[2024-01-24 13:31:33,058] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:33,063] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:33,063] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e8bcc0e-5f89-40a7-9c2a-8c481c538691/dqc_reference
[2024-01-24 13:31:34,504] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:34,505] [INFO] Task started: Prodigal
[2024-01-24 13:31:34,505] [INFO] Running command: gunzip -c /var/lib/cwl/stg18ac6fc8-7583-4f00-9661-dac636f9970f/GCF_000429085.1_ASM42908v1_genomic.fna.gz | prodigal -d GCF_000429085.1_ASM42908v1_genomic.fna/cds.fna -a GCF_000429085.1_ASM42908v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:55,435] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:55,436] [INFO] Task started: HMMsearch
[2024-01-24 13:31:55,436] [INFO] Running command: hmmsearch --tblout GCF_000429085.1_ASM42908v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e8bcc0e-5f89-40a7-9c2a-8c481c538691/dqc_reference/reference_markers.hmm GCF_000429085.1_ASM42908v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:55,781] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:55,783] [INFO] Found 6/6 markers.
[2024-01-24 13:31:55,844] [INFO] Query marker FASTA was written to GCF_000429085.1_ASM42908v1_genomic.fna/markers.fasta
[2024-01-24 13:31:55,845] [INFO] Task started: Blastn
[2024-01-24 13:31:55,845] [INFO] Running command: blastn -query GCF_000429085.1_ASM42908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e8bcc0e-5f89-40a7-9c2a-8c481c538691/dqc_reference/reference_markers.fasta -out GCF_000429085.1_ASM42908v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:57,034] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:57,038] [INFO] Selected 15 target genomes.
[2024-01-24 13:31:57,038] [INFO] Target genome list was writen to GCF_000429085.1_ASM42908v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:57,043] [INFO] Task started: fastANI
[2024-01-24 13:31:57,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg18ac6fc8-7583-4f00-9661-dac636f9970f/GCF_000429085.1_ASM42908v1_genomic.fna.gz --refList GCF_000429085.1_ASM42908v1_genomic.fna/target_genomes.txt --output GCF_000429085.1_ASM42908v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:24,617] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:24,618] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e8bcc0e-5f89-40a7-9c2a-8c481c538691/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:24,619] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e8bcc0e-5f89-40a7-9c2a-8c481c538691/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:24,644] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:24,644] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:24,644] [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 flavidovirens	strain=DSM 40150	GCA_000429085.1	67298	67298	type	True	100.0	2328	2333	95	conclusive
Streptomyces chryseus	strain=DSM 40420	GCA_005981935.1	68186	68186	type	True	90.5598	1295	2333	95	below_threshold
Streptomyces chryseus	strain=JCM 4737	GCA_014650755.1	68186	68186	type	True	90.5465	1747	2333	95	below_threshold
Streptomyces albidochromogenes	strain=DSM 41800	GCA_005981925.1	329524	329524	type	True	90.3656	1470	2333	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.9491	1427	2333	95	below_threshold
Streptomyces finlayi	strain=JCM 4637	GCA_014650515.1	67296	67296	type	True	82.9468	1393	2333	95	below_threshold
Streptomyces gelaticus	strain=JCM 4376	GCA_014649535.1	285446	285446	type	True	82.9193	1315	2333	95	below_threshold
Streptomyces scopuliridis	strain=NRRL B-24574	GCA_000718095.1	452529	452529	type	True	82.862	1318	2333	95	below_threshold
Streptomyces candidus	strain=JCM 4629	GCA_014655855.1	67283	67283	type	True	82.8027	1335	2333	95	below_threshold
Streptomyces candidus	strain=DSM 40141	GCA_014207445.1	67283	67283	type	True	82.7992	1325	2333	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	82.4052	1406	2333	95	below_threshold
Streptomyces wuyuanensis	strain=CGMCC 4.7042	GCA_900103455.1	1196353	1196353	type	True	82.3346	1380	2333	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	81.7319	1161	2333	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	81.5949	1202	2333	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	81.3814	1328	2333	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:24,647] [INFO] DFAST Taxonomy check result was written to GCF_000429085.1_ASM42908v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:24,648] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:24,648] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:24,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e8bcc0e-5f89-40a7-9c2a-8c481c538691/dqc_reference/checkm_data
[2024-01-24 13:32:24,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:24,724] [INFO] Task started: CheckM
[2024-01-24 13:32:24,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429085.1_ASM42908v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429085.1_ASM42908v1_genomic.fna/checkm_input GCF_000429085.1_ASM42908v1_genomic.fna/checkm_result
[2024-01-24 13:33:29,550] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:29,552] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:29,574] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:29,575] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:29,575] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429085.1_ASM42908v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:29,576] [INFO] Task started: Blastn
[2024-01-24 13:33:29,576] [INFO] Running command: blastn -query GCF_000429085.1_ASM42908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e8bcc0e-5f89-40a7-9c2a-8c481c538691/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429085.1_ASM42908v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:31,496] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:31,498] [INFO] Selected 7 target genomes.
[2024-01-24 13:33:31,499] [INFO] Target genome list was writen to GCF_000429085.1_ASM42908v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:31,507] [INFO] Task started: fastANI
[2024-01-24 13:33:31,508] [INFO] Running command: fastANI --query /var/lib/cwl/stg18ac6fc8-7583-4f00-9661-dac636f9970f/GCF_000429085.1_ASM42908v1_genomic.fna.gz --refList GCF_000429085.1_ASM42908v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429085.1_ASM42908v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:46,014] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:46,021] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:46,021] [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_000429085.1	s__Streptomyces flavidovirens	100.0	2328	2333	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.95	95.95	0.82	0.82	2	conclusive
GCF_018614615.1	s__Streptomyces sp018614615	90.853	1742	2333	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018614035.1	s__Streptomyces sp018614035	90.7541	1758	2333	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650755.1	s__Streptomyces chryseus	90.5328	1748	2333	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5104	99.26	99.24	0.89	0.85	3	-
GCF_001746415.1	s__Streptomyces agglomeratus	90.4818	1832	2333	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	99.39	0.92	0.91	5	-
GCF_005981925.1	s__Streptomyces albidochromogenes	90.3498	1472	2333	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5104	N/A	N/A	N/A	N/A	1	-
GCA_003719395.1	s__Streptomyces altiplanensis	89.9961	1564	2333	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.26	96.26	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:46,023] [INFO] GTDB search result was written to GCF_000429085.1_ASM42908v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:46,023] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:46,028] [INFO] DFAST_QC result json was written to GCF_000429085.1_ASM42908v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:46,028] [INFO] DFAST_QC completed!
[2024-01-24 13:33:46,028] [INFO] Total running time: 0h2m13s