[2024-01-24 11:58:57,099] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:57,101] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:57,101] [INFO] DQC Reference Directory: /var/lib/cwl/stga31e578b-69a4-4f9b-9340-c21c41c4a29b/dqc_reference
[2024-01-24 11:58:58,436] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:58,437] [INFO] Task started: Prodigal
[2024-01-24 11:58:58,437] [INFO] Running command: gunzip -c /var/lib/cwl/stg7120d59c-9948-4aca-b879-a1b45292a094/GCF_003725545.1_ASM372554v1_genomic.fna.gz | prodigal -d GCF_003725545.1_ASM372554v1_genomic.fna/cds.fna -a GCF_003725545.1_ASM372554v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:13,407] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:13,408] [INFO] Task started: HMMsearch
[2024-01-24 11:59:13,408] [INFO] Running command: hmmsearch --tblout GCF_003725545.1_ASM372554v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga31e578b-69a4-4f9b-9340-c21c41c4a29b/dqc_reference/reference_markers.hmm GCF_003725545.1_ASM372554v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:13,772] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:13,773] [INFO] Found 6/6 markers.
[2024-01-24 11:59:13,836] [INFO] Query marker FASTA was written to GCF_003725545.1_ASM372554v1_genomic.fna/markers.fasta
[2024-01-24 11:59:13,837] [INFO] Task started: Blastn
[2024-01-24 11:59:13,837] [INFO] Running command: blastn -query GCF_003725545.1_ASM372554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga31e578b-69a4-4f9b-9340-c21c41c4a29b/dqc_reference/reference_markers.fasta -out GCF_003725545.1_ASM372554v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:15,119] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:15,123] [INFO] Selected 23 target genomes.
[2024-01-24 11:59:15,123] [INFO] Target genome list was writen to GCF_003725545.1_ASM372554v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:15,135] [INFO] Task started: fastANI
[2024-01-24 11:59:15,136] [INFO] Running command: fastANI --query /var/lib/cwl/stg7120d59c-9948-4aca-b879-a1b45292a094/GCF_003725545.1_ASM372554v1_genomic.fna.gz --refList GCF_003725545.1_ASM372554v1_genomic.fna/target_genomes.txt --output GCF_003725545.1_ASM372554v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:55,043] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:55,043] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga31e578b-69a4-4f9b-9340-c21c41c4a29b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:55,043] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga31e578b-69a4-4f9b-9340-c21c41c4a29b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:55,061] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:59:55,062] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:59:55,062] [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 auratinigra	strain=DSM 44815	GCA_900089595.1	261654	261654	type	True	89.5492	1443	1870	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	89.3997	1447	1870	95	below_threshold
Micromonospora chersina	strain=DSM 44151	GCA_900091475.1	47854	47854	type	True	89.2358	1445	1870	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	89.1212	1397	1870	95	below_threshold
Micromonospora terminaliae	strain=TMS7	GCA_010671825.1	1914461	1914461	type	True	89.0044	1414	1870	95	below_threshold
Micromonospora terminaliae	strain=DSM 101760	GCA_009671205.1	1914461	1914461	type	True	88.9481	1413	1870	95	below_threshold
Micromonospora eburnea	strain=DSM 44814	GCA_900090225.1	227316	227316	type	True	88.429	1380	1870	95	below_threshold
Micromonospora viridifaciens	strain=DSM 43909	GCA_900091545.1	1881	1881	type	True	88.4168	1302	1870	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	87.5782	1381	1870	95	below_threshold
Micromonospora rhizosphaerae	strain=DSM 45431	GCA_900091465.1	568872	568872	type	True	87.4725	1274	1870	95	below_threshold
Micromonospora halophytica	strain=DSM 43171	GCA_900090245.1	47864	47864	type	True	86.6275	1282	1870	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	86.35	1023	1870	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	85.4119	1151	1870	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	85.4091	1289	1870	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	85.3598	1282	1870	95	below_threshold
Micromonospora rifamycinica	strain=AM105	GCA_001542325.1	291594	291594	type	True	85.3381	1163	1870	95	below_threshold
Micromonospora rifamycinica	strain=DSM 44983	GCA_900090265.1	291594	291594	type	True	85.3288	1245	1870	95	below_threshold
Micromonospora nigra	strain=DSM 43818	GCA_900091585.1	145857	145857	type	True	84.3984	1181	1870	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.9014	1155	1870	95	below_threshold
Micromonospora tarapacensis	strain=Llam7	GCA_019697375.1	2835305	2835305	type	True	83.7368	1151	1870	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	83.6828	1149	1870	95	below_threshold
Micromonospora maris	strain=AB-18-032	GCA_000204155.1	1003110	1003110	type	True	83.6824	1153	1870	95	below_threshold
Micromonospora fiedleri	strain=MG-37	GCA_016774385.1	1157498	1157498	type	True	83.5545	1205	1870	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:55,064] [INFO] DFAST Taxonomy check result was written to GCF_003725545.1_ASM372554v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:55,065] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:55,065] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:55,066] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga31e578b-69a4-4f9b-9340-c21c41c4a29b/dqc_reference/checkm_data
[2024-01-24 11:59:55,067] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:55,122] [INFO] Task started: CheckM
[2024-01-24 11:59:55,122] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003725545.1_ASM372554v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003725545.1_ASM372554v1_genomic.fna/checkm_input GCF_003725545.1_ASM372554v1_genomic.fna/checkm_result
[2024-01-24 12:00:48,333] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:48,334] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:48,354] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:48,355] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:48,355] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003725545.1_ASM372554v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:48,355] [INFO] Task started: Blastn
[2024-01-24 12:00:48,355] [INFO] Running command: blastn -query GCF_003725545.1_ASM372554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga31e578b-69a4-4f9b-9340-c21c41c4a29b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003725545.1_ASM372554v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:50,148] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:50,151] [INFO] Selected 18 target genomes.
[2024-01-24 12:00:50,151] [INFO] Target genome list was writen to GCF_003725545.1_ASM372554v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:50,176] [INFO] Task started: fastANI
[2024-01-24 12:00:50,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg7120d59c-9948-4aca-b879-a1b45292a094/GCF_003725545.1_ASM372554v1_genomic.fna.gz --refList GCF_003725545.1_ASM372554v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003725545.1_ASM372554v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:21,969] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:21,984] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:21,984] [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_003725545.1	s__Micromonospora sp003725545	100.0	1860	1870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.98	99.95	0.98	0.97	4	conclusive
GCF_900089595.1	s__Micromonospora auratinigra	89.4881	1451	1870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648395.1	s__Micromonospora fulviviridis	89.4006	1447	1870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.01	95.01	0.74	0.74	2	-
GCF_900091475.1	s__Micromonospora chersina	89.2403	1444	1870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.87	95.82	0.87	0.87	3	-
GCF_000982955.1	s__Micromonospora sp000982955	89.2119	1349	1870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008868175.1	s__Micromonospora sp008868175	89.1242	1287	1870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091435.1	s__Micromonospora chaiyaphumensis	89.0776	1402	1870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.16	95.15	0.86	0.86	3	-
GCF_008119785.1	s__Micromonospora sp008119785	88.7648	1368	1870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905095.1	s__Micromonospora sp001905095	88.5471	1377	1870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091545.1	s__Micromonospora viridifaciens	88.4701	1297	1870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090225.1	s__Micromonospora eburnea	88.4527	1377	1870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091465.1	s__Micromonospora rhizosphaerae	87.4481	1277	1870	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	86.6503	1280	1870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090265.1	s__Micromonospora rifamycinica	85.3562	1242	1870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010560025.1	s__Micromonospora sp010560025	83.7365	1134	1870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.75	99.70	1.00	1.00	3	-
GCF_016863495.1	s__Micromonospora andamanensis	83.5791	1153	1870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.71	95.67	0.86	0.84	3	-
GCF_009712475.1	s__Micromonospora sp009712475	83.5789	1111	1870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012726175.1	s__Micromonospora sp012726175	82.7075	936	1870	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 12:01:21,986] [INFO] GTDB search result was written to GCF_003725545.1_ASM372554v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:21,986] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:21,990] [INFO] DFAST_QC result json was written to GCF_003725545.1_ASM372554v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:21,990] [INFO] DFAST_QC completed!
[2024-01-24 12:01:21,990] [INFO] Total running time: 0h2m25s