[2024-01-25 17:58:35,728] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:58:35,729] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:58:35,729] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3b897b2-56b8-4c21-a99d-af7ed3efd65b/dqc_reference
[2024-01-25 17:58:36,886] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:58:36,888] [INFO] Task started: Prodigal
[2024-01-25 17:58:36,888] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c82e30c-83ed-432c-af39-6c5e64b9c71c/GCF_001418385.1_ASM141838v1_genomic.fna.gz | prodigal -d GCF_001418385.1_ASM141838v1_genomic.fna/cds.fna -a GCF_001418385.1_ASM141838v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:58:54,144] [INFO] Task succeeded: Prodigal
[2024-01-25 17:58:54,144] [INFO] Task started: HMMsearch
[2024-01-25 17:58:54,145] [INFO] Running command: hmmsearch --tblout GCF_001418385.1_ASM141838v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3b897b2-56b8-4c21-a99d-af7ed3efd65b/dqc_reference/reference_markers.hmm GCF_001418385.1_ASM141838v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:58:54,462] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:58:54,463] [INFO] Found 6/6 markers.
[2024-01-25 17:58:54,522] [INFO] Query marker FASTA was written to GCF_001418385.1_ASM141838v1_genomic.fna/markers.fasta
[2024-01-25 17:58:54,523] [INFO] Task started: Blastn
[2024-01-25 17:58:54,523] [INFO] Running command: blastn -query GCF_001418385.1_ASM141838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3b897b2-56b8-4c21-a99d-af7ed3efd65b/dqc_reference/reference_markers.fasta -out GCF_001418385.1_ASM141838v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:58:55,747] [INFO] Task succeeded: Blastn
[2024-01-25 17:58:55,750] [INFO] Selected 13 target genomes.
[2024-01-25 17:58:55,750] [INFO] Target genome list was writen to GCF_001418385.1_ASM141838v1_genomic.fna/target_genomes.txt
[2024-01-25 17:58:55,761] [INFO] Task started: fastANI
[2024-01-25 17:58:55,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c82e30c-83ed-432c-af39-6c5e64b9c71c/GCF_001418385.1_ASM141838v1_genomic.fna.gz --refList GCF_001418385.1_ASM141838v1_genomic.fna/target_genomes.txt --output GCF_001418385.1_ASM141838v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:59:22,074] [INFO] Task succeeded: fastANI
[2024-01-25 17:59:22,074] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3b897b2-56b8-4c21-a99d-af7ed3efd65b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:59:22,075] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3b897b2-56b8-4c21-a99d-af7ed3efd65b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:59:22,083] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:59:22,084] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:59:22,084] [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 alboniger	strain=NRRL B-1832	GCA_001418385.1	132473	132473	type	True	100.0	2186	2206	95	conclusive
Streptomyces alboniger	strain=ATCC 12461	GCA_008704395.1	132473	132473	type	True	99.9839	2205	2206	95	conclusive
Streptomyces silaceus	strain=NRRL B-24166	GCA_001419745.1	545123	545123	type	True	88.5124	1506	2206	95	below_threshold
Streptomyces atriruber	strain=NRRL B-24165	GCA_001418325.1	545121	545121	type	True	88.3919	1510	2206	95	below_threshold
Streptomyces alfalfae	strain=XY25	GCA_004212445.1	1642299	1642299	type	True	88.3827	1540	2206	95	below_threshold
Streptomyces alfalfae	strain=XY25	GCA_004127445.1	1642299	1642299	type	True	88.3623	1591	2206	95	below_threshold
Streptomyces kanamyceticus	strain=ATCC 12853	GCA_008704495.1	1967	1967	type	True	87.8594	1668	2206	95	below_threshold
Streptomyces kanamyceticus	strain=NRRL B-2535	GCA_001418465.1	1967	1967	type	True	87.7746	1519	2206	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	86.0246	1588	2206	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	84.8457	1534	2206	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	82.9082	1295	2206	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	82.8767	1162	2206	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	82.8076	1279	2206	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:59:22,085] [INFO] DFAST Taxonomy check result was written to GCF_001418385.1_ASM141838v1_genomic.fna/tc_result.tsv
[2024-01-25 17:59:22,086] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:59:22,086] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:59:22,086] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3b897b2-56b8-4c21-a99d-af7ed3efd65b/dqc_reference/checkm_data
[2024-01-25 17:59:22,087] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:59:22,157] [INFO] Task started: CheckM
[2024-01-25 17:59:22,157] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001418385.1_ASM141838v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001418385.1_ASM141838v1_genomic.fna/checkm_input GCF_001418385.1_ASM141838v1_genomic.fna/checkm_result
[2024-01-25 18:00:22,168] [INFO] Task succeeded: CheckM
[2024-01-25 18:00:22,169] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:00:22,196] [INFO] ===== Completeness check finished =====
[2024-01-25 18:00:22,196] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:00:22,197] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001418385.1_ASM141838v1_genomic.fna/markers.fasta)
[2024-01-25 18:00:22,197] [INFO] Task started: Blastn
[2024-01-25 18:00:22,197] [INFO] Running command: blastn -query GCF_001418385.1_ASM141838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3b897b2-56b8-4c21-a99d-af7ed3efd65b/dqc_reference/reference_markers_gtdb.fasta -out GCF_001418385.1_ASM141838v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:24,238] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:24,247] [INFO] Selected 10 target genomes.
[2024-01-25 18:00:24,248] [INFO] Target genome list was writen to GCF_001418385.1_ASM141838v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:00:24,255] [INFO] Task started: fastANI
[2024-01-25 18:00:24,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c82e30c-83ed-432c-af39-6c5e64b9c71c/GCF_001418385.1_ASM141838v1_genomic.fna.gz --refList GCF_001418385.1_ASM141838v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001418385.1_ASM141838v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:00:44,631] [INFO] Task succeeded: fastANI
[2024-01-25 18:00:44,639] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:00:44,639] [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_008704395.1	s__Streptomyces alboniger	99.9839	2205	2206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.40	96.83	0.93	0.87	3	conclusive
GCF_003945545.1	s__Streptomyces sp003945545	92.7722	1779	2206	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	90.1798	1580	2206	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	90.1631	1586	2206	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	88.5318	1504	2206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.58	99.58	0.96	0.96	2	-
GCF_004127445.1	s__Streptomyces alfalfae	88.3777	1589	2206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.46	98.55	0.94	0.88	8	-
GCF_001418325.1	s__Streptomyces atriruber	88.3362	1517	2206	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	88.0557	1583	2206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.58	99.56	0.88	0.87	4	-
GCF_008704495.1	s__Streptomyces kanamyceticus	87.8526	1669	2206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
GCF_004684775.1	s__Streptomyces sp004684775	86.3821	1411	2206	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 18:00:44,640] [INFO] GTDB search result was written to GCF_001418385.1_ASM141838v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:00:44,641] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:00:44,644] [INFO] DFAST_QC result json was written to GCF_001418385.1_ASM141838v1_genomic.fna/dqc_result.json
[2024-01-25 18:00:44,644] [INFO] DFAST_QC completed!
[2024-01-25 18:00:44,644] [INFO] Total running time: 0h2m9s