[2024-01-25 19:07:50,523] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:07:50,526] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:07:50,526] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a48b55d-de9b-4665-a4fb-8401af0fe549/dqc_reference
[2024-01-25 19:07:51,716] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:07:51,716] [INFO] Task started: Prodigal
[2024-01-25 19:07:51,717] [INFO] Running command: gunzip -c /var/lib/cwl/stgacb0e153-9873-4102-a85d-1de6c089e650/GCF_014649775.1_ASM1464977v1_genomic.fna.gz | prodigal -d GCF_014649775.1_ASM1464977v1_genomic.fna/cds.fna -a GCF_014649775.1_ASM1464977v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:08:21,023] [INFO] Task succeeded: Prodigal
[2024-01-25 19:08:21,024] [INFO] Task started: HMMsearch
[2024-01-25 19:08:21,024] [INFO] Running command: hmmsearch --tblout GCF_014649775.1_ASM1464977v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a48b55d-de9b-4665-a4fb-8401af0fe549/dqc_reference/reference_markers.hmm GCF_014649775.1_ASM1464977v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:08:21,459] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:08:21,460] [INFO] Found 6/6 markers.
[2024-01-25 19:08:21,539] [INFO] Query marker FASTA was written to GCF_014649775.1_ASM1464977v1_genomic.fna/markers.fasta
[2024-01-25 19:08:21,539] [INFO] Task started: Blastn
[2024-01-25 19:08:21,539] [INFO] Running command: blastn -query GCF_014649775.1_ASM1464977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a48b55d-de9b-4665-a4fb-8401af0fe549/dqc_reference/reference_markers.fasta -out GCF_014649775.1_ASM1464977v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:22,779] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:22,783] [INFO] Selected 19 target genomes.
[2024-01-25 19:08:22,783] [INFO] Target genome list was writen to GCF_014649775.1_ASM1464977v1_genomic.fna/target_genomes.txt
[2024-01-25 19:08:22,803] [INFO] Task started: fastANI
[2024-01-25 19:08:22,803] [INFO] Running command: fastANI --query /var/lib/cwl/stgacb0e153-9873-4102-a85d-1de6c089e650/GCF_014649775.1_ASM1464977v1_genomic.fna.gz --refList GCF_014649775.1_ASM1464977v1_genomic.fna/target_genomes.txt --output GCF_014649775.1_ASM1464977v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:09:02,508] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:02,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a48b55d-de9b-4665-a4fb-8401af0fe549/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:09:02,509] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a48b55d-de9b-4665-a4fb-8401af0fe549/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:09:02,521] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:09:02,521] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:09:02,521] [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 longisporoflavus	strain=JCM 4396	GCA_014649775.1	28044	28044	type	True	100.0	3188	3196	95	conclusive
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	90.6822	2418	3196	95	below_threshold
Streptomyces silaceus	strain=NRRL B-24166	GCA_001419745.1	545123	545123	type	True	85.8088	1722	3196	95	below_threshold
Streptomyces alboniger	strain=NRRL B-1832	GCA_001418385.1	132473	132473	type	True	85.7566	1534	3196	95	below_threshold
Streptomyces atriruber	strain=NRRL B-24165	GCA_001418325.1	545121	545121	type	True	85.6814	1745	3196	95	below_threshold
Streptomyces alboniger	strain=ATCC 12461	GCA_008704395.1	132473	132473	type	True	85.6678	1811	3196	95	below_threshold
Streptomyces kanamyceticus	strain=ATCC 12853	GCA_008704495.1	1967	1967	type	True	85.6661	2027	3196	95	below_threshold
Streptomyces kanamyceticus	strain=NRRL B-2535	GCA_001418465.1	1967	1967	type	True	85.6633	1763	3196	95	below_threshold
Streptomyces alfalfae	strain=XY25	GCA_004212445.1	1642299	1642299	type	True	85.1957	1776	3196	95	below_threshold
Streptomyces alfalfae	strain=XY25	GCA_004127445.1	1642299	1642299	type	True	85.1405	1834	3196	95	below_threshold
Streptomyces aureoverticillatus	strain=JCM 4347	GCA_014649395.1	66871	66871	type	True	84.3502	1944	3196	95	below_threshold
Streptomyces lasiicapitis	strain=CGMCC 4.7349	GCA_014646335.1	1923961	1923961	type	True	84.1859	1893	3196	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	83.6999	1867	3196	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	82.3862	1493	3196	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	81.8655	1396	3196	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	81.6581	1639	3196	95	below_threshold
Streptomyces microflavus	strain=JCM 4496	GCA_014650075.1	1919	1919	type	True	81.6157	1483	3196	95	below_threshold
Streptomyces nitrosporeus	strain=ATCC 12769	GCA_008704555.1	28894	28894	type	True	80.9921	1330	3196	95	below_threshold
Streptomyces zagrosensis	strain=CECT 8305	GCA_014203645.1	1042984	1042984	type	True	79.3739	1133	3196	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:09:02,523] [INFO] DFAST Taxonomy check result was written to GCF_014649775.1_ASM1464977v1_genomic.fna/tc_result.tsv
[2024-01-25 19:09:02,523] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:09:02,523] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:09:02,524] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a48b55d-de9b-4665-a4fb-8401af0fe549/dqc_reference/checkm_data
[2024-01-25 19:09:02,524] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:09:02,613] [INFO] Task started: CheckM
[2024-01-25 19:09:02,614] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649775.1_ASM1464977v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649775.1_ASM1464977v1_genomic.fna/checkm_input GCF_014649775.1_ASM1464977v1_genomic.fna/checkm_result
[2024-01-25 19:10:50,933] [INFO] Task succeeded: CheckM
[2024-01-25 19:10:50,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:10:50,959] [INFO] ===== Completeness check finished =====
[2024-01-25 19:10:50,959] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:10:50,960] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649775.1_ASM1464977v1_genomic.fna/markers.fasta)
[2024-01-25 19:10:50,960] [INFO] Task started: Blastn
[2024-01-25 19:10:50,960] [INFO] Running command: blastn -query GCF_014649775.1_ASM1464977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a48b55d-de9b-4665-a4fb-8401af0fe549/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649775.1_ASM1464977v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:53,026] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:53,029] [INFO] Selected 17 target genomes.
[2024-01-25 19:10:53,029] [INFO] Target genome list was writen to GCF_014649775.1_ASM1464977v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:10:53,055] [INFO] Task started: fastANI
[2024-01-25 19:10:53,055] [INFO] Running command: fastANI --query /var/lib/cwl/stgacb0e153-9873-4102-a85d-1de6c089e650/GCF_014649775.1_ASM1464977v1_genomic.fna.gz --refList GCF_014649775.1_ASM1464977v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649775.1_ASM1464977v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:11:32,196] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:32,207] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:11:32,207] [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_014649775.1	s__Streptomyces longisporoflavus	100.0	3188	3196	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_009769735.1	s__Streptomyces sp009769735	90.4708	2329	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684775.1	s__Streptomyces sp004684775	88.4175	1854	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704495.1	s__Streptomyces kanamyceticus	85.6671	2027	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
GCF_001418325.1	s__Streptomyces atriruber	85.6632	1748	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704395.1	s__Streptomyces alboniger	85.6555	1814	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.40	96.83	0.93	0.87	3	-
GCF_002556545.1	s__Streptomyces formicae	85.6291	2002	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003945545.1	s__Streptomyces sp003945545	85.6289	1840	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016905445.1	s__Streptomyces sp016905445	85.5102	1663	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008642335.1	s__Streptomyces venezuelae_F	85.4218	1919	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008642355.1	s__Streptomyces venezuelae_B	85.3362	1880	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.58	99.56	0.88	0.87	4	-
GCF_004127445.1	s__Streptomyces alfalfae	85.1666	1829	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.46	98.55	0.94	0.88	8	-
GCF_014649395.1	s__Streptomyces aureoverticillatus	84.3467	1946	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646335.1	s__Streptomyces lasiicapitis	84.1991	1890	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.86	98.86	0.95	0.95	2	-
GCF_008905045.1	s__Streptomyces albicerus	82.4293	1829	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905365.1	s__Streptomyces sp001905365	81.466	1496	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203645.1	s__Streptomyces zagrosensis	79.4135	1125	3196	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 19:11:32,208] [INFO] GTDB search result was written to GCF_014649775.1_ASM1464977v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:11:32,209] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:11:32,212] [INFO] DFAST_QC result json was written to GCF_014649775.1_ASM1464977v1_genomic.fna/dqc_result.json
[2024-01-25 19:11:32,213] [INFO] DFAST_QC completed!
[2024-01-25 19:11:32,213] [INFO] Total running time: 0h3m42s