[2024-01-25 20:03:20,664] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:20,665] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:20,665] [INFO] DQC Reference Directory: /var/lib/cwl/stg79bcf8fd-2403-4d6f-b4ca-e7127148be7a/dqc_reference
[2024-01-25 20:03:21,855] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:21,857] [INFO] Task started: Prodigal
[2024-01-25 20:03:21,858] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2f672b0-87dc-409b-a939-7a50ec937899/GCF_017813245.1_ASM1781324v1_genomic.fna.gz | prodigal -d GCF_017813245.1_ASM1781324v1_genomic.fna/cds.fna -a GCF_017813245.1_ASM1781324v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:38,896] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:38,897] [INFO] Task started: HMMsearch
[2024-01-25 20:03:38,897] [INFO] Running command: hmmsearch --tblout GCF_017813245.1_ASM1781324v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79bcf8fd-2403-4d6f-b4ca-e7127148be7a/dqc_reference/reference_markers.hmm GCF_017813245.1_ASM1781324v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:39,197] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:39,199] [INFO] Found 6/6 markers.
[2024-01-25 20:03:39,256] [INFO] Query marker FASTA was written to GCF_017813245.1_ASM1781324v1_genomic.fna/markers.fasta
[2024-01-25 20:03:39,257] [INFO] Task started: Blastn
[2024-01-25 20:03:39,257] [INFO] Running command: blastn -query GCF_017813245.1_ASM1781324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79bcf8fd-2403-4d6f-b4ca-e7127148be7a/dqc_reference/reference_markers.fasta -out GCF_017813245.1_ASM1781324v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:40,517] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:40,520] [INFO] Selected 24 target genomes.
[2024-01-25 20:03:40,521] [INFO] Target genome list was writen to GCF_017813245.1_ASM1781324v1_genomic.fna/target_genomes.txt
[2024-01-25 20:03:40,540] [INFO] Task started: fastANI
[2024-01-25 20:03:40,540] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2f672b0-87dc-409b-a939-7a50ec937899/GCF_017813245.1_ASM1781324v1_genomic.fna.gz --refList GCF_017813245.1_ASM1781324v1_genomic.fna/target_genomes.txt --output GCF_017813245.1_ASM1781324v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:04:20,506] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:20,506] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79bcf8fd-2403-4d6f-b4ca-e7127148be7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:04:20,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79bcf8fd-2403-4d6f-b4ca-e7127148be7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:04:20,523] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:04:20,523] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:04:20,524] [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 montanisoli	strain=MMS17-BM035	GCA_017813245.1	2798581	2798581	type	True	100.0	2187	2216	95	conclusive
Streptomyces fuscigenes	strain=JBL-20	GCA_021556455.1	1528880	1528880	type	True	85.3053	1126	2216	95	below_threshold
Streptomyces liangshanensis	strain=QMT-12	GCA_011694815.1	2717324	2717324	type	True	81.7188	1134	2216	95	below_threshold
Streptomyces lushanensis	strain=NRRL B-24994	GCA_001700515.1	1434255	1434255	type	True	81.3296	952	2216	95	below_threshold
Streptomyces scopuliridis	strain=RB72	GCA_003073355.1	452529	452529	type	True	81.308	1063	2216	95	below_threshold
Streptomyces scopuliridis	strain=NRRL B-24574	GCA_000718095.1	452529	452529	type	True	81.2431	1118	2216	95	below_threshold
Streptomyces badius	strain=JCM 4350	GCA_014649415.1	1941	1941	type	True	80.9116	1024	2216	95	below_threshold
Streptomyces vietnamensis	strain=GIM4.0001	GCA_000830005.1	362257	362257	type	True	80.8125	1103	2216	95	below_threshold
Streptomyces litmocidini	strain=JCM 4394	GCA_014649755.1	67318	67318	type	True	80.7592	1063	2216	95	below_threshold
Streptomyces microflavus	strain=JCM 4496	GCA_014650075.1	1919	1919	type	True	80.7428	1064	2216	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	80.733	1096	2216	95	below_threshold
Streptomyces griseus	strain=DSM 40236	GCA_900105705.1	1911	1911	type	True	80.7289	1099	2216	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	80.6908	1129	2216	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	80.574	1019	2216	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	80.5421	1070	2216	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	80.4733	978	2216	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	80.4271	993	2216	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	80.3692	1087	2216	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	80.2401	1126	2216	95	below_threshold
Streptomyces triticiradicis	strain=NEAU-H2	GCA_008868685.1	2651189	2651189	type	True	80.1359	1107	2216	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	80.133	1074	2216	95	below_threshold
Streptomyces populi	strain=A249	GCA_002911015.1	2058924	2058924	type	True	80.1175	1088	2216	95	below_threshold
Streptomyces olivochromogenes	strain=DSM 40451	GCA_001514115.1	1963	1963	type	True	80.1092	1123	2216	95	below_threshold
Streptomyces physcomitrii	strain=LD120	GCA_012273655.1	2724184	2724184	type	True	80.0501	1008	2216	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:04:20,525] [INFO] DFAST Taxonomy check result was written to GCF_017813245.1_ASM1781324v1_genomic.fna/tc_result.tsv
[2024-01-25 20:04:20,525] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:04:20,526] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:04:20,526] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79bcf8fd-2403-4d6f-b4ca-e7127148be7a/dqc_reference/checkm_data
[2024-01-25 20:04:20,527] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:04:20,594] [INFO] Task started: CheckM
[2024-01-25 20:04:20,595] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017813245.1_ASM1781324v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017813245.1_ASM1781324v1_genomic.fna/checkm_input GCF_017813245.1_ASM1781324v1_genomic.fna/checkm_result
[2024-01-25 20:05:49,480] [INFO] Task succeeded: CheckM
[2024-01-25 20:05:49,481] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:05:49,509] [INFO] ===== Completeness check finished =====
[2024-01-25 20:05:49,509] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:05:49,510] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017813245.1_ASM1781324v1_genomic.fna/markers.fasta)
[2024-01-25 20:05:49,510] [INFO] Task started: Blastn
[2024-01-25 20:05:49,510] [INFO] Running command: blastn -query GCF_017813245.1_ASM1781324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79bcf8fd-2403-4d6f-b4ca-e7127148be7a/dqc_reference/reference_markers_gtdb.fasta -out GCF_017813245.1_ASM1781324v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:51,611] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:51,613] [INFO] Selected 23 target genomes.
[2024-01-25 20:05:51,613] [INFO] Target genome list was writen to GCF_017813245.1_ASM1781324v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:05:51,658] [INFO] Task started: fastANI
[2024-01-25 20:05:51,658] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2f672b0-87dc-409b-a939-7a50ec937899/GCF_017813245.1_ASM1781324v1_genomic.fna.gz --refList GCF_017813245.1_ASM1781324v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017813245.1_ASM1781324v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:06:30,654] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:30,671] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:06:30,671] [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_017813245.1	s__Streptomyces bomunensis	100.0	2187	2216	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_000721265.1	s__Streptomyces sp000721265	94.077	1818	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000818175.1	s__Streptomyces sp000818175	81.9458	1271	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011694815.1	s__Streptomyces liangshanensis	81.7017	1136	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004151105.1	s__Streptomyces sp004151105	81.3221	1138	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001700515.1	s__Streptomyces lushanensis	81.312	954	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009739905.1	s__Streptomyces ficellus	81.2673	1046	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718095.1	s__Streptomyces scopuliridis	81.2186	1123	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000719775.1	s__Streptomyces sp000719775	81.1829	1119	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001646665.1	s__Streptomyces albulus_A	81.164	1050	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353505.1	s__Streptomyces sp004353505	81.1121	1064	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.86	0.97	0.92	4	-
GCF_002982015.1	s__Streptomyces sp002982015	81.0837	845	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013387495.1	s__Streptomyces sp013387495	81.0609	1028	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010384365.1	s__Streptomyces sp010384365	81.0605	1112	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.09	98.09	0.85	0.85	2	-
GCF_000377145.1	s__Streptomyces sp000377145	81.0462	999	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373645.1	s__Streptomyces sp000373645	81.0123	1063	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018614575.1	s__Streptomyces sp018614575	80.9928	994	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004117935.1	s__Streptomyces roseicoloratus	80.8628	1055	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649875.1	s__Streptomyces rubiginosohelvolus	80.7776	1091	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.09	96.67	0.91	0.87	22	-
GCF_900105415.1	s__Streptomyces sp900105415	80.6456	1086	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.85	0.85	2	-
GCF_002911015.1	s__Streptomyces populi	80.1286	1086	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.82	0.82	2	-
GCF_001514115.1	s__Streptomyces olivochromogenes	80.0922	1126	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2382	97.99	96.97	0.89	0.84	4	-
GCF_012273535.1	s__Streptomyces sp002846625	80.0773	1121	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.4492	97.43	96.23	0.83	0.78	4	-
--------------------------------------------------------------------------------
[2024-01-25 20:06:30,673] [INFO] GTDB search result was written to GCF_017813245.1_ASM1781324v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:06:30,673] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:06:30,677] [INFO] DFAST_QC result json was written to GCF_017813245.1_ASM1781324v1_genomic.fna/dqc_result.json
[2024-01-25 20:06:30,677] [INFO] DFAST_QC completed!
[2024-01-25 20:06:30,677] [INFO] Total running time: 0h3m10s