[2024-01-24 11:21:07,408] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:21:07,409] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:21:07,410] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d0521d1-d0c8-4f84-b196-ef1c65ab51aa/dqc_reference
[2024-01-24 11:21:11,962] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:21:11,963] [INFO] Task started: Prodigal
[2024-01-24 11:21:11,964] [INFO] Running command: gunzip -c /var/lib/cwl/stgce2238d5-0b75-4a9a-9571-38f4a29fd45c/GCF_014201145.1_ASM1420114v1_genomic.fna.gz | prodigal -d GCF_014201145.1_ASM1420114v1_genomic.fna/cds.fna -a GCF_014201145.1_ASM1420114v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:34,014] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:34,015] [INFO] Task started: HMMsearch
[2024-01-24 11:21:34,015] [INFO] Running command: hmmsearch --tblout GCF_014201145.1_ASM1420114v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d0521d1-d0c8-4f84-b196-ef1c65ab51aa/dqc_reference/reference_markers.hmm GCF_014201145.1_ASM1420114v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:34,330] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:34,332] [INFO] Found 6/6 markers.
[2024-01-24 11:21:34,389] [INFO] Query marker FASTA was written to GCF_014201145.1_ASM1420114v1_genomic.fna/markers.fasta
[2024-01-24 11:21:34,390] [INFO] Task started: Blastn
[2024-01-24 11:21:34,390] [INFO] Running command: blastn -query GCF_014201145.1_ASM1420114v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d0521d1-d0c8-4f84-b196-ef1c65ab51aa/dqc_reference/reference_markers.fasta -out GCF_014201145.1_ASM1420114v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:35,543] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:35,547] [INFO] Selected 16 target genomes.
[2024-01-24 11:21:35,548] [INFO] Target genome list was writen to GCF_014201145.1_ASM1420114v1_genomic.fna/target_genomes.txt
[2024-01-24 11:21:35,557] [INFO] Task started: fastANI
[2024-01-24 11:21:35,557] [INFO] Running command: fastANI --query /var/lib/cwl/stgce2238d5-0b75-4a9a-9571-38f4a29fd45c/GCF_014201145.1_ASM1420114v1_genomic.fna.gz --refList GCF_014201145.1_ASM1420114v1_genomic.fna/target_genomes.txt --output GCF_014201145.1_ASM1420114v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:22:04,100] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:04,100] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d0521d1-d0c8-4f84-b196-ef1c65ab51aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:22:04,101] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d0521d1-d0c8-4f84-b196-ef1c65ab51aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:22:04,114] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:22:04,114] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:22:04,115] [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 parathelypteridis	strain=DSM 103125	GCA_014201145.1	1839617	1839617	type	True	100.0	2337	2338	95	conclusive
Micromonospora parathelypteridis	strain=CGMCC 4.7347	GCA_014646315.1	1839617	1839617	type	True	99.9906	2319	2338	95	conclusive
Micromonospora luteifusca	strain=DSM 100204	GCA_016907275.1	709860	709860	type	True	93.9941	1924	2338	95	below_threshold
Micromonospora jinlongensis	strain=DSM 45876	GCA_013410645.1	1287877	1287877	type	True	90.6215	1802	2338	95	below_threshold
Micromonospora saelicesensis	strain=DSM 44871	GCA_900091575.1	285676	285676	type	True	90.6196	1833	2338	95	below_threshold
Micromonospora zamorensis	strain=DSM 45600	GCA_900090275.1	709883	709883	type	True	90.5967	1811	2338	95	below_threshold
Micromonospora noduli	strain=GUI43	GCA_003264365.1	709876	709876	type	True	90.5541	1773	2338	95	below_threshold
Micromonospora vinacea	strain=DSM 101695	GCA_015751785.1	709878	709878	type	True	90.5063	1872	2338	95	below_threshold
Micromonospora ureilytica	strain=DSM 101692	GCA_015751765.1	709868	709868	type	True	90.4582	1794	2338	95	below_threshold
Micromonospora inaquosa	strain=LB39	GCA_003857055.1	2203716	2203716	type	True	90.1718	1605	2338	95	below_threshold
Micromonospora cremea	strain=DSM 45599	GCA_900143515.1	709881	709881	type	True	89.3556	1732	2338	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	89.2238	1530	2338	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	85.3516	1108	2338	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	83.7339	1422	2338	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	83.7323	1409	2338	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	82.9849	1354	2338	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:22:04,116] [INFO] DFAST Taxonomy check result was written to GCF_014201145.1_ASM1420114v1_genomic.fna/tc_result.tsv
[2024-01-24 11:22:04,117] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:22:04,117] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:22:04,117] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d0521d1-d0c8-4f84-b196-ef1c65ab51aa/dqc_reference/checkm_data
[2024-01-24 11:22:04,118] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:22:04,179] [INFO] Task started: CheckM
[2024-01-24 11:22:04,179] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201145.1_ASM1420114v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201145.1_ASM1420114v1_genomic.fna/checkm_input GCF_014201145.1_ASM1420114v1_genomic.fna/checkm_result
[2024-01-24 11:23:24,694] [INFO] Task succeeded: CheckM
[2024-01-24 11:23:24,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:23:24,717] [INFO] ===== Completeness check finished =====
[2024-01-24 11:23:24,718] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:23:24,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201145.1_ASM1420114v1_genomic.fna/markers.fasta)
[2024-01-24 11:23:24,719] [INFO] Task started: Blastn
[2024-01-24 11:23:24,720] [INFO] Running command: blastn -query GCF_014201145.1_ASM1420114v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d0521d1-d0c8-4f84-b196-ef1c65ab51aa/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201145.1_ASM1420114v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:26,445] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:26,449] [INFO] Selected 13 target genomes.
[2024-01-24 11:23:26,449] [INFO] Target genome list was writen to GCF_014201145.1_ASM1420114v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:23:26,458] [INFO] Task started: fastANI
[2024-01-24 11:23:26,458] [INFO] Running command: fastANI --query /var/lib/cwl/stgce2238d5-0b75-4a9a-9571-38f4a29fd45c/GCF_014201145.1_ASM1420114v1_genomic.fna.gz --refList GCF_014201145.1_ASM1420114v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201145.1_ASM1420114v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:23:50,144] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:50,158] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:23:50,159] [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_014201145.1	s__Micromonospora parathelypteridis	100.0	2338	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_016907275.1	s__Micromonospora luteifusca	94.0073	1925	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003205615.1	s__Micromonospora arborensis	93.943	1843	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091575.1	s__Micromonospora saelicesensis	90.6155	1833	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	96.6221	98.85	97.77	0.96	0.92	6	-
GCF_900090275.1	s__Micromonospora zamorensis	90.5974	1813	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.71	96.30	0.91	0.89	6	-
GCF_003264365.1	s__Micromonospora noduli	90.5503	1775	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	96.6221	98.92	97.90	0.94	0.91	8	-
GCF_000718555.1	s__Micromonospora chokoriensis_B	90.5359	1712	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015751785.1	s__Micromonospora vinacea	90.4882	1875	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015751765.1	s__Micromonospora ureilytica	90.4775	1791	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	97.34	0.88	0.87	3	-
GCF_018070325.1	s__Micromonospora sp018070325	90.4279	1731	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.6333	N/A	N/A	N/A	N/A	1	-
GCF_003857055.1	s__Micromonospora inaquosa	90.1811	1605	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667505.1	s__Micromonospora sp003667505	89.4036	1637	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.83	98.83	0.94	0.94	2	-
GCF_003172955.1	s__Micromonospora sp003172955	89.2625	1525	2338	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 11:23:50,160] [INFO] GTDB search result was written to GCF_014201145.1_ASM1420114v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:23:50,161] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:23:50,164] [INFO] DFAST_QC result json was written to GCF_014201145.1_ASM1420114v1_genomic.fna/dqc_result.json
[2024-01-24 11:23:50,165] [INFO] DFAST_QC completed!
[2024-01-24 11:23:50,165] [INFO] Total running time: 0h2m43s