[2024-01-24 12:21:44,786] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:44,788] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:44,788] [INFO] DQC Reference Directory: /var/lib/cwl/stge573ff0d-b381-4c7b-8868-080b0f6c7c70/dqc_reference
[2024-01-24 12:21:46,266] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:46,267] [INFO] Task started: Prodigal
[2024-01-24 12:21:46,267] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b727f2f-43b5-4add-98e1-e790863b2c37/GCF_002262875.1_ASM226287v1_genomic.fna.gz | prodigal -d GCF_002262875.1_ASM226287v1_genomic.fna/cds.fna -a GCF_002262875.1_ASM226287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:06,857] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:06,857] [INFO] Task started: HMMsearch
[2024-01-24 12:22:06,858] [INFO] Running command: hmmsearch --tblout GCF_002262875.1_ASM226287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge573ff0d-b381-4c7b-8868-080b0f6c7c70/dqc_reference/reference_markers.hmm GCF_002262875.1_ASM226287v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:07,275] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:07,277] [INFO] Found 6/6 markers.
[2024-01-24 12:22:07,347] [INFO] Query marker FASTA was written to GCF_002262875.1_ASM226287v1_genomic.fna/markers.fasta
[2024-01-24 12:22:07,347] [INFO] Task started: Blastn
[2024-01-24 12:22:07,347] [INFO] Running command: blastn -query GCF_002262875.1_ASM226287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge573ff0d-b381-4c7b-8868-080b0f6c7c70/dqc_reference/reference_markers.fasta -out GCF_002262875.1_ASM226287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:08,698] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:08,703] [INFO] Selected 26 target genomes.
[2024-01-24 12:22:08,704] [INFO] Target genome list was writen to GCF_002262875.1_ASM226287v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:08,713] [INFO] Task started: fastANI
[2024-01-24 12:22:08,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b727f2f-43b5-4add-98e1-e790863b2c37/GCF_002262875.1_ASM226287v1_genomic.fna.gz --refList GCF_002262875.1_ASM226287v1_genomic.fna/target_genomes.txt --output GCF_002262875.1_ASM226287v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:53,270] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:53,271] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge573ff0d-b381-4c7b-8868-080b0f6c7c70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:53,271] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge573ff0d-b381-4c7b-8868-080b0f6c7c70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:53,292] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:22:53,293] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:22:53,293] [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 albispora	strain=WP1	GCA_003312875.1	1804986	1804986	type	True	80.3071	1097	2087	95	below_threshold
Amycolatopsis nigrescens	strain=CSC17Ta-90	GCA_000384315.1	381445	381445	type	True	80.2982	1092	2087	95	below_threshold
Amycolatopsis magusensis	strain=DSM 45510	GCA_017875555.1	882444	882444	type	True	80.2169	1086	2087	95	below_threshold
Amycolatopsis anabasis	strain=EGI 650086	GCA_009765355.1	1840409	1840409	type	True	80.0548	1087	2087	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	79.988	934	2087	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	79.9793	937	2087	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.8574	893	2087	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000371885.1	1814	1814	type	True	79.7363	905	2087	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000739085.1	1814	1814	type	True	79.7028	925	2087	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	79.6953	961	2087	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.6477	956	2087	95	below_threshold
Amycolatopsis palatopharyngis	strain=DSM 44832	GCA_003385185.1	187982	187982	type	True	79.6309	860	2087	95	below_threshold
Amycolatopsis marina	strain=CGMCC 4.3568	GCA_900111885.1	490629	490629	type	True	79.6115	904	2087	95	below_threshold
Amycolatopsis thermoflava	strain=N1165	GCA_000473265.1	84480	84480	type	True	79.5981	964	2087	95	below_threshold
Amycolatopsis saalfeldensis	strain=DSM 44993	GCA_900110575.1	394193	394193	type	True	79.5861	1006	2087	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_001995215.1	36819	36819	type	True	79.5748	987	2087	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_000340415.1	36819	36819	type	True	79.5702	992	2087	95	below_threshold
Amycolatopsis keratiniphila subsp. nogabecina	strain=FH 1893	GCA_001953855.1	208442	129921	type	True	79.5443	985	2087	95	below_threshold
Amycolatopsis sacchari	strain=DSM 44468	GCA_900114035.1	115433	115433	type	True	79.5307	874	2087	95	below_threshold
Amycolatopsis endophytica	strain=DSM 104006	GCA_013410405.1	860233	860233	type	True	79.5247	887	2087	95	below_threshold
Amycolatopsis keratiniphila subsp. keratiniphila	strain=DSM 44409	GCA_001620365.2	227715	129921	type	True	79.4941	978	2087	95	below_threshold
Amycolatopsis xylanica	strain=CPCC 202699	GCA_900107045.1	589385	589385	type	True	79.4378	987	2087	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	79.3878	1031	2087	95	below_threshold
Amycolatopsis kentuckyensis	strain=NRRL B-24129	GCA_002155975.1	218823	218823	type	True	79.3664	937	2087	95	below_threshold
Amycolatopsis acidicola	strain=K81G1	GCA_007713735.2	2596893	2596893	type	True	79.363	859	2087	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.3358	688	2087	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:53,295] [INFO] DFAST Taxonomy check result was written to GCF_002262875.1_ASM226287v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:53,296] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:53,296] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:53,296] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge573ff0d-b381-4c7b-8868-080b0f6c7c70/dqc_reference/checkm_data
[2024-01-24 12:22:53,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:53,366] [INFO] Task started: CheckM
[2024-01-24 12:22:53,366] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002262875.1_ASM226287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002262875.1_ASM226287v1_genomic.fna/checkm_input GCF_002262875.1_ASM226287v1_genomic.fna/checkm_result
[2024-01-24 12:24:00,216] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:00,218] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:00,247] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:00,248] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:00,248] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002262875.1_ASM226287v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:00,249] [INFO] Task started: Blastn
[2024-01-24 12:24:00,249] [INFO] Running command: blastn -query GCF_002262875.1_ASM226287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge573ff0d-b381-4c7b-8868-080b0f6c7c70/dqc_reference/reference_markers_gtdb.fasta -out GCF_002262875.1_ASM226287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:02,368] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:02,372] [INFO] Selected 21 target genomes.
[2024-01-24 12:24:02,372] [INFO] Target genome list was writen to GCF_002262875.1_ASM226287v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:02,395] [INFO] Task started: fastANI
[2024-01-24 12:24:02,395] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b727f2f-43b5-4add-98e1-e790863b2c37/GCF_002262875.1_ASM226287v1_genomic.fna.gz --refList GCF_002262875.1_ASM226287v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002262875.1_ASM226287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:37,742] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:37,758] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:37,759] [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_002262875.1	s__Amycolatopsis antarctica	100.0	2084	2087	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	80.2998	1091	2087	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	80.2903	1103	2087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009429145.1	s__Amycolatopsis sp009429145	80.2267	1110	2087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765355.1	s__Amycolatopsis anabasis	80.098	1079	2087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115565.1	s__Yuhushiella arida	79.9857	935	2087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_016464705.1	s__Saccharomonospora sp016464705	79.8611	899	2087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000231075.2	s__Amycolatopsis sp000231075	79.752	953	2087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.4849	N/A	N/A	N/A	N/A	1	-
GCF_000739085.1	s__Amycolatopsis methanolica	79.7053	925	2087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	96.3446	100.00	100.00	1.00	1.00	2	-
GCF_018736145.1	s__Amycolatopsis sp018736145	79.6871	1071	2087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385185.1	s__Amycolatopsis_D palatopharyngis	79.6353	860	2087	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_900110575.1	s__Amycolatopsis saalfeldensis	79.622	999	2087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111885.1	s__Amycolatopsis_D marina	79.6174	903	2087	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_014654365.1	s__Amycolatopsis oliviviridis	79.5101	1013	2087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114035.1	s__Amycolatopsis sacchari	79.508	878	2087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107045.1	s__Amycolatopsis xylanica	79.4429	984	2087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654205.1	s__Amycolatopsis bullii	79.3797	980	2087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002904295.1	s__Amycolatopsis sp002904295	79.3525	1007	2087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902497555.1	s__Amycolatopsis sp902497555	79.351	1040	2087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007713735.2	s__Amycolatopsis acidicola	79.3438	863	2087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002904335.1	s__Amycolatopsis sp002904335	79.3422	1012	2087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:37,760] [INFO] GTDB search result was written to GCF_002262875.1_ASM226287v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:37,761] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:37,766] [INFO] DFAST_QC result json was written to GCF_002262875.1_ASM226287v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:37,766] [INFO] DFAST_QC completed!
[2024-01-24 12:24:37,766] [INFO] Total running time: 0h2m53s