[2024-01-24 15:02:24,209] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:24,213] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:24,214] [INFO] DQC Reference Directory: /var/lib/cwl/stgc10e6737-6c89-4ac1-a664-faf0c64acaa7/dqc_reference
[2024-01-24 15:02:26,425] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:26,426] [INFO] Task started: Prodigal
[2024-01-24 15:02:26,426] [INFO] Running command: gunzip -c /var/lib/cwl/stg0654db42-a3b2-4858-9642-1fe712324fe6/GCF_014205155.1_ASM1420515v1_genomic.fna.gz | prodigal -d GCF_014205155.1_ASM1420515v1_genomic.fna/cds.fna -a GCF_014205155.1_ASM1420515v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:54,992] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:54,993] [INFO] Task started: HMMsearch
[2024-01-24 15:02:54,993] [INFO] Running command: hmmsearch --tblout GCF_014205155.1_ASM1420515v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc10e6737-6c89-4ac1-a664-faf0c64acaa7/dqc_reference/reference_markers.hmm GCF_014205155.1_ASM1420515v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:55,447] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:55,449] [INFO] Found 6/6 markers.
[2024-01-24 15:02:55,523] [INFO] Query marker FASTA was written to GCF_014205155.1_ASM1420515v1_genomic.fna/markers.fasta
[2024-01-24 15:02:55,523] [INFO] Task started: Blastn
[2024-01-24 15:02:55,523] [INFO] Running command: blastn -query GCF_014205155.1_ASM1420515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc10e6737-6c89-4ac1-a664-faf0c64acaa7/dqc_reference/reference_markers.fasta -out GCF_014205155.1_ASM1420515v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:56,859] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:56,863] [INFO] Selected 17 target genomes.
[2024-01-24 15:02:56,863] [INFO] Target genome list was writen to GCF_014205155.1_ASM1420515v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:56,870] [INFO] Task started: fastANI
[2024-01-24 15:02:56,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg0654db42-a3b2-4858-9642-1fe712324fe6/GCF_014205155.1_ASM1420515v1_genomic.fna.gz --refList GCF_014205155.1_ASM1420515v1_genomic.fna/target_genomes.txt --output GCF_014205155.1_ASM1420515v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:38,162] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:38,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc10e6737-6c89-4ac1-a664-faf0c64acaa7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:38,163] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc10e6737-6c89-4ac1-a664-faf0c64acaa7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:38,178] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:38,178] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:38,178] [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 umgeniensis	strain=DSM 45272	GCA_014205155.1	336628	336628	type	True	100.0	3074	3075	95	conclusive
Amycolatopsis alba	strain=DSM 44262	GCA_000384215.1	76020	76020	type	True	91.6728	2466	3075	95	below_threshold
Amycolatopsis alba	strain=DSM 44262	GCA_002234385.1	76020	76020	type	True	91.5772	2315	3075	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_001995215.1	36819	36819	type	True	91.5541	2496	3075	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_000340415.1	36819	36819	type	True	91.5109	2471	3075	95	below_threshold
Amycolatopsis thailandensis	strain=JCM 16380	GCA_002234405.1	589330	589330	type	True	91.4179	2287	3075	95	below_threshold
Amycolatopsis coloradensis	strain=DSM 44225	GCA_001953865.1	76021	76021	type	True	90.8876	2293	3075	95	below_threshold
Amycolatopsis keratiniphila subsp. nogabecina	strain=FH 1893	GCA_001953855.1	208442	129921	type	True	90.5824	2413	3075	95	below_threshold
Amycolatopsis orientalis	strain=KCTC 9412	GCA_000478275.1	31958	31958	type	True	90.4284	2309	3075	95	below_threshold
Amycolatopsis pittospori	strain=PIP199	GCA_013870525.1	2749434	2749434	type	True	90.2517	2206	3075	95	below_threshold
Amycolatopsis regifaucium	strain=GY080	GCA_001558125.2	546365	546365	type	True	90.1254	2183	3075	95	below_threshold
Amycolatopsis regifaucium	strain=GY080	GCA_001613935.1	546365	546365	type	True	90.083	2198	3075	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	81.4726	1717	3075	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.6723	1080	3075	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	78.9007	1018	3075	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	78.7663	1036	3075	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	77.891	824	3075	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:38,180] [INFO] DFAST Taxonomy check result was written to GCF_014205155.1_ASM1420515v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:38,181] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:38,181] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:38,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc10e6737-6c89-4ac1-a664-faf0c64acaa7/dqc_reference/checkm_data
[2024-01-24 15:03:38,182] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:38,270] [INFO] Task started: CheckM
[2024-01-24 15:03:38,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014205155.1_ASM1420515v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014205155.1_ASM1420515v1_genomic.fna/checkm_input GCF_014205155.1_ASM1420515v1_genomic.fna/checkm_result
[2024-01-24 15:05:26,821] [INFO] Task succeeded: CheckM
[2024-01-24 15:05:26,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.94%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:05:26,852] [INFO] ===== Completeness check finished =====
[2024-01-24 15:05:26,852] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:05:26,853] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014205155.1_ASM1420515v1_genomic.fna/markers.fasta)
[2024-01-24 15:05:26,853] [INFO] Task started: Blastn
[2024-01-24 15:05:26,853] [INFO] Running command: blastn -query GCF_014205155.1_ASM1420515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc10e6737-6c89-4ac1-a664-faf0c64acaa7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014205155.1_ASM1420515v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:05:28,988] [INFO] Task succeeded: Blastn
[2024-01-24 15:05:28,993] [INFO] Selected 15 target genomes.
[2024-01-24 15:05:28,993] [INFO] Target genome list was writen to GCF_014205155.1_ASM1420515v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:05:29,031] [INFO] Task started: fastANI
[2024-01-24 15:05:29,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg0654db42-a3b2-4858-9642-1fe712324fe6/GCF_014205155.1_ASM1420515v1_genomic.fna.gz --refList GCF_014205155.1_ASM1420515v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014205155.1_ASM1420515v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:06:04,161] [INFO] Task succeeded: fastANI
[2024-01-24 15:06:04,176] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:06:04,176] [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_014205155.1	s__Amycolatopsis umgeniensis	100.0	3075	3075	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_002849735.1	s__Amycolatopsis sp002849735	93.2183	2597	3075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000384215.1	s__Amycolatopsis alba	91.6728	2466	3075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001995215.1	s__Amycolatopsis azurea	91.5611	2495	3075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014654365.1	s__Amycolatopsis oliviviridis	91.5203	2482	3075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002234405.1	s__Amycolatopsis thailandensis	91.4264	2286	3075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003947415.1	s__Amycolatopsis sp003947415	90.9989	2393	3075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	96.38	96.38	0.89	0.88	3	-
GCF_001953865.1	s__Amycolatopsis coloradensis	90.8787	2294	3075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000478275.1	s__Amycolatopsis orientalis	90.454	2305	3075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	96.64	96.64	0.89	0.89	2	-
GCF_013870525.1	s__Amycolatopsis pittospori	90.2418	2208	3075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613935.1	s__Amycolatopsis regifaucium	90.1033	2195	3075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	0.99	0.99	3	-
GCF_014084125.1	s__Streptacidiphilus sp014084125	76.2934	562	3075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005879585.1	s__DP-3 sp005879585	74.8686	198	3075	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__DP-6;g__DP-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903897935.1	s__CAIUDO01 sp903897935	74.6337	249	3075	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__CAIUDO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:06:04,178] [INFO] GTDB search result was written to GCF_014205155.1_ASM1420515v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:06:04,179] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:06:04,183] [INFO] DFAST_QC result json was written to GCF_014205155.1_ASM1420515v1_genomic.fna/dqc_result.json
[2024-01-24 15:06:04,183] [INFO] DFAST_QC completed!
[2024-01-24 15:06:04,183] [INFO] Total running time: 0h3m40s