[2024-01-25 17:34:07,121] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,125] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,125] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b04ed92-ed42-4070-9d2c-a6e2067c811e/dqc_reference
[2024-01-25 17:34:08,953] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:08,954] [INFO] Task started: Prodigal
[2024-01-25 17:34:08,955] [INFO] Running command: gunzip -c /var/lib/cwl/stgc036935b-fcf7-4be5-936a-3f4c22259540/GCF_003721415.1_ASM372141v1_genomic.fna.gz | prodigal -d GCF_003721415.1_ASM372141v1_genomic.fna/cds.fna -a GCF_003721415.1_ASM372141v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:28,226] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:28,226] [INFO] Task started: HMMsearch
[2024-01-25 17:34:28,226] [INFO] Running command: hmmsearch --tblout GCF_003721415.1_ASM372141v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b04ed92-ed42-4070-9d2c-a6e2067c811e/dqc_reference/reference_markers.hmm GCF_003721415.1_ASM372141v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:28,601] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:28,602] [INFO] Found 6/6 markers.
[2024-01-25 17:34:28,670] [INFO] Query marker FASTA was written to GCF_003721415.1_ASM372141v1_genomic.fna/markers.fasta
[2024-01-25 17:34:28,670] [INFO] Task started: Blastn
[2024-01-25 17:34:28,671] [INFO] Running command: blastn -query GCF_003721415.1_ASM372141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b04ed92-ed42-4070-9d2c-a6e2067c811e/dqc_reference/reference_markers.fasta -out GCF_003721415.1_ASM372141v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:29,896] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:29,898] [INFO] Selected 17 target genomes.
[2024-01-25 17:34:29,899] [INFO] Target genome list was writen to GCF_003721415.1_ASM372141v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:29,904] [INFO] Task started: fastANI
[2024-01-25 17:34:29,904] [INFO] Running command: fastANI --query /var/lib/cwl/stgc036935b-fcf7-4be5-936a-3f4c22259540/GCF_003721415.1_ASM372141v1_genomic.fna.gz --refList GCF_003721415.1_ASM372141v1_genomic.fna/target_genomes.txt --output GCF_003721415.1_ASM372141v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:35:06,133] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:06,134] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b04ed92-ed42-4070-9d2c-a6e2067c811e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:35:06,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b04ed92-ed42-4070-9d2c-a6e2067c811e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:35:06,145] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 17:35:06,145] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 17:35:06,145] [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 aurantiaca	strain=ATCC 27029	GCA_003721415.1	47850	47850	type	True	100.0	2440	2447	95	inconclusive
Micromonospora aurantiaca	strain=ATCC 27029	GCA_000145235.1	47850	47850	type	True	98.5907	2124	2447	95	inconclusive
Micromonospora tulbaghiae	strain=DSM 45142	GCA_900091605.1	479978	479978	type	True	95.1635	1877	2447	95	inconclusive
Micromonospora marina	strain=DSM 45555	GCA_900091565.1	307120	307120	type	True	94.2784	1692	2447	95	below_threshold
Micromonospora chalcea	strain=DSM 43026	GCA_002926165.1	1874	1874	type	True	93.7477	1813	2447	95	below_threshold
Micromonospora sediminicola	strain=DSM 45794	GCA_900089585.1	946078	946078	type	True	89.7905	1720	2447	95	below_threshold
Micromonospora maritima		GCA_902825405.1	986711	986711	type	True	89.6604	1233	2447	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	89.226	1682	2447	95	below_threshold
Micromonospora humi	strain=DSM 45647	GCA_900090105.1	745366	745366	type	True	89.1473	1693	2447	95	below_threshold
Micromonospora terminaliae	strain=DSM 101760	GCA_009671205.1	1914461	1914461	type	True	87.3436	1586	2447	95	below_threshold
Micromonospora terminaliae	strain=TMS7	GCA_010671825.1	1914461	1914461	type	True	87.331	1572	2447	95	below_threshold
Micromonospora eburnea	strain=DSM 44814	GCA_900090225.1	227316	227316	type	True	85.911	1452	2447	95	below_threshold
Micromonospora viridifaciens	strain=DSM 43909	GCA_900091545.1	1881	1881	type	True	85.8723	1414	2447	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	85.0057	1091	2447	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	84.5713	1494	2447	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	84.4447	1267	2447	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.2039	1311	2447	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:35:06,146] [INFO] DFAST Taxonomy check result was written to GCF_003721415.1_ASM372141v1_genomic.fna/tc_result.tsv
[2024-01-25 17:35:06,147] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:35:06,147] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:35:06,147] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b04ed92-ed42-4070-9d2c-a6e2067c811e/dqc_reference/checkm_data
[2024-01-25 17:35:06,148] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:35:06,215] [INFO] Task started: CheckM
[2024-01-25 17:35:06,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003721415.1_ASM372141v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003721415.1_ASM372141v1_genomic.fna/checkm_input GCF_003721415.1_ASM372141v1_genomic.fna/checkm_result
[2024-01-25 17:36:23,658] [INFO] Task succeeded: CheckM
[2024-01-25 17:36:23,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:36:23,676] [INFO] ===== Completeness check finished =====
[2024-01-25 17:36:23,677] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:36:23,678] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003721415.1_ASM372141v1_genomic.fna/markers.fasta)
[2024-01-25 17:36:23,678] [INFO] Task started: Blastn
[2024-01-25 17:36:23,678] [INFO] Running command: blastn -query GCF_003721415.1_ASM372141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b04ed92-ed42-4070-9d2c-a6e2067c811e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003721415.1_ASM372141v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:25,674] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:25,677] [INFO] Selected 12 target genomes.
[2024-01-25 17:36:25,678] [INFO] Target genome list was writen to GCF_003721415.1_ASM372141v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:36:25,684] [INFO] Task started: fastANI
[2024-01-25 17:36:25,685] [INFO] Running command: fastANI --query /var/lib/cwl/stgc036935b-fcf7-4be5-936a-3f4c22259540/GCF_003721415.1_ASM372141v1_genomic.fna.gz --refList GCF_003721415.1_ASM372141v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003721415.1_ASM372141v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:36:52,370] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:52,382] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:36:52,382] [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_000145235.1	s__Micromonospora aurantiaca	98.5794	2125	2447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.1942	98.37	95.58	0.90	0.84	15	conclusive
GCF_900091605.1	s__Micromonospora tulbaghiae	95.1744	1876	2447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.1942	97.73	96.20	0.92	0.87	5	-
GCF_900091565.1	s__Micromonospora marina	94.2317	1696	2447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.54	95.96	0.90	0.86	3	-
GCF_002926165.1	s__Micromonospora chalcea	93.7271	1816	2447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	95.31	0.89	0.84	18	-
GCF_900089585.1	s__Micromonospora sediminicola	89.7468	1725	2447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.55	97.81	0.94	0.92	3	-
GCF_902825405.1	s__Micromonospora maritima	89.6415	1235	2447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090105.1	s__Micromonospora humi	89.118	1697	2447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003027925.1	s__Micromonospora sp003027925	88.9621	1685	2447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002140155.1	s__Micromonospora sp002140155	88.7971	1598	2447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008119785.1	s__Micromonospora sp008119785	86.0081	1518	2447	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	85.8867	1548	2447	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	85.8184	1421	2447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:36:52,383] [INFO] GTDB search result was written to GCF_003721415.1_ASM372141v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:36:52,384] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:36:52,387] [INFO] DFAST_QC result json was written to GCF_003721415.1_ASM372141v1_genomic.fna/dqc_result.json
[2024-01-25 17:36:52,387] [INFO] DFAST_QC completed!
[2024-01-25 17:36:52,387] [INFO] Total running time: 0h2m45s