[2024-01-24 14:14:00,944] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:00,945] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:00,946] [INFO] DQC Reference Directory: /var/lib/cwl/stg352887d1-c48d-490a-bf2f-88c3790d030a/dqc_reference
[2024-01-24 14:14:02,229] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:02,230] [INFO] Task started: Prodigal
[2024-01-24 14:14:02,230] [INFO] Running command: gunzip -c /var/lib/cwl/stgdcefa899-2ec1-42c5-a7e4-fd6424ed9f4b/GCF_002154505.1_ASM215450v1_genomic.fna.gz | prodigal -d GCF_002154505.1_ASM215450v1_genomic.fna/cds.fna -a GCF_002154505.1_ASM215450v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:33,114] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:33,114] [INFO] Task started: HMMsearch
[2024-01-24 14:14:33,115] [INFO] Running command: hmmsearch --tblout GCF_002154505.1_ASM215450v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg352887d1-c48d-490a-bf2f-88c3790d030a/dqc_reference/reference_markers.hmm GCF_002154505.1_ASM215450v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:33,836] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:33,844] [INFO] Found 6/6 markers.
[2024-01-24 14:14:33,989] [INFO] Query marker FASTA was written to GCF_002154505.1_ASM215450v1_genomic.fna/markers.fasta
[2024-01-24 14:14:33,989] [INFO] Task started: Blastn
[2024-01-24 14:14:33,989] [INFO] Running command: blastn -query GCF_002154505.1_ASM215450v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg352887d1-c48d-490a-bf2f-88c3790d030a/dqc_reference/reference_markers.fasta -out GCF_002154505.1_ASM215450v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:35,671] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:35,675] [INFO] Selected 16 target genomes.
[2024-01-24 14:14:35,676] [INFO] Target genome list was writen to GCF_002154505.1_ASM215450v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:35,689] [INFO] Task started: fastANI
[2024-01-24 14:14:35,689] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcefa899-2ec1-42c5-a7e4-fd6424ed9f4b/GCF_002154505.1_ASM215450v1_genomic.fna.gz --refList GCF_002154505.1_ASM215450v1_genomic.fna/target_genomes.txt --output GCF_002154505.1_ASM215450v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:09,168] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:09,169] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg352887d1-c48d-490a-bf2f-88c3790d030a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:09,169] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg352887d1-c48d-490a-bf2f-88c3790d030a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:09,185] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:09,185] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:09,185] [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 carpinensis	strain=NRRL B-16921	GCA_002154505.1	66369	66369	type	True	100.0	3065	3095	95	conclusive
Streptomyces spiralis	strain=JCM 3302	GCA_014654675.1	66376	66376	type	True	91.0587	2096	3095	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	87.5133	1535	3095	95	below_threshold
Streptomyces anandii	strain=JCM 4720	GCA_014650655.1	285454	285454	type	True	87.4396	1689	3095	95	below_threshold
Streptomyces kebangsaanensis	strain=SUK12	GCA_001906585.1	864058	864058	type	True	87.3785	1582	3095	95	below_threshold
Streptomyces naganishii	strain=JCM 4654	GCA_014650575.1	285447	285447	type	True	87.3571	1684	3095	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	85.9661	1439	3095	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.1117	1655	3095	95	below_threshold
Streptomyces cellostaticus	strain=DSM 40189	GCA_001513965.1	67285	67285	type	True	85.0759	1646	3095	95	below_threshold
Streptomyces canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	84.9913	1713	3095	95	below_threshold
Streptomyces puniciscabiei	strain=DSM 41929	GCA_006715785.1	164348	164348	type	True	84.9561	1696	3095	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	84.8741	1554	3095	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	84.8175	1542	3095	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.8106	1336	3095	95	below_threshold
Streptomyces echinatus	strain=JCM4574	GCA_020400685.1	67293	67293	type	True	84.5858	1641	3095	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.2965	1442	3095	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:09,188] [INFO] DFAST Taxonomy check result was written to GCF_002154505.1_ASM215450v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:09,189] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:09,189] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:09,190] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg352887d1-c48d-490a-bf2f-88c3790d030a/dqc_reference/checkm_data
[2024-01-24 14:15:09,192] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:09,295] [INFO] Task started: CheckM
[2024-01-24 14:15:09,295] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002154505.1_ASM215450v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002154505.1_ASM215450v1_genomic.fna/checkm_input GCF_002154505.1_ASM215450v1_genomic.fna/checkm_result
[2024-01-24 14:16:37,727] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:37,729] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:37,758] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:37,759] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:37,760] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002154505.1_ASM215450v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:37,760] [INFO] Task started: Blastn
[2024-01-24 14:16:37,760] [INFO] Running command: blastn -query GCF_002154505.1_ASM215450v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg352887d1-c48d-490a-bf2f-88c3790d030a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002154505.1_ASM215450v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:39,971] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:39,975] [INFO] Selected 15 target genomes.
[2024-01-24 14:16:39,975] [INFO] Target genome list was writen to GCF_002154505.1_ASM215450v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:39,991] [INFO] Task started: fastANI
[2024-01-24 14:16:39,991] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcefa899-2ec1-42c5-a7e4-fd6424ed9f4b/GCF_002154505.1_ASM215450v1_genomic.fna.gz --refList GCF_002154505.1_ASM215450v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002154505.1_ASM215450v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:13,004] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:13,018] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:13,018] [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_002154505.1	s__Streptomyces carpinensis	100.0	3065	3095	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_014654675.1	s__Streptomyces spiralis	91.0399	2098	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.07	98.07	0.87	0.87	2	-
GCF_902506575.1	s__Streptomyces mexicanus	87.825	1720	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.95	96.19	0.87	0.78	3	-
GCF_014650655.1	s__Streptomyces anandii	87.4145	1693	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001906585.1	s__Streptomyces kebangsaanensis	87.3913	1580	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650575.1	s__Streptomyces naganishii	87.3414	1685	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383935.1	s__Streptomyces sp000383935	87.3257	1655	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.62	97.70	0.92	0.84	4	-
GCF_000720185.1	s__Streptomyces sp000720185	87.2472	1734	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364255.1	s__Streptomyces seoulensis_A	87.1537	1653	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002803075.1	s__Streptomyces sp002803075	86.7718	1657	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017526105.1	s__Streptomyces cyanogenus	85.1098	1581	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155905.1	s__Streptomyces tricolor	85.0291	1363	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	98.00	0.86	0.72	5	-
GCF_006715785.1	s__Streptomyces puniciscabiei	84.9204	1702	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.70	95.42	0.91	0.82	3	-
GCF_000716535.1	s__Streptomyces flaveolus_A	84.8841	1773	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.84	0.94	0.91	9	-
GCF_001905845.1	s__Streptomyces sp001905845	84.7379	1588	3095	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 14:17:13,022] [INFO] GTDB search result was written to GCF_002154505.1_ASM215450v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:13,023] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:13,028] [INFO] DFAST_QC result json was written to GCF_002154505.1_ASM215450v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:13,028] [INFO] DFAST_QC completed!
[2024-01-24 14:17:13,028] [INFO] Total running time: 0h3m12s