[2024-01-24 13:56:27,230] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:27,232] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:27,232] [INFO] DQC Reference Directory: /var/lib/cwl/stg9eff3dd0-8638-4f03-b0c3-a1604d1b6c9e/dqc_reference
[2024-01-24 13:56:28,450] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:28,451] [INFO] Task started: Prodigal
[2024-01-24 13:56:28,451] [INFO] Running command: gunzip -c /var/lib/cwl/stge328b96a-e1a7-4f74-94b2-2bb4281aefe4/GCF_007830095.1_ASM783009v1_genomic.fna.gz | prodigal -d GCF_007830095.1_ASM783009v1_genomic.fna/cds.fna -a GCF_007830095.1_ASM783009v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:59,421] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:59,422] [INFO] Task started: HMMsearch
[2024-01-24 13:56:59,422] [INFO] Running command: hmmsearch --tblout GCF_007830095.1_ASM783009v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9eff3dd0-8638-4f03-b0c3-a1604d1b6c9e/dqc_reference/reference_markers.hmm GCF_007830095.1_ASM783009v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:59,752] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:59,754] [INFO] Found 6/6 markers.
[2024-01-24 13:56:59,816] [INFO] Query marker FASTA was written to GCF_007830095.1_ASM783009v1_genomic.fna/markers.fasta
[2024-01-24 13:56:59,817] [INFO] Task started: Blastn
[2024-01-24 13:56:59,817] [INFO] Running command: blastn -query GCF_007830095.1_ASM783009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9eff3dd0-8638-4f03-b0c3-a1604d1b6c9e/dqc_reference/reference_markers.fasta -out GCF_007830095.1_ASM783009v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:01,007] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:01,011] [INFO] Selected 20 target genomes.
[2024-01-24 13:57:01,012] [INFO] Target genome list was writen to GCF_007830095.1_ASM783009v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:01,029] [INFO] Task started: fastANI
[2024-01-24 13:57:01,029] [INFO] Running command: fastANI --query /var/lib/cwl/stge328b96a-e1a7-4f74-94b2-2bb4281aefe4/GCF_007830095.1_ASM783009v1_genomic.fna.gz --refList GCF_007830095.1_ASM783009v1_genomic.fna/target_genomes.txt --output GCF_007830095.1_ASM783009v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:39,496] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:39,496] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9eff3dd0-8638-4f03-b0c3-a1604d1b6c9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:39,497] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9eff3dd0-8638-4f03-b0c3-a1604d1b6c9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:39,520] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:39,521] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:57:39,521] [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 taraxaci	strain=DSM 45885	GCA_007830095.1	1316803	1316803	type	True	100.0	2401	2402	95	inconclusive
Micromonospora chokoriensis	strain=DSM 45160	GCA_900091505.1	356851	356851	type	True	95.0326	2054	2402	95	inconclusive
Micromonospora jinlongensis	strain=DSM 45876	GCA_013410645.1	1287877	1287877	type	True	91.0738	1927	2402	95	below_threshold
Micromonospora zamorensis	strain=DSM 45600	GCA_900090275.1	709883	709883	type	True	90.8435	1964	2402	95	below_threshold
Micromonospora vinacea	strain=DSM 101695	GCA_015751785.1	709878	709878	type	True	90.3927	1956	2402	95	below_threshold
Micromonospora saelicesensis	strain=DSM 44871	GCA_900091575.1	285676	285676	type	True	90.3799	1940	2402	95	below_threshold
Micromonospora arida	strain=LB32	GCA_003857035.1	2203715	2203715	type	True	90.2377	1765	2402	95	below_threshold
Micromonospora violae	strain=DSM 45888	GCA_004217135.1	1278207	1278207	type	True	89.9968	1887	2402	95	below_threshold
Micromonospora parathelypteridis	strain=DSM 103125	GCA_014201145.1	1839617	1839617	type	True	89.9239	1867	2402	95	below_threshold
Micromonospora inaquosa	strain=LB39	GCA_003857055.1	2203716	2203716	type	True	89.9123	1718	2402	95	below_threshold
Micromonospora orduensis	strain=S2509	GCA_006228125.1	1420891	1420891	type	True	89.0901	1635	2402	95	below_threshold
Micromonospora coriariae	strain=DSM 44875	GCA_900091455.1	285665	285665	type	True	88.5942	1684	2402	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	88.5504	1527	2402	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	85.156	1127	2402	95	below_threshold
Micromonospora peucetia	strain=DSM 43363	GCA_900091625.1	47871	47871	type	True	84.2735	1447	2402	95	below_threshold
Micromonospora mirobrigensis	strain=DSM 44830	GCA_900091555.1	262898	262898	type	True	84.2123	1370	2402	95	below_threshold
Micromonospora siamensis	strain=DSM 45097	GCA_900090305.1	299152	299152	type	True	84.1421	1372	2402	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	83.6961	1471	2402	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	83.6818	1476	2402	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.2528	1342	2402	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:39,522] [INFO] DFAST Taxonomy check result was written to GCF_007830095.1_ASM783009v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:39,523] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:39,523] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:39,523] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9eff3dd0-8638-4f03-b0c3-a1604d1b6c9e/dqc_reference/checkm_data
[2024-01-24 13:57:39,524] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:39,598] [INFO] Task started: CheckM
[2024-01-24 13:57:39,598] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830095.1_ASM783009v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830095.1_ASM783009v1_genomic.fna/checkm_input GCF_007830095.1_ASM783009v1_genomic.fna/checkm_result
[2024-01-24 13:59:35,441] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:35,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:35,468] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:35,468] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:35,469] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830095.1_ASM783009v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:35,469] [INFO] Task started: Blastn
[2024-01-24 13:59:35,469] [INFO] Running command: blastn -query GCF_007830095.1_ASM783009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9eff3dd0-8638-4f03-b0c3-a1604d1b6c9e/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830095.1_ASM783009v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:37,308] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:37,312] [INFO] Selected 21 target genomes.
[2024-01-24 13:59:37,312] [INFO] Target genome list was writen to GCF_007830095.1_ASM783009v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:37,381] [INFO] Task started: fastANI
[2024-01-24 13:59:37,381] [INFO] Running command: fastANI --query /var/lib/cwl/stge328b96a-e1a7-4f74-94b2-2bb4281aefe4/GCF_007830095.1_ASM783009v1_genomic.fna.gz --refList GCF_007830095.1_ASM783009v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830095.1_ASM783009v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:17,187] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:17,204] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:17,204] [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_900091505.1	s__Micromonospora chokoriensis	95.0204	2055	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.10	95.10	0.89	0.89	2	conclusive
GCF_900090275.1	s__Micromonospora zamorensis	90.8436	1964	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.71	96.30	0.91	0.89	6	-
GCF_900091575.1	s__Micromonospora saelicesensis	90.3846	1939	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	96.6221	98.85	97.77	0.96	0.92	6	-
GCF_015751785.1	s__Micromonospora vinacea	90.3603	1960	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003264365.1	s__Micromonospora noduli	90.2234	1873	2402	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	90.2099	1769	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	96.1103	N/A	N/A	N/A	N/A	1	-
GCF_000718555.1	s__Micromonospora chokoriensis_B	90.1496	1814	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718515.1	s__Micromonospora parva	90.1225	1889	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.24	99.24	0.97	0.97	2	-
GCF_004217135.1	s__Micromonospora violae	89.9744	1888	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201145.1	s__Micromonospora parathelypteridis	89.936	1866	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003857055.1	s__Micromonospora inaquosa	89.8931	1720	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803395.1	s__Micromonospora sp016803395	89.8626	1614	2402	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	89.7788	1796	2402	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	89.6624	1786	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016802865.1	s__Micromonospora sp016802865	88.8543	1537	2402	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	88.609	1612	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.83	98.83	0.94	0.94	2	-
GCF_900091455.1	s__Micromonospora coriariae	88.5624	1690	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070045.1	s__Micromonospora sp018070045	88.4637	1705	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000297395.2	s__Micromonospora lupini	88.2634	1853	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090305.1	s__Micromonospora siamensis	84.1713	1367	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091555.1	s__Micromonospora mirobrigensis	84.1629	1378	2402	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 14:00:17,206] [INFO] GTDB search result was written to GCF_007830095.1_ASM783009v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:17,207] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:17,211] [INFO] DFAST_QC result json was written to GCF_007830095.1_ASM783009v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:17,211] [INFO] DFAST_QC completed!
[2024-01-24 14:00:17,212] [INFO] Total running time: 0h3m50s