[2024-01-24 14:05:36,721] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:36,723] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:36,723] [INFO] DQC Reference Directory: /var/lib/cwl/stg05c2ae06-33d5-4c92-ba32-4969a257d0cb/dqc_reference
[2024-01-24 14:05:38,105] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:38,106] [INFO] Task started: Prodigal
[2024-01-24 14:05:38,106] [INFO] Running command: gunzip -c /var/lib/cwl/stgee48ba0e-e2c4-4484-8d50-30ca69032b4b/GCF_010671795.1_ASM1067179v1_genomic.fna.gz | prodigal -d GCF_010671795.1_ASM1067179v1_genomic.fna/cds.fna -a GCF_010671795.1_ASM1067179v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:53,716] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:53,717] [INFO] Task started: HMMsearch
[2024-01-24 14:05:53,717] [INFO] Running command: hmmsearch --tblout GCF_010671795.1_ASM1067179v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05c2ae06-33d5-4c92-ba32-4969a257d0cb/dqc_reference/reference_markers.hmm GCF_010671795.1_ASM1067179v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:54,051] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:54,053] [INFO] Found 6/6 markers.
[2024-01-24 14:05:54,104] [INFO] Query marker FASTA was written to GCF_010671795.1_ASM1067179v1_genomic.fna/markers.fasta
[2024-01-24 14:05:54,105] [INFO] Task started: Blastn
[2024-01-24 14:05:54,105] [INFO] Running command: blastn -query GCF_010671795.1_ASM1067179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05c2ae06-33d5-4c92-ba32-4969a257d0cb/dqc_reference/reference_markers.fasta -out GCF_010671795.1_ASM1067179v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:55,356] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:55,359] [INFO] Selected 23 target genomes.
[2024-01-24 14:05:55,360] [INFO] Target genome list was writen to GCF_010671795.1_ASM1067179v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:55,378] [INFO] Task started: fastANI
[2024-01-24 14:05:55,378] [INFO] Running command: fastANI --query /var/lib/cwl/stgee48ba0e-e2c4-4484-8d50-30ca69032b4b/GCF_010671795.1_ASM1067179v1_genomic.fna.gz --refList GCF_010671795.1_ASM1067179v1_genomic.fna/target_genomes.txt --output GCF_010671795.1_ASM1067179v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:36,932] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:36,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05c2ae06-33d5-4c92-ba32-4969a257d0cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:36,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05c2ae06-33d5-4c92-ba32-4969a257d0cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:36,950] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:36,951] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:36,951] [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	89.4999	1449	1870	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	89.3659	1450	1870	95	below_threshold
Micromonospora chersina	strain=DSM 44151	GCA_900091475.1	47854	47854	type	True	89.2198	1446	1870	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	89.1084	1399	1870	95	below_threshold
Micromonospora terminaliae	strain=TMS7	GCA_010671825.1	1914461	1914461	type	True	88.9845	1416	1870	95	below_threshold
Micromonospora terminaliae	strain=DSM 101760	GCA_009671205.1	1914461	1914461	type	True	88.9539	1412	1870	95	below_threshold
Micromonospora eburnea	strain=DSM 44814	GCA_900090225.1	227316	227316	type	True	88.4576	1376	1870	95	below_threshold
Micromonospora viridifaciens	strain=DSM 43909	GCA_900091545.1	1881	1881	type	True	88.4188	1302	1870	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	87.5409	1385	1870	95	below_threshold
Micromonospora rhizosphaerae	strain=DSM 45431	GCA_900091465.1	568872	568872	type	True	87.4823	1273	1870	95	below_threshold
Micromonospora halophytica	strain=DSM 43171	GCA_900090245.1	47864	47864	type	True	86.579	1287	1870	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	86.3076	1027	1870	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	85.4459	1148	1870	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	85.4439	1285	1870	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	85.3715	1281	1870	95	below_threshold
Micromonospora rifamycinica	strain=AM105	GCA_001542325.1	291594	291594	type	True	85.3371	1163	1870	95	below_threshold
Micromonospora rifamycinica	strain=DSM 44983	GCA_900090265.1	291594	291594	type	True	85.3076	1248	1870	95	below_threshold
Micromonospora nigra	strain=DSM 43818	GCA_900091585.1	145857	145857	type	True	84.3846	1183	1870	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.9357	1151	1870	95	below_threshold
Micromonospora tarapacensis	strain=Llam7	GCA_019697375.1	2835305	2835305	type	True	83.767	1147	1870	95	below_threshold
Micromonospora maris	strain=AB-18-032	GCA_000204155.1	1003110	1003110	type	True	83.7225	1148	1870	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	83.6837	1149	1870	95	below_threshold
Micromonospora fiedleri	strain=MG-37	GCA_016774385.1	1157498	1157498	type	True	83.5792	1201	1870	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:36,952] [INFO] DFAST Taxonomy check result was written to GCF_010671795.1_ASM1067179v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:36,953] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:36,953] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:36,953] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05c2ae06-33d5-4c92-ba32-4969a257d0cb/dqc_reference/checkm_data
[2024-01-24 14:06:36,954] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:37,011] [INFO] Task started: CheckM
[2024-01-24 14:06:37,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010671795.1_ASM1067179v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010671795.1_ASM1067179v1_genomic.fna/checkm_input GCF_010671795.1_ASM1067179v1_genomic.fna/checkm_result
[2024-01-24 14:07:32,272] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:32,273] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:32,297] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:32,297] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:32,298] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010671795.1_ASM1067179v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:32,298] [INFO] Task started: Blastn
[2024-01-24 14:07:32,298] [INFO] Running command: blastn -query GCF_010671795.1_ASM1067179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05c2ae06-33d5-4c92-ba32-4969a257d0cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_010671795.1_ASM1067179v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:34,204] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:34,208] [INFO] Selected 18 target genomes.
[2024-01-24 14:07:34,209] [INFO] Target genome list was writen to GCF_010671795.1_ASM1067179v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:34,225] [INFO] Task started: fastANI
[2024-01-24 14:07:34,226] [INFO] Running command: fastANI --query /var/lib/cwl/stgee48ba0e-e2c4-4484-8d50-30ca69032b4b/GCF_010671795.1_ASM1067179v1_genomic.fna.gz --refList GCF_010671795.1_ASM1067179v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010671795.1_ASM1067179v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:06,045] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:06,065] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:06,066] [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	89.6064	1439	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	89.4202	1445	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_000982955.1	s__Micromonospora sp000982955	89.2607	1344	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_900091475.1	s__Micromonospora chersina	89.2245	1446	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_008868175.1	s__Micromonospora sp008868175	89.0954	1289	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	89.0812	1401	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	88.7965	1365	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	88.5516	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_900090225.1	s__Micromonospora eburnea	88.4306	1380	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	88.3451	1308	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	87.4827	1273	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	86.6134	1283	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	85.376	1240	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	83.7608	1131	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_009712475.1	s__Micromonospora sp009712475	83.6042	1108	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_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_012726175.1	s__Micromonospora sp012726175	82.7428	932	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 14:08:06,068] [INFO] GTDB search result was written to GCF_010671795.1_ASM1067179v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:06,068] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:06,073] [INFO] DFAST_QC result json was written to GCF_010671795.1_ASM1067179v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:06,073] [INFO] DFAST_QC completed!
[2024-01-24 14:08:06,073] [INFO] Total running time: 0h2m29s