[2024-01-24 13:18:40,713] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:40,715] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:40,715] [INFO] DQC Reference Directory: /var/lib/cwl/stg30fada61-bedc-4944-b3c3-1aebe8ca8f9f/dqc_reference
[2024-01-24 13:18:41,997] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:41,998] [INFO] Task started: Prodigal
[2024-01-24 13:18:41,998] [INFO] Running command: gunzip -c /var/lib/cwl/stg063007b8-ae5e-4bd9-819b-7940d4d657f4/GCF_013389765.1_ASM1338976v1_genomic.fna.gz | prodigal -d GCF_013389765.1_ASM1338976v1_genomic.fna/cds.fna -a GCF_013389765.1_ASM1338976v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:05,070] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:05,070] [INFO] Task started: HMMsearch
[2024-01-24 13:19:05,071] [INFO] Running command: hmmsearch --tblout GCF_013389765.1_ASM1338976v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30fada61-bedc-4944-b3c3-1aebe8ca8f9f/dqc_reference/reference_markers.hmm GCF_013389765.1_ASM1338976v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:05,425] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:05,426] [INFO] Found 6/6 markers.
[2024-01-24 13:19:05,484] [INFO] Query marker FASTA was written to GCF_013389765.1_ASM1338976v1_genomic.fna/markers.fasta
[2024-01-24 13:19:05,485] [INFO] Task started: Blastn
[2024-01-24 13:19:05,485] [INFO] Running command: blastn -query GCF_013389765.1_ASM1338976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30fada61-bedc-4944-b3c3-1aebe8ca8f9f/dqc_reference/reference_markers.fasta -out GCF_013389765.1_ASM1338976v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:06,833] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:06,838] [INFO] Selected 15 target genomes.
[2024-01-24 13:19:06,839] [INFO] Target genome list was writen to GCF_013389765.1_ASM1338976v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:06,847] [INFO] Task started: fastANI
[2024-01-24 13:19:06,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg063007b8-ae5e-4bd9-819b-7940d4d657f4/GCF_013389765.1_ASM1338976v1_genomic.fna.gz --refList GCF_013389765.1_ASM1338976v1_genomic.fna/target_genomes.txt --output GCF_013389765.1_ASM1338976v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:44,255] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:44,255] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30fada61-bedc-4944-b3c3-1aebe8ca8f9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:44,256] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30fada61-bedc-4944-b3c3-1aebe8ca8f9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:44,269] [INFO] Found 15 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:19:44,269] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:19:44,270] [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 carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	100.0	2509	2509	95	inconclusive
Micromonospora carbonacea	strain=DSM 43815	GCA_014205165.1	47853	47853	type	True	99.999	2508	2509	95	inconclusive
Micromonospora carbonacea	strain=DSM 43168	GCA_900091535.1	47853	47853	type	True	98.3671	2284	2509	95	inconclusive
Micromonospora haikouensis	strain=DSM 45626	GCA_900091595.1	686309	686309	type	True	95.4958	2063	2509	95	inconclusive
Micromonospora rubida	strain=NEAU-HG-1	GCA_009908295.1	2697657	2697657	type	True	88.2445	1645	2509	95	below_threshold
Micromonospora olivasterospora	strain=DSM 43868	GCA_007830265.1	1880	1880	type	True	87.002	1422	2509	95	below_threshold
Micromonospora halophytica	strain=DSM 43171	GCA_900090245.1	47864	47864	type	True	86.111	1422	2509	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	85.9234	1644	2509	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	85.625	1079	2509	95	below_threshold
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	85.3591	1463	2509	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	84.9966	1545	2509	95	below_threshold
Micromonospora narathiwatensis	strain=DSM 45248	GCA_900089605.1	299146	299146	type	True	84.9099	1413	2509	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	84.6841	1275	2509	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.5693	1337	2509	95	below_threshold
Micromonospora fiedleri	strain=MG-37	GCA_016774385.1	1157498	1157498	type	True	83.4543	1356	2509	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:44,272] [INFO] DFAST Taxonomy check result was written to GCF_013389765.1_ASM1338976v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:44,273] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:44,273] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:44,274] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30fada61-bedc-4944-b3c3-1aebe8ca8f9f/dqc_reference/checkm_data
[2024-01-24 13:19:44,275] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:44,344] [INFO] Task started: CheckM
[2024-01-24 13:19:44,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013389765.1_ASM1338976v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013389765.1_ASM1338976v1_genomic.fna/checkm_input GCF_013389765.1_ASM1338976v1_genomic.fna/checkm_result
[2024-01-24 13:21:19,190] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:19,191] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:21:19,212] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:19,213] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:19,213] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013389765.1_ASM1338976v1_genomic.fna/markers.fasta)
[2024-01-24 13:21:19,214] [INFO] Task started: Blastn
[2024-01-24 13:21:19,214] [INFO] Running command: blastn -query GCF_013389765.1_ASM1338976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30fada61-bedc-4944-b3c3-1aebe8ca8f9f/dqc_reference/reference_markers_gtdb.fasta -out GCF_013389765.1_ASM1338976v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:21,508] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:21,512] [INFO] Selected 12 target genomes.
[2024-01-24 13:21:21,513] [INFO] Target genome list was writen to GCF_013389765.1_ASM1338976v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:21,550] [INFO] Task started: fastANI
[2024-01-24 13:21:21,551] [INFO] Running command: fastANI --query /var/lib/cwl/stg063007b8-ae5e-4bd9-819b-7940d4d657f4/GCF_013389765.1_ASM1338976v1_genomic.fna.gz --refList GCF_013389765.1_ASM1338976v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013389765.1_ASM1338976v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:51,507] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:51,520] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:21:51,520] [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_014205165.1	s__Micromonospora carbonacea	99.9991	2507	2509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	conclusive
GCF_900091595.1	s__Micromonospora haikouensis	95.4956	2063	2509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	97.81	97.42	0.87	0.87	3	-
GCF_000158815.1	s__Micromonospora sp000158815	91.6319	1693	2509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.02	97.02	0.80	0.80	2	-
GCF_003434305.1	s__Micromonospora sp003434305	88.8805	1643	2509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009908295.1	s__Micromonospora rubida	88.1971	1651	2509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830265.1	s__Micromonospora olivasterospora	86.9414	1429	2509	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	86.1171	1421	2509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664255.1	s__Micromonospora sp003664255	85.4072	1557	2509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090235.1	s__Micromonospora echinaurantiaca	85.2876	1472	2509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.93	95.22	0.84	0.83	3	-
GCF_002926165.1	s__Micromonospora chalcea	84.9441	1449	2509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	95.31	0.89	0.84	18	-
GCF_900089605.1	s__Micromonospora narathiwatensis	84.9031	1413	2509	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	84.6576	1414	2509	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 13:21:51,522] [INFO] GTDB search result was written to GCF_013389765.1_ASM1338976v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:51,523] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:51,526] [INFO] DFAST_QC result json was written to GCF_013389765.1_ASM1338976v1_genomic.fna/dqc_result.json
[2024-01-24 13:21:51,526] [INFO] DFAST_QC completed!
[2024-01-24 13:21:51,526] [INFO] Total running time: 0h3m11s