025.1_ASM1807002v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:41,275] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:41,279] [INFO] Selected 23 target genomes.
[2024-01-24 13:32:41,280] [INFO] Target genome list was writen to GCF_018070025.1_ASM1807002v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:41,299] [INFO] Task started: fastANI
[2024-01-24 13:32:41,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg91ead76a-505c-464a-8160-1446cefe2ca2/GCF_018070025.1_ASM1807002v1_genomic.fna.gz --refList GCF_018070025.1_ASM1807002v1_genomic.fna/target_genomes.txt --output GCF_018070025.1_ASM1807002v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:32,124] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:32,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a09b669-8e19-41bb-ab82-2ccf0c569916/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:32,125] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a09b669-8e19-41bb-ab82-2ccf0c569916/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:32,146] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:33:32,147] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:33:32,147] [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 aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	89.8357	2063	3708	95	below_threshold
Streptomyces phaeochromogenes	strain=NRRL B-1248	GCA_001418655.1	1923	1923	type	True	87.9711	2173	3708	95	below_threshold
Streptomyces umbrinus	strain=JCM 4521	GCA_014650195.1	67370	67370	type	True	87.9613	2443	3708	95	below_threshold
Streptomyces fructofermentans	strain=JCM 4956	GCA_014651055.1	152141	152141	type	True	86.1283	2124	3708	95	below_threshold
Streptomyces scabichelini	strain=HC44	GCA_011045015.1	2711217	2711217	type	True	85.1523	1978	3708	95	below_threshold
Streptomyces avermitilis	strain=MA-4680	GCA_000009765.2	33903	33903	type	True	84.6783	1917	3708	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	84.5752	1916	3708	95	below_threshold
Streptomyces mirabilis	strain=JCM 4551	GCA_014650275.1	68239	68239	suspected-type	True	84.5361	2078	3708	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	84.3958	2036	3708	95	below_threshold
Streptomyces avermitilis	strain=MA-4680	GCA_000968255.1	33903	33903	type	True	84.3541	2010	3708	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	83.5902	2035	3708	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	83.5787	1976	3708	95	below_threshold
Streptomyces davaonensis	strain=JCM 4913	GCA_000349325.1	348043	348043	type	True	83.4248	1919	3708	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	83.4132	1699	3708	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	83.3654	1444	3708	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	83.3462	1522	3708	95	below_threshold
Streptomyces prunicolor	strain=NBRC 13075	GCA_000367365.1	67348	67348	type	True	83.2807	1995	3708	95	below_threshold
Streptomyces kanamyceticus	strain=NRRL B-2535	GCA_001418465.1	1967	1967	type	True	82.6814	1545	3708	95	below_threshold
Streptomyces boluensis	strain=YC537	GCA_009908195.1	1775135	1775135	type	True	82.0577	1380	3708	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	81.4567	1220	3708	95	below_threshold
Streptomyces parvus	strain=NRRL B-1455	GCA_008632535.1	66428	66428	type	True	81.1907	1407	3708	95	below_threshold
Streptomyces cavourensis	strain=DSM 41795	GCA_006788935.1	67258	67258	type	True	81.1569	1476	3708	95	below_threshold
Streptomyces cavourensis	strain=JCM 4298	GCA_014649215.1	67258	67258	type	True	81.1533	1432	3708	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:32,150] [INFO] DFAST Taxonomy check result was written to GCF_018070025.1_ASM1807002v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:32,150] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:32,150] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:32,151] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a09b669-8e19-41bb-ab82-2ccf0c569916/dqc_reference/checkm_data
[2024-01-24 13:33:32,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:32,261] [INFO] Task started: CheckM
[2024-01-24 13:33:32,262] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018070025.1_ASM1807002v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018070025.1_ASM1807002v1_genomic.fna/checkm_input GCF_018070025.1_ASM1807002v1_genomic.fna/checkm_result
[2024-01-24 13:36:54,844] [INFO] Task succeeded: CheckM
[2024-01-24 13:36:54,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:36:54,869] [INFO] ===== Completeness check finished =====
[2024-01-24 13:36:54,870] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:36:54,870] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018070025.1_ASM1807002v1_genomic.fna/markers.fasta)
[2024-01-24 13:36:54,871] [INFO] Task started: Blastn
[2024-01-24 13:36:54,871] [INFO] Running command: blastn -query GCF_018070025.1_ASM1807002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a09b669-8e19-41bb-ab82-2ccf0c569916/dqc_reference/reference_markers_gtdb.fasta -out GCF_018070025.1_ASM1807002v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:57,929] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:57,933] [INFO] Selected 11 target genomes.
[2024-01-24 13:36:57,933] [INFO] Target genome list was writen to GCF_018070025.1_ASM1807002v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:36:57,943] [INFO] Task started: fastANI
[2024-01-24 13:36:57,943] [INFO] Running command: fastANI --query /var/lib/cwl/stg91ead76a-505c-464a-8160-1446cefe2ca2/GCF_018070025.1_ASM1807002v1_genomic.fna.gz --refList GCF_018070025.1_ASM1807002v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018070025.1_ASM1807002v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:28,206] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:28,221] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:28,222] [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_018070025.1	s__Streptomyces sp018070025	100.0	3707	3708	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_003024195.1	s__Streptomyces dioscori	94.524	2925	3708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650955.1	s__Streptomyces tauricus	93.4195	2720	3708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418335.1	s__Streptomyces aurantiacus	89.8338	2063	3708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.25	99.25	0.97	0.97	2	-
GCF_008369065.1	s__Streptomyces sp008369065	89.4527	2310	3708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019090165.1	s__Streptomyces sp019090165	89.1709	2223	3708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418655.1	s__Streptomyces phaeochromogenes	87.9242	2182	3708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.97	95.89	0.88	0.87	3	-
GCF_008905045.1	s__Streptomyces albicerus	87.6049	2250	3708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651055.1	s__Streptomyces fructofermentans	86.1307	2123	3708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687325.1	s__Streptomyces sp001687325	81.2664	1493	3708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002082585.1	s__Streptomyces albolongus	81.176	1480	3708	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 13:37:28,223] [INFO] GTDB search result was written to GCF_018070025.1_ASM1807002v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:28,224] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:28,228] [INFO] DFAST_QC result json was written to GCF_018070025.1_ASM1807002v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:28,228] [INFO] DFAST_QC completed!
[2024-01-24 13:37:28,228] [INFO] Total running time: 0h5m44s