[2024-01-24 11:59:12,984] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:12,986] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:12,986] [INFO] DQC Reference Directory: /var/lib/cwl/stg084ede02-5d61-4bd7-82ca-4efc2549ea1d/dqc_reference
[2024-01-24 11:59:14,258] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:14,259] [INFO] Task started: Prodigal
[2024-01-24 11:59:14,259] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5d1d02d-9405-4c83-a3c3-be71ca92a43f/GCF_014650615.1_ASM1465061v1_genomic.fna.gz | prodigal -d GCF_014650615.1_ASM1465061v1_genomic.fna/cds.fna -a GCF_014650615.1_ASM1465061v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:37,838] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:37,839] [INFO] Task started: HMMsearch
[2024-01-24 11:59:37,839] [INFO] Running command: hmmsearch --tblout GCF_014650615.1_ASM1465061v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg084ede02-5d61-4bd7-82ca-4efc2549ea1d/dqc_reference/reference_markers.hmm GCF_014650615.1_ASM1465061v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:38,340] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:38,342] [INFO] Found 6/6 markers.
[2024-01-24 11:59:38,421] [INFO] Query marker FASTA was written to GCF_014650615.1_ASM1465061v1_genomic.fna/markers.fasta
[2024-01-24 11:59:38,421] [INFO] Task started: Blastn
[2024-01-24 11:59:38,422] [INFO] Running command: blastn -query GCF_014650615.1_ASM1465061v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg084ede02-5d61-4bd7-82ca-4efc2549ea1d/dqc_reference/reference_markers.fasta -out GCF_014650615.1_ASM1465061v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:39,812] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:39,815] [INFO] Selected 22 target genomes.
[2024-01-24 11:59:39,816] [INFO] Target genome list was writen to GCF_014650615.1_ASM1465061v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:39,824] [INFO] Task started: fastANI
[2024-01-24 11:59:39,825] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5d1d02d-9405-4c83-a3c3-be71ca92a43f/GCF_014650615.1_ASM1465061v1_genomic.fna.gz --refList GCF_014650615.1_ASM1465061v1_genomic.fna/target_genomes.txt --output GCF_014650615.1_ASM1465061v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:21,686] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:21,687] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg084ede02-5d61-4bd7-82ca-4efc2549ea1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:21,687] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg084ede02-5d61-4bd7-82ca-4efc2549ea1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:21,709] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:00:21,709] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:21,709] [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 albaduncus	strain=JCM 4715	GCA_014650615.1	68172	68172	type	True	100.0	2591	2594	95	conclusive
Streptomyces albaduncus	strain=CECT 3226	GCA_014203495.1	68172	68172	type	True	99.9867	2576	2594	95	conclusive
Streptomyces capillispiralis	strain=DSM 41695	GCA_007829875.1	68182	68182	type	True	92.8759	2156	2594	95	below_threshold
Streptomyces capillispiralis	strain=JCM 5075	GCA_014656315.1	68182	68182	type	True	92.8619	2144	2594	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	91.1787	2044	2594	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	90.0292	1868	2594	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	89.9655	1887	2594	95	below_threshold
Streptomyces viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	89.3748	1507	2594	95	below_threshold
Streptomyces griseoflavus	strain=JCM 4479	GCA_014649995.1	35619	35619	type	True	89.0571	1809	2594	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	86.4433	1783	2594	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	86.2308	1762	2594	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	86.184	1768	2594	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	86.1411	1715	2594	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.6017	1489	2594	95	below_threshold
Streptomyces daghestanicus	strain=JCM 4365	GCA_014649475.1	66885	66885	suspected-type	True	85.3237	1607	2594	95	below_threshold
Streptomyces daghestanicus	strain=NBRC 12762	GCA_020521275.1	66885	66885	suspected-type	True	85.3129	1648	2594	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.965	1551	2594	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	81.4668	1351	2594	95	below_threshold
Motilibacter deserti	strain=E257	GCA_011250635.1	2714956	2714956	type	True	76.6242	462	2594	95	below_threshold
Marmoricola aurantiacus	strain=DSM 12652	GCA_003752505.1	86796	86796	type	True	76.5584	445	2594	95	below_threshold
Marmoricola aequoreus	strain=NRRL B-24464	GCA_000720335.1	397278	397278	type	True	76.5069	431	2594	95	below_threshold
Cellulomonas rhizosphaerae	strain=NEAU-TCZ24	GCA_003470205.1	2293719	2293719	type	True	76.4015	353	2594	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:21,711] [INFO] DFAST Taxonomy check result was written to GCF_014650615.1_ASM1465061v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:21,711] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:21,712] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:21,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg084ede02-5d61-4bd7-82ca-4efc2549ea1d/dqc_reference/checkm_data
[2024-01-24 12:00:21,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:21,788] [INFO] Task started: CheckM
[2024-01-24 12:00:21,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650615.1_ASM1465061v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650615.1_ASM1465061v1_genomic.fna/checkm_input GCF_014650615.1_ASM1465061v1_genomic.fna/checkm_result
[2024-01-24 12:02:09,828] [INFO] Task succeeded: CheckM
[2024-01-24 12:02:09,830] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:02:09,861] [INFO] ===== Completeness check finished =====
[2024-01-24 12:02:09,861] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:02:09,862] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650615.1_ASM1465061v1_genomic.fna/markers.fasta)
[2024-01-24 12:02:09,862] [INFO] Task started: Blastn
[2024-01-24 12:02:09,863] [INFO] Running command: blastn -query GCF_014650615.1_ASM1465061v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg084ede02-5d61-4bd7-82ca-4efc2549ea1d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650615.1_ASM1465061v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:02:11,837] [INFO] Task succeeded: Blastn
[2024-01-24 12:02:11,841] [INFO] Selected 21 target genomes.
[2024-01-24 12:02:11,842] [INFO] Target genome list was writen to GCF_014650615.1_ASM1465061v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:02:11,857] [INFO] Task started: fastANI
[2024-01-24 12:02:11,857] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5d1d02d-9405-4c83-a3c3-be71ca92a43f/GCF_014650615.1_ASM1465061v1_genomic.fna.gz --refList GCF_014650615.1_ASM1465061v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650615.1_ASM1465061v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:02:53,080] [INFO] Task succeeded: fastANI
[2024-01-24 12:02:53,100] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:02:53,100] [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
GCA_014650015.1	s__Streptomyces griseoloalbus	99.1738	2428	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.17	99.17	0.94	0.94	3	conclusive
GCF_007829875.1	s__Streptomyces capillispiralis	92.8675	2157	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006782915.1	s__Streptomyces calvus	91.0687	2047	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.66	99.31	0.97	0.96	5	-
GCF_019049255.1	s__Streptomyces sp019049255	90.7781	1977	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905725.1	s__Streptomyces sp001905725	90.579	1972	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721605.1	s__Streptomyces sp000721605	90.5174	1943	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008312835.1	s__Streptomyces marokkonensis	90.4152	1881	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009852415.1	s__Streptomyces sp009852415	90.1301	1940	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003665435.1	s__Streptomyces fungicidicus_A	90.0742	1907	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.86	98.42	0.93	0.90	4	-
GCF_000718785.1	s__Streptomyces sp000718785	89.3644	1831	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649995.1	s__Streptomyces griseoflavus	89.0474	1810	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018638295.1	s__Streptomyces sp018638295	88.7494	1720	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648815.1	s__Streptomyces flaveolus	86.1537	1713	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717055.1	s__Streptomyces iakyrus	86.0041	1768	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	96.00	95.60	0.85	0.85	3	-
GCF_000931445.1	s__Streptomyces cyaneogriseus	85.701	1665	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.603	N/A	N/A	N/A	N/A	1	-
GCF_018614415.1	s__Streptomyces sp018614415	85.3923	1635	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014649155.1	s__Streptomyces griseoviridis	85.3566	1638	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.52	99.48	0.96	0.96	3	-
GCF_002291145.1	s__Streptomyces sp002291145	85.2444	1712	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103455.1	s__Streptomyces wuyuanensis	81.5502	1321	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001704635.1	s__Streptomyces sparsogenes	80.7389	1294	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.81	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:02:53,103] [INFO] GTDB search result was written to GCF_014650615.1_ASM1465061v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:02:53,103] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:02:53,108] [INFO] DFAST_QC result json was written to GCF_014650615.1_ASM1465061v1_genomic.fna/dqc_result.json
[2024-01-24 12:02:53,108] [INFO] DFAST_QC completed!
[2024-01-24 12:02:53,108] [INFO] Total running time: 0h3m40s