[2024-01-24 13:48:59,872] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,874] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,874] [INFO] DQC Reference Directory: /var/lib/cwl/stg76f19cfd-a6c3-41c4-bf56-890b255bc7fa/dqc_reference
[2024-01-24 13:49:01,268] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,269] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,269] [INFO] Running command: gunzip -c /var/lib/cwl/stg0adacc29-68ed-4f86-a3d6-5e09b1ebd389/GCF_000721075.1_ASM72107v1_genomic.fna.gz | prodigal -d GCF_000721075.1_ASM72107v1_genomic.fna/cds.fna -a GCF_000721075.1_ASM72107v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:28,417] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:28,418] [INFO] Task started: HMMsearch
[2024-01-24 13:49:28,418] [INFO] Running command: hmmsearch --tblout GCF_000721075.1_ASM72107v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76f19cfd-a6c3-41c4-bf56-890b255bc7fa/dqc_reference/reference_markers.hmm GCF_000721075.1_ASM72107v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:28,882] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:28,883] [INFO] Found 6/6 markers.
[2024-01-24 13:49:28,972] [INFO] Query marker FASTA was written to GCF_000721075.1_ASM72107v1_genomic.fna/markers.fasta
[2024-01-24 13:49:28,972] [INFO] Task started: Blastn
[2024-01-24 13:49:28,972] [INFO] Running command: blastn -query GCF_000721075.1_ASM72107v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76f19cfd-a6c3-41c4-bf56-890b255bc7fa/dqc_reference/reference_markers.fasta -out GCF_000721075.1_ASM72107v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:30,329] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:30,332] [INFO] Selected 27 target genomes.
[2024-01-24 13:49:30,333] [INFO] Target genome list was writen to GCF_000721075.1_ASM72107v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:30,342] [INFO] Task started: fastANI
[2024-01-24 13:49:30,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg0adacc29-68ed-4f86-a3d6-5e09b1ebd389/GCF_000721075.1_ASM72107v1_genomic.fna.gz --refList GCF_000721075.1_ASM72107v1_genomic.fna/target_genomes.txt --output GCF_000721075.1_ASM72107v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:13,482] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:13,483] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76f19cfd-a6c3-41c4-bf56-890b255bc7fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:13,483] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76f19cfd-a6c3-41c4-bf56-890b255bc7fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:13,506] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:13,506] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:13,506] [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
Streptosporangium amethystogenes	strain=NRRL B-2639	GCA_000721075.1	2002	2002	type	True	100.0	3056	3064	95	conclusive
Streptosporangium canum	strain=CGMCC 4.2126	GCA_900113865.1	324952	324952	type	True	85.341	1858	3064	95	below_threshold
Streptosporangium roseum	strain=DSM 43021	GCA_000024865.1	2001	2001	type	True	85.241	1918	3064	95	below_threshold
Streptosporangium minutum	strain=M26	GCA_002149035.1	569862	569862	type	True	85.1042	1803	3064	95	below_threshold
Streptosporangium becharense	strain=DSM 46887	GCA_014204985.1	1816182	1816182	type	True	85.0231	1679	3064	95	below_threshold
Streptosporangium becharense	strain=CECT 8961	GCA_014191075.1	1816182	1816182	type	True	84.9936	1652	3064	95	below_threshold
Streptosporangium album	strain=DSM 43023	GCA_014203795.1	47479	47479	type	True	84.3548	1662	3064	95	below_threshold
Streptosporangium pseudovulgare	strain=JCM 3115	GCA_014648055.1	35765	35765	type	True	83.4247	1579	3064	95	below_threshold
Planomonospora sphaerica	strain=JCM 9374	GCA_001653075.1	161355	161355	type	True	83.3143	1520	3064	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=JCM 3094	GCA_014647955.1	97193	58119	type	True	83.3007	1520	3064	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=NBRC 15869	GCA_016863235.1	97193	58119	type	True	83.254	1501	3064	95	below_threshold
Planobispora rosea	strain=NBRC 15558	GCA_016863155.1	35762	35762	type	True	82.9844	1525	3064	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	80.2248	902	3064	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	80.0556	1331	3064	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	79.5599	1379	3064	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	79.5596	1362	3064	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	79.4039	1310	3064	95	below_threshold
Motilibacter peucedani	strain=RP-AC37	GCA_003634695.1	598650	598650	type	True	76.7735	403	3064	95	below_threshold
Mangrovactinospora gilvigriseus	strain=MUSC 26	GCA_001879105.1	1428644	1428644	type	True	76.6728	453	3064	95	below_threshold
Kibdelosporangium persicum	strain=4NS15	GCA_013280595.1	2698649	2698649	type	True	76.4726	515	3064	95	below_threshold
Ruania alba	strain=DSM 21368	GCA_900105765.1	648782	648782	type	True	75.9932	205	3064	95	below_threshold
Leifsonia xyli subsp. cynodontis	strain=DSM 46306	GCA_000470775.1	31966	1575	type	True	75.9732	145	3064	95	below_threshold
Ruania albidiflava	strain=DSM 18029	GCA_000421225.1	366586	366586	type	True	75.949	254	3064	95	below_threshold
Leifsonia naganoensis	strain=DSM 15166	GCA_013410615.1	150025	150025	type	True	75.8892	266	3064	95	below_threshold
Rathayibacter caricis	strain=DSM 15933	GCA_003044275.1	110936	110936	type	True	75.822	260	3064	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	75.7925	228	3064	95	below_threshold
Rathayibacter festucae	strain=DSM 15932	GCA_004011135.1	110937	110937	type	True	75.7651	332	3064	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:13,508] [INFO] DFAST Taxonomy check result was written to GCF_000721075.1_ASM72107v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:13,509] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:13,509] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:13,509] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76f19cfd-a6c3-41c4-bf56-890b255bc7fa/dqc_reference/checkm_data
[2024-01-24 13:50:13,510] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:13,595] [INFO] Task started: CheckM
[2024-01-24 13:50:13,596] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000721075.1_ASM72107v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000721075.1_ASM72107v1_genomic.fna/checkm_input GCF_000721075.1_ASM72107v1_genomic.fna/checkm_result
[2024-01-24 13:51:34,890] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:34,891] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.13%
Strain heterogeneity: 58.33%
--------------------------------------------------------------------------------
[2024-01-24 13:51:34,918] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:34,918] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:34,918] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000721075.1_ASM72107v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:34,919] [INFO] Task started: Blastn
[2024-01-24 13:51:34,919] [INFO] Running command: blastn -query GCF_000721075.1_ASM72107v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76f19cfd-a6c3-41c4-bf56-890b255bc7fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_000721075.1_ASM72107v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:36,897] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:36,900] [INFO] Selected 19 target genomes.
[2024-01-24 13:51:36,901] [INFO] Target genome list was writen to GCF_000721075.1_ASM72107v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:36,952] [INFO] Task started: fastANI
[2024-01-24 13:51:36,952] [INFO] Running command: fastANI --query /var/lib/cwl/stg0adacc29-68ed-4f86-a3d6-5e09b1ebd389/GCF_000721075.1_ASM72107v1_genomic.fna.gz --refList GCF_000721075.1_ASM72107v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000721075.1_ASM72107v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:08,067] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:08,089] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:08,089] [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_000721075.1	s__Streptosporangium amethystogenes	100.0	3056	3064	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900113865.1	s__Streptosporangium canum	85.3446	1856	3064	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	96.48	96.48	0.86	0.86	2	-
GCF_000024865.1	s__Streptosporangium roseum	85.2531	1915	3064	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002149035.1	s__Streptosporangium minutum	85.1053	1804	3064	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	N/A	N/A	N/A	N/A	1	-
GCF_014204985.1	s__Streptosporangium becharense	85.0207	1679	3064	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900188345.1	s__Streptosporangium subroseum	84.9492	1789	3064	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	95.81	95.81	0.87	0.87	2	-
GCF_014203795.1	s__Streptosporangium album	84.3638	1659	3064	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015711605.1	s__Planomonospora_A sp015711605	83.5397	1557	3064	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203605.1	s__Planomonospora_A venezuelensis	83.4805	1578	3064	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648055.1	s__Streptosporangium pseudovulgare	83.4289	1576	3064	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	-
GCA_014647935.1	s__Planomonospora parontospora	83.2665	1525	3064	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	97.40	95.90	0.89	0.84	6	-
GCF_015711645.1	s__Planomonospora sp015711645	83.0885	1498	3064	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634695.1	s__Motilibacter peucedani	76.7264	413	3064	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Motilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879105.1	s__Streptomyces_G gilvigriseus	76.6364	459	3064	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013811715.1	s__JACCUS01 sp013811715	76.4471	176	3064	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JACCUS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015690345.1	s__Plantactinospora sp015690345	76.3702	593	3064	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002583555.1	s__Pseudonocardia sp002583555	76.0089	508	3064	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000470775.1	s__Leifsonia cynodontis	75.9628	146	3064	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217625.1	s__Leifsonia shinshuensis_A	75.9203	304	3064	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:08,091] [INFO] GTDB search result was written to GCF_000721075.1_ASM72107v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:08,092] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:08,101] [INFO] DFAST_QC result json was written to GCF_000721075.1_ASM72107v1_genomic.fna/dqc_result.json
[2024-01-24 13:52:08,102] [INFO] DFAST_QC completed!
[2024-01-24 13:52:08,102] [INFO] Total running time: 0h3m8s