[2024-01-24 13:50:25,990] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:50:25,992] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:50:25,992] [INFO] DQC Reference Directory: /var/lib/cwl/stg5cf8fe82-135b-4e0b-8920-d1a6914c0ff4/dqc_reference
[2024-01-24 13:50:27,186] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:50:27,187] [INFO] Task started: Prodigal
[2024-01-24 13:50:27,187] [INFO] Running command: gunzip -c /var/lib/cwl/stg3899d1de-8078-476e-a5f9-d067416e7ba7/GCF_004127445.1_ASM412744v1_genomic.fna.gz | prodigal -d GCF_004127445.1_ASM412744v1_genomic.fna/cds.fna -a GCF_004127445.1_ASM412744v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:50,566] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:50,567] [INFO] Task started: HMMsearch
[2024-01-24 13:50:50,567] [INFO] Running command: hmmsearch --tblout GCF_004127445.1_ASM412744v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5cf8fe82-135b-4e0b-8920-d1a6914c0ff4/dqc_reference/reference_markers.hmm GCF_004127445.1_ASM412744v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:50,915] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:50,916] [INFO] Found 6/6 markers.
[2024-01-24 13:50:50,982] [INFO] Query marker FASTA was written to GCF_004127445.1_ASM412744v1_genomic.fna/markers.fasta
[2024-01-24 13:50:50,982] [INFO] Task started: Blastn
[2024-01-24 13:50:50,983] [INFO] Running command: blastn -query GCF_004127445.1_ASM412744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cf8fe82-135b-4e0b-8920-d1a6914c0ff4/dqc_reference/reference_markers.fasta -out GCF_004127445.1_ASM412744v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:52,229] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:52,235] [INFO] Selected 13 target genomes.
[2024-01-24 13:50:52,235] [INFO] Target genome list was writen to GCF_004127445.1_ASM412744v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:52,275] [INFO] Task started: fastANI
[2024-01-24 13:50:52,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg3899d1de-8078-476e-a5f9-d067416e7ba7/GCF_004127445.1_ASM412744v1_genomic.fna.gz --refList GCF_004127445.1_ASM412744v1_genomic.fna/target_genomes.txt --output GCF_004127445.1_ASM412744v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:51:20,627] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:20,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5cf8fe82-135b-4e0b-8920-d1a6914c0ff4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:51:20,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5cf8fe82-135b-4e0b-8920-d1a6914c0ff4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:51:20,645] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:51:20,645] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:51:20,646] [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 alfalfae	strain=XY25	GCA_004127445.1	1642299	1642299	type	True	100.0	2682	2730	95	conclusive
Streptomyces alfalfae	strain=XY25	GCA_004212445.1	1642299	1642299	type	True	99.9539	2530	2730	95	conclusive
Streptomyces alboniger	strain=NRRL B-1832	GCA_001418385.1	132473	132473	type	True	88.2962	1574	2730	95	below_threshold
Streptomyces alboniger	strain=ATCC 12461	GCA_008704395.1	132473	132473	type	True	88.2521	1871	2730	95	below_threshold
Streptomyces silaceus	strain=NRRL B-24166	GCA_001419745.1	545123	545123	type	True	87.6067	1655	2730	95	below_threshold
Streptomyces atriruber	strain=NRRL B-24165	GCA_001418325.1	545121	545121	type	True	87.5483	1646	2730	95	below_threshold
Streptomyces kanamyceticus	strain=ATCC 12853	GCA_008704495.1	1967	1967	type	True	86.9828	1895	2730	95	below_threshold
Streptomyces kanamyceticus	strain=NRRL B-2535	GCA_001418465.1	1967	1967	type	True	86.9455	1679	2730	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	85.4128	1846	2730	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	84.1756	1783	2730	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	82.5201	1352	2730	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	82.4926	1545	2730	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	82.1652	1530	2730	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:51:20,648] [INFO] DFAST Taxonomy check result was written to GCF_004127445.1_ASM412744v1_genomic.fna/tc_result.tsv
[2024-01-24 13:51:20,648] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:51:20,648] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:51:20,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5cf8fe82-135b-4e0b-8920-d1a6914c0ff4/dqc_reference/checkm_data
[2024-01-24 13:51:20,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:51:20,724] [INFO] Task started: CheckM
[2024-01-24 13:51:20,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004127445.1_ASM412744v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004127445.1_ASM412744v1_genomic.fna/checkm_input GCF_004127445.1_ASM412744v1_genomic.fna/checkm_result
[2024-01-24 13:53:19,086] [INFO] Task succeeded: CheckM
[2024-01-24 13:53:19,088] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:53:19,122] [INFO] ===== Completeness check finished =====
[2024-01-24 13:53:19,123] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:53:19,123] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004127445.1_ASM412744v1_genomic.fna/markers.fasta)
[2024-01-24 13:53:19,124] [INFO] Task started: Blastn
[2024-01-24 13:53:19,124] [INFO] Running command: blastn -query GCF_004127445.1_ASM412744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cf8fe82-135b-4e0b-8920-d1a6914c0ff4/dqc_reference/reference_markers_gtdb.fasta -out GCF_004127445.1_ASM412744v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:53:21,159] [INFO] Task succeeded: Blastn
[2024-01-24 13:53:21,163] [INFO] Selected 12 target genomes.
[2024-01-24 13:53:21,163] [INFO] Target genome list was writen to GCF_004127445.1_ASM412744v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:53:21,207] [INFO] Task started: fastANI
[2024-01-24 13:53:21,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg3899d1de-8078-476e-a5f9-d067416e7ba7/GCF_004127445.1_ASM412744v1_genomic.fna.gz --refList GCF_004127445.1_ASM412744v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004127445.1_ASM412744v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:53:47,996] [INFO] Task succeeded: fastANI
[2024-01-24 13:53:48,021] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:53:48,021] [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_004127445.1	s__Streptomyces alfalfae	100.0	2679	2730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.46	98.55	0.94	0.88	8	conclusive
GCF_003945545.1	s__Streptomyces sp003945545	88.3518	1880	2730	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	88.2646	1869	2730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.40	96.83	0.93	0.87	3	-
GCF_016905445.1	s__Streptomyces sp016905445	88.1373	1759	2730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004010275.1	s__Streptomyces huasconensis	88.0432	1837	2730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001419745.1	s__Streptomyces silaceus	87.6052	1656	2730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.58	99.58	0.96	0.96	2	-
GCF_001418325.1	s__Streptomyces atriruber	87.5364	1648	2730	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	87.4365	1875	2730	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	87.2697	1889	2730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.58	99.56	0.88	0.87	4	-
GCF_008642315.1	s__Streptomyces venezuelae_D	87.1568	1921	2730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002556545.1	s__Streptomyces formicae	86.9812	1917	2730	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	86.9642	1898	2730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:53:48,023] [INFO] GTDB search result was written to GCF_004127445.1_ASM412744v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:53:48,024] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:53:48,028] [INFO] DFAST_QC result json was written to GCF_004127445.1_ASM412744v1_genomic.fna/dqc_result.json
[2024-01-24 13:53:48,028] [INFO] DFAST_QC completed!
[2024-01-24 13:53:48,028] [INFO] Total running time: 0h3m22s