[2024-01-24 11:43:34,998] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:35,000] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:35,001] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc7b624f-a811-46cb-86c3-22e202df8a42/dqc_reference
[2024-01-24 11:43:36,209] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:36,209] [INFO] Task started: Prodigal
[2024-01-24 11:43:36,210] [INFO] Running command: gunzip -c /var/lib/cwl/stg178d24fd-6ca6-443c-859d-217841017e6e/GCF_003857055.1_ASM385705v1_genomic.fna.gz | prodigal -d GCF_003857055.1_ASM385705v1_genomic.fna/cds.fna -a GCF_003857055.1_ASM385705v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:57,212] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:57,213] [INFO] Task started: HMMsearch
[2024-01-24 11:43:57,213] [INFO] Running command: hmmsearch --tblout GCF_003857055.1_ASM385705v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc7b624f-a811-46cb-86c3-22e202df8a42/dqc_reference/reference_markers.hmm GCF_003857055.1_ASM385705v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:57,561] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:57,563] [INFO] Found 6/6 markers.
[2024-01-24 11:43:57,628] [INFO] Query marker FASTA was written to GCF_003857055.1_ASM385705v1_genomic.fna/markers.fasta
[2024-01-24 11:43:57,628] [INFO] Task started: Blastn
[2024-01-24 11:43:57,628] [INFO] Running command: blastn -query GCF_003857055.1_ASM385705v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc7b624f-a811-46cb-86c3-22e202df8a42/dqc_reference/reference_markers.fasta -out GCF_003857055.1_ASM385705v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:58,791] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:58,795] [INFO] Selected 14 target genomes.
[2024-01-24 11:43:58,796] [INFO] Target genome list was writen to GCF_003857055.1_ASM385705v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:58,802] [INFO] Task started: fastANI
[2024-01-24 11:43:58,802] [INFO] Running command: fastANI --query /var/lib/cwl/stg178d24fd-6ca6-443c-859d-217841017e6e/GCF_003857055.1_ASM385705v1_genomic.fna.gz --refList GCF_003857055.1_ASM385705v1_genomic.fna/target_genomes.txt --output GCF_003857055.1_ASM385705v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:24,720] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:24,721] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc7b624f-a811-46cb-86c3-22e202df8a42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:24,722] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc7b624f-a811-46cb-86c3-22e202df8a42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:24,740] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:24,740] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:24,740] [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
Micromonospora inaquosa	strain=LB39	GCA_003857055.1	2203716	2203716	type	True	100.0	2368	2386	95	conclusive
Micromonospora saelicesensis	strain=DSM 44871	GCA_900091575.1	285676	285676	type	True	92.9969	1810	2386	95	below_threshold
Micromonospora ureilytica	strain=DSM 101692	GCA_015751765.1	709868	709868	type	True	92.9898	1723	2386	95	below_threshold
Micromonospora noduli	strain=GUI43	GCA_003264365.1	709876	709876	type	True	92.9416	1759	2386	95	below_threshold
Micromonospora arida	strain=LB32	GCA_003857035.1	2203715	2203715	type	True	92.9108	1651	2386	95	below_threshold
Micromonospora vinacea	strain=DSM 101695	GCA_015751785.1	709878	709878	type	True	92.8246	1799	2386	95	below_threshold
Micromonospora violae	strain=DSM 45888	GCA_004217135.1	1278207	1278207	type	True	92.3796	1780	2386	95	below_threshold
Micromonospora luteifusca	strain=DSM 100204	GCA_016907275.1	709860	709860	type	True	89.9934	1685	2386	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	88.6502	1438	2386	95	below_threshold
Micromonospora cremea	strain=DSM 45599	GCA_900143515.1	709881	709881	type	True	88.3595	1622	2386	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	85.1367	1073	2386	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	83.6488	1355	2386	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	76.3966	499	2386	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	76.3104	512	2386	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:24,742] [INFO] DFAST Taxonomy check result was written to GCF_003857055.1_ASM385705v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:24,743] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:24,743] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:24,743] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc7b624f-a811-46cb-86c3-22e202df8a42/dqc_reference/checkm_data
[2024-01-24 11:44:24,744] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:24,815] [INFO] Task started: CheckM
[2024-01-24 11:44:24,815] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003857055.1_ASM385705v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003857055.1_ASM385705v1_genomic.fna/checkm_input GCF_003857055.1_ASM385705v1_genomic.fna/checkm_result
[2024-01-24 11:45:34,396] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:34,398] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:34,424] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:34,424] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:34,424] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003857055.1_ASM385705v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:34,425] [INFO] Task started: Blastn
[2024-01-24 11:45:34,425] [INFO] Running command: blastn -query GCF_003857055.1_ASM385705v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc7b624f-a811-46cb-86c3-22e202df8a42/dqc_reference/reference_markers_gtdb.fasta -out GCF_003857055.1_ASM385705v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:36,188] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:36,192] [INFO] Selected 15 target genomes.
[2024-01-24 11:45:36,193] [INFO] Target genome list was writen to GCF_003857055.1_ASM385705v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:36,204] [INFO] Task started: fastANI
[2024-01-24 11:45:36,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg178d24fd-6ca6-443c-859d-217841017e6e/GCF_003857055.1_ASM385705v1_genomic.fna.gz --refList GCF_003857055.1_ASM385705v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003857055.1_ASM385705v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:01,745] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:01,768] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:01,769] [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_003857055.1	s__Micromonospora inaquosa	100.0	2368	2386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000718515.1	s__Micromonospora parva	93.4066	1827	2386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.24	99.24	0.97	0.97	2	-
GCF_900091575.1	s__Micromonospora saelicesensis	93.0071	1809	2386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	96.6221	98.85	97.77	0.96	0.92	6	-
GCF_015751765.1	s__Micromonospora ureilytica	92.9944	1722	2386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	97.34	0.88	0.87	3	-
GCF_003264365.1	s__Micromonospora noduli	92.9482	1758	2386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	96.6221	98.92	97.90	0.94	0.91	8	-
GCF_003857035.1	s__Micromonospora arida	92.9135	1650	2386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	96.1103	N/A	N/A	N/A	N/A	1	-
GCF_018070325.1	s__Micromonospora sp018070325	92.8473	1731	2386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.6333	N/A	N/A	N/A	N/A	1	-
GCF_015751785.1	s__Micromonospora vinacea	92.8347	1798	2386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217135.1	s__Micromonospora violae	92.3898	1779	2386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718555.1	s__Micromonospora chokoriensis_B	91.7587	1663	2386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907275.1	s__Micromonospora luteifusca	90.0128	1683	2386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091505.1	s__Micromonospora chokoriensis	89.5917	1670	2386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.10	95.10	0.89	0.89	2	-
GCF_003172955.1	s__Micromonospora sp003172955	88.6597	1437	2386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090245.1	s__Micromonospora halophytica	84.169	1261	2386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900089595.1	s__Micromonospora auratinigra	84.0975	1323	2386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:01,770] [INFO] GTDB search result was written to GCF_003857055.1_ASM385705v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:01,774] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:01,778] [INFO] DFAST_QC result json was written to GCF_003857055.1_ASM385705v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:01,778] [INFO] DFAST_QC completed!
[2024-01-24 11:46:01,778] [INFO] Total running time: 0h2m27s