[2024-01-24 13:57:15,708] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:15,724] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:15,724] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c39893e-be15-40fb-a169-92253fbb162d/dqc_reference
[2024-01-24 13:57:17,025] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:17,026] [INFO] Task started: Prodigal
[2024-01-24 13:57:17,026] [INFO] Running command: gunzip -c /var/lib/cwl/stg18b4c139-a405-4394-8309-4702cecc28e5/GCF_009765355.1_ASM976535v1_genomic.fna.gz | prodigal -d GCF_009765355.1_ASM976535v1_genomic.fna/cds.fna -a GCF_009765355.1_ASM976535v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:58,420] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:58,421] [INFO] Task started: HMMsearch
[2024-01-24 13:57:58,421] [INFO] Running command: hmmsearch --tblout GCF_009765355.1_ASM976535v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c39893e-be15-40fb-a169-92253fbb162d/dqc_reference/reference_markers.hmm GCF_009765355.1_ASM976535v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:58,858] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:58,860] [INFO] Found 6/6 markers.
[2024-01-24 13:57:58,950] [INFO] Query marker FASTA was written to GCF_009765355.1_ASM976535v1_genomic.fna/markers.fasta
[2024-01-24 13:57:58,950] [INFO] Task started: Blastn
[2024-01-24 13:57:58,950] [INFO] Running command: blastn -query GCF_009765355.1_ASM976535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c39893e-be15-40fb-a169-92253fbb162d/dqc_reference/reference_markers.fasta -out GCF_009765355.1_ASM976535v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:00,343] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:00,346] [INFO] Selected 20 target genomes.
[2024-01-24 13:58:00,346] [INFO] Target genome list was writen to GCF_009765355.1_ASM976535v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:00,354] [INFO] Task started: fastANI
[2024-01-24 13:58:00,355] [INFO] Running command: fastANI --query /var/lib/cwl/stg18b4c139-a405-4394-8309-4702cecc28e5/GCF_009765355.1_ASM976535v1_genomic.fna.gz --refList GCF_009765355.1_ASM976535v1_genomic.fna/target_genomes.txt --output GCF_009765355.1_ASM976535v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:40,776] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:40,777] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c39893e-be15-40fb-a169-92253fbb162d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:40,778] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c39893e-be15-40fb-a169-92253fbb162d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:40,797] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:40,797] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:40,797] [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
Amycolatopsis anabasis	strain=EGI 650086	GCA_009765355.1	1840409	1840409	type	True	100.0	3549	3556	95	conclusive
Amycolatopsis nigrescens	strain=CSC17Ta-90	GCA_000384315.1	381445	381445	type	True	82.0365	1757	3556	95	below_threshold
Amycolatopsis albispora	strain=WP1	GCA_003312875.1	1804986	1804986	type	True	80.7563	1511	3556	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	80.5919	1270	3556	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	80.576	1234	3556	95	below_threshold
Amycolatopsis magusensis	strain=DSM 45510	GCA_017875555.1	882444	882444	type	True	80.5465	1526	3556	95	below_threshold
Amycolatopsis viridis	strain=DSM 45668	GCA_011758765.1	185678	185678	type	True	80.3664	1143	3556	95	below_threshold
Amycolatopsis acididurans	strain=K13G38	GCA_012328925.1	2724524	2724524	type	True	80.3339	1149	3556	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000371885.1	1814	1814	type	True	80.2758	1266	3556	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000739085.1	1814	1814	type	True	80.2372	1285	3556	95	below_threshold
Amycolatopsis rhizosphaerae	strain=TBRC 6029	GCA_007713715.1	2053003	2053003	type	True	80.2255	990	3556	95	below_threshold
Amycolatopsis sacchari	strain=DSM 44468	GCA_900114035.1	115433	115433	type	True	80.1917	1214	3556	95	below_threshold
Amycolatopsis thermoflava	strain=N1165	GCA_000473265.1	84480	84480	type	True	80.1858	1353	3556	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	80.1527	1330	3556	95	below_threshold
Amycolatopsis acidicola	strain=K81G1	GCA_007713735.2	2596893	2596893	type	True	79.9946	1216	3556	95	below_threshold
Amycolatopsis sulphurea	strain=DSM 46092	GCA_002564045.1	76022	76022	type	True	79.8765	1054	3556	95	below_threshold
Amycolatopsis taiwanensis	strain=DSM 45107	GCA_000519205.1	342230	342230	type	True	79.6804	1105	3556	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	78.0568	946	3556	95	below_threshold
Kibdelosporangium philippinense	strain=ATCC 49844	GCA_021390435.3	211113	211113	type	True	77.6576	875	3556	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	76.3601	553	3556	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:40,799] [INFO] DFAST Taxonomy check result was written to GCF_009765355.1_ASM976535v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:40,800] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:40,800] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:40,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c39893e-be15-40fb-a169-92253fbb162d/dqc_reference/checkm_data
[2024-01-24 13:58:40,802] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:40,902] [INFO] Task started: CheckM
[2024-01-24 13:58:40,902] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009765355.1_ASM976535v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009765355.1_ASM976535v1_genomic.fna/checkm_input GCF_009765355.1_ASM976535v1_genomic.fna/checkm_result
[2024-01-24 14:00:51,578] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:51,579] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:51,604] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:51,605] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:51,605] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009765355.1_ASM976535v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:51,605] [INFO] Task started: Blastn
[2024-01-24 14:00:51,606] [INFO] Running command: blastn -query GCF_009765355.1_ASM976535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c39893e-be15-40fb-a169-92253fbb162d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009765355.1_ASM976535v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:53,714] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:53,717] [INFO] Selected 18 target genomes.
[2024-01-24 14:00:53,717] [INFO] Target genome list was writen to GCF_009765355.1_ASM976535v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:53,797] [INFO] Task started: fastANI
[2024-01-24 14:00:53,797] [INFO] Running command: fastANI --query /var/lib/cwl/stg18b4c139-a405-4394-8309-4702cecc28e5/GCF_009765355.1_ASM976535v1_genomic.fna.gz --refList GCF_009765355.1_ASM976535v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009765355.1_ASM976535v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:01:30,753] [INFO] Task succeeded: fastANI
[2024-01-24 14:01:30,772] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:01:30,772] [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_009765355.1	s__Amycolatopsis anabasis	100.0	3549	3556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000384315.1	s__Amycolatopsis nigrescens	82.0326	1759	3556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003312875.1	s__Amycolatopsis albispora	80.7931	1503	3556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018736145.1	s__Amycolatopsis sp018736145	80.7182	1634	3556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017309385.1	s__Amycolatopsis sp017309385	80.5692	1606	3556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011758765.1	s__Amycolatopsis viridis	80.3549	1144	3556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.9842	N/A	N/A	N/A	N/A	1	-
GCF_012328925.1	s__Amycolatopsis acididurans	80.2815	1160	3556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739085.1	s__Amycolatopsis methanolica	80.276	1277	3556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	96.3446	100.00	100.00	1.00	1.00	2	-
GCF_000231075.2	s__Amycolatopsis sp000231075	80.239	1341	3556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.4849	N/A	N/A	N/A	N/A	1	-
GCF_900114035.1	s__Amycolatopsis sacchari	80.2269	1206	3556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007713715.1	s__Amycolatopsis rhizosphaerae	80.225	990	3556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473265.1	s__Amycolatopsis thermoflava	80.2009	1349	3556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	96.3446	98.72	98.72	0.92	0.92	2	-
GCF_018885265.1	s__Amycolatopsis_D sp018885265	80.1555	1330	3556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002564045.1	s__Amycolatopsis sulphurea	79.8506	1058	3556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	95.19	95.19	0.83	0.83	2	-
GCF_000519205.1	s__Amycolatopsis taiwanensis	79.6826	1105	3556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107925.1	s__Amycolatopsis pretoriensis	79.6319	1452	3556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900103775.1	s__Allokutzneria albata	77.9916	1025	3556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Allokutzneria	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014204915.1	s__Crossiella cryophila	77.6457	1204	3556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Crossiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:01:30,774] [INFO] GTDB search result was written to GCF_009765355.1_ASM976535v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:01:30,774] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:01:30,778] [INFO] DFAST_QC result json was written to GCF_009765355.1_ASM976535v1_genomic.fna/dqc_result.json
[2024-01-24 14:01:30,779] [INFO] DFAST_QC completed!
[2024-01-24 14:01:30,779] [INFO] Total running time: 0h4m15s