[2024-01-25 18:25:20,586] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:25:20,587] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:25:20,587] [INFO] DQC Reference Directory: /var/lib/cwl/stg6734e047-4ea2-448a-8665-d2973b1ca3b5/dqc_reference
[2024-01-25 18:25:21,758] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:25:21,758] [INFO] Task started: Prodigal
[2024-01-25 18:25:21,759] [INFO] Running command: gunzip -c /var/lib/cwl/stg434c885a-e4c7-44e0-8a46-865a327b4da2/GCF_000384295.1_ASM38429v1_genomic.fna.gz | prodigal -d GCF_000384295.1_ASM38429v1_genomic.fna/cds.fna -a GCF_000384295.1_ASM38429v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:25:50,552] [INFO] Task succeeded: Prodigal
[2024-01-25 18:25:50,552] [INFO] Task started: HMMsearch
[2024-01-25 18:25:50,552] [INFO] Running command: hmmsearch --tblout GCF_000384295.1_ASM38429v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6734e047-4ea2-448a-8665-d2973b1ca3b5/dqc_reference/reference_markers.hmm GCF_000384295.1_ASM38429v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:25:51,050] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:25:51,051] [INFO] Found 6/6 markers.
[2024-01-25 18:25:51,130] [INFO] Query marker FASTA was written to GCF_000384295.1_ASM38429v1_genomic.fna/markers.fasta
[2024-01-25 18:25:51,130] [INFO] Task started: Blastn
[2024-01-25 18:25:51,130] [INFO] Running command: blastn -query GCF_000384295.1_ASM38429v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6734e047-4ea2-448a-8665-d2973b1ca3b5/dqc_reference/reference_markers.fasta -out GCF_000384295.1_ASM38429v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:25:52,427] [INFO] Task succeeded: Blastn
[2024-01-25 18:25:52,430] [INFO] Selected 16 target genomes.
[2024-01-25 18:25:52,431] [INFO] Target genome list was writen to GCF_000384295.1_ASM38429v1_genomic.fna/target_genomes.txt
[2024-01-25 18:25:52,450] [INFO] Task started: fastANI
[2024-01-25 18:25:52,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg434c885a-e4c7-44e0-8a46-865a327b4da2/GCF_000384295.1_ASM38429v1_genomic.fna.gz --refList GCF_000384295.1_ASM38429v1_genomic.fna/target_genomes.txt --output GCF_000384295.1_ASM38429v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:26:35,466] [INFO] Task succeeded: fastANI
[2024-01-25 18:26:35,466] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6734e047-4ea2-448a-8665-d2973b1ca3b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:26:35,467] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6734e047-4ea2-448a-8665-d2973b1ca3b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:26:35,477] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:26:35,477] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:26:35,478] [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 balhimycina	strain=DSM 44591	GCA_000384295.1	208443	208443	type	True	100.0	3615	3619	95	conclusive
Amycolatopsis vastitatis	strain=H5	GCA_002234595.1	1905142	1905142	type	True	93.3854	2679	3619	95	below_threshold
Amycolatopsis mediterranei	strain=S699	GCA_000220945.1	33910	33910	type	True	89.9656	2529	3619	95	below_threshold
Amycolatopsis kentuckyensis	strain=NRRL B-24129	GCA_002155975.1	218823	218823	type	True	89.7727	2139	3619	95	below_threshold
Amycolatopsis rifamycinica	strain=DSM 46095	GCA_000695625.1	287986	287986	type	True	89.6842	2289	3619	95	below_threshold
Amycolatopsis vancoresmycina	strain=NRRL B-24208	GCA_000716785.1	208444	208444	type	True	89.6204	2425	3619	95	below_threshold
Amycolatopsis vancoresmycina	strain=DSM 44592	GCA_000388135.1	208444	208444	type	True	89.5918	2029	3619	95	below_threshold
Amycolatopsis tolypomycina	strain=DSM 44544	GCA_900105945.1	208445	208445	type	True	89.4706	2475	3619	95	below_threshold
Amycolatopsis lexingtonensis	strain=NRRL B-24131	GCA_002156005.1	218822	218822	type	True	88.6068	2134	3619	95	below_threshold
Amycolatopsis eburnea	strain=GLM-1	GCA_003937945.1	2267691	2267691	type	True	88.5584	2372	3619	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	88.5534	2461	3619	95	below_threshold
Amycolatopsis pretoriensis	strain=NRRL B-24133	GCA_002156025.1	218821	218821	type	True	88.3035	2144	3619	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	80.2532	1245	3619	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.0718	1118	3619	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	78.5956	1121	3619	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.1294	956	3619	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:26:35,479] [INFO] DFAST Taxonomy check result was written to GCF_000384295.1_ASM38429v1_genomic.fna/tc_result.tsv
[2024-01-25 18:26:35,479] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:26:35,480] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:26:35,480] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6734e047-4ea2-448a-8665-d2973b1ca3b5/dqc_reference/checkm_data
[2024-01-25 18:26:35,481] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:26:35,577] [INFO] Task started: CheckM
[2024-01-25 18:26:35,577] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000384295.1_ASM38429v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000384295.1_ASM38429v1_genomic.fna/checkm_input GCF_000384295.1_ASM38429v1_genomic.fna/checkm_result
[2024-01-25 18:29:21,482] [INFO] Task succeeded: CheckM
[2024-01-25 18:29:21,484] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:29:21,504] [INFO] ===== Completeness check finished =====
[2024-01-25 18:29:21,504] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:29:21,505] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000384295.1_ASM38429v1_genomic.fna/markers.fasta)
[2024-01-25 18:29:21,505] [INFO] Task started: Blastn
[2024-01-25 18:29:21,505] [INFO] Running command: blastn -query GCF_000384295.1_ASM38429v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6734e047-4ea2-448a-8665-d2973b1ca3b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000384295.1_ASM38429v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:29:23,473] [INFO] Task succeeded: Blastn
[2024-01-25 18:29:23,476] [INFO] Selected 13 target genomes.
[2024-01-25 18:29:23,476] [INFO] Target genome list was writen to GCF_000384295.1_ASM38429v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:29:23,487] [INFO] Task started: fastANI
[2024-01-25 18:29:23,487] [INFO] Running command: fastANI --query /var/lib/cwl/stg434c885a-e4c7-44e0-8a46-865a327b4da2/GCF_000384295.1_ASM38429v1_genomic.fna.gz --refList GCF_000384295.1_ASM38429v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000384295.1_ASM38429v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:30:04,984] [INFO] Task succeeded: fastANI
[2024-01-25 18:30:05,005] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:30:05,005] [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_000384295.1	s__Amycolatopsis balhimycina	100.0	3615	3619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_002234595.1	s__Amycolatopsis vastitatis	93.3749	2680	3619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220945.1	s__Amycolatopsis mediterranei	89.9647	2529	3619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	0.99	7	-
GCF_002904335.1	s__Amycolatopsis sp002904335	89.7713	2441	3619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155975.1	s__Amycolatopsis kentuckyensis	89.7357	2143	3619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716785.1	s__Amycolatopsis vancoresmycina	89.6787	2416	3619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000695625.1	s__Amycolatopsis rifamycinica	89.6764	2290	3619	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	89.6714	2319	3619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017308975.1	s__Amycolatopsis sp017308975	89.5019	2468	3619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105945.1	s__Amycolatopsis tolypomycina	89.4566	2475	3619	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	89.2451	2342	3619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364075.1	s__Amycolatopsis sp013364075	89.09	2507	3619	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	88.5411	2464	3619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:30:05,006] [INFO] GTDB search result was written to GCF_000384295.1_ASM38429v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:30:05,007] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:30:05,011] [INFO] DFAST_QC result json was written to GCF_000384295.1_ASM38429v1_genomic.fna/dqc_result.json
[2024-01-25 18:30:05,011] [INFO] DFAST_QC completed!
[2024-01-25 18:30:05,011] [INFO] Total running time: 0h4m44s