[2024-01-24 11:35:10,457] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:10,461] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:10,461] [INFO] DQC Reference Directory: /var/lib/cwl/stg437a8c7e-163f-4b4b-bb06-b0d47fad9c6c/dqc_reference
[2024-01-24 11:35:11,812] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:11,813] [INFO] Task started: Prodigal
[2024-01-24 11:35:11,813] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9be2457-dc0d-43c7-9d34-6a84aec3f5ac/GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna/cds.fna -a GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:39,695] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:39,695] [INFO] Task started: HMMsearch
[2024-01-24 11:35:39,695] [INFO] Running command: hmmsearch --tblout GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg437a8c7e-163f-4b4b-bb06-b0d47fad9c6c/dqc_reference/reference_markers.hmm GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:40,040] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:40,041] [INFO] Found 6/6 markers.
[2024-01-24 11:35:40,096] [INFO] Query marker FASTA was written to GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 11:35:40,096] [INFO] Task started: Blastn
[2024-01-24 11:35:40,096] [INFO] Running command: blastn -query GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg437a8c7e-163f-4b4b-bb06-b0d47fad9c6c/dqc_reference/reference_markers.fasta -out GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:41,411] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:41,415] [INFO] Selected 10 target genomes.
[2024-01-24 11:35:41,416] [INFO] Target genome list was writen to GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 11:35:41,423] [INFO] Task started: fastANI
[2024-01-24 11:35:41,423] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9be2457-dc0d-43c7-9d34-6a84aec3f5ac/GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna.gz --refList GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:04,026] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:04,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg437a8c7e-163f-4b4b-bb06-b0d47fad9c6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:04,027] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg437a8c7e-163f-4b4b-bb06-b0d47fad9c6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:04,037] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:36:04,037] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:36:04,037] [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 rifamycinica	strain=DSM 44983	GCA_900090265.1	291594	291594	type	True	100.0	2336	2337	95	conclusive
Micromonospora rifamycinica	strain=AM105	GCA_001542325.1	291594	291594	type	True	99.8697	2063	2337	95	conclusive
Micromonospora matsumotoense	strain=DSM 44100	GCA_900091525.1	121616	121616	type	True	91.8442	1848	2337	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	91.8132	1900	2337	95	below_threshold
Micromonospora wenchangensis	strain=CCTCC AA 2012002	GCA_002210435.1	1185415	1185415	type	True	91.8017	1845	2337	95	below_threshold
Micromonospora halophytica	strain=DSM 43171	GCA_900090245.1	47864	47864	type	True	86.2522	1425	2337	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	84.9535	1033	2337	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	84.7758	1454	2337	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	84.6018	1178	2337	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.2948	1300	2337	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:04,040] [INFO] DFAST Taxonomy check result was written to GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 11:36:04,041] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:04,041] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:04,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg437a8c7e-163f-4b4b-bb06-b0d47fad9c6c/dqc_reference/checkm_data
[2024-01-24 11:36:04,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:04,119] [INFO] Task started: CheckM
[2024-01-24 11:36:04,120] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna/checkm_input GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 11:37:51,360] [INFO] Task succeeded: CheckM
[2024-01-24 11:37:51,361] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:37:51,386] [INFO] ===== Completeness check finished =====
[2024-01-24 11:37:51,386] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:37:51,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 11:37:51,387] [INFO] Task started: Blastn
[2024-01-24 11:37:51,387] [INFO] Running command: blastn -query GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg437a8c7e-163f-4b4b-bb06-b0d47fad9c6c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:53,260] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:53,264] [INFO] Selected 10 target genomes.
[2024-01-24 11:37:53,265] [INFO] Target genome list was writen to GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:53,273] [INFO] Task started: fastANI
[2024-01-24 11:37:53,273] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9be2457-dc0d-43c7-9d34-6a84aec3f5ac/GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna.gz --refList GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:38:15,380] [INFO] Task succeeded: fastANI
[2024-01-24 11:38:15,393] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:38:15,393] [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_900090265.1	s__Micromonospora rifamycinica	100.0	2336	2337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900091525.1	s__Micromonospora matsumotoense	91.8422	1848	2337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017599305.1	s__Micromonospora sp017599305	91.8258	1899	2337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210435.1	s__Micromonospora wenchangensis	91.7618	1850	2337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.84	95.43	0.85	0.83	5	-
GCF_900091515.1	s__Micromonospora purpureochromogenes	86.4415	1412	2337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.27	95.68	0.85	0.81	4	-
GCF_900090295.1	s__Micromonospora coxensis	86.3636	1464	2337	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	86.2076	1430	2337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003434305.1	s__Micromonospora sp003434305	85.2451	1388	2337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070575.1	s__Micromonospora sp018070575	84.5389	1339	2337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001567585.1	s__Micromonospora rosaria	84.2725	1342	2337	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 11:38:15,395] [INFO] GTDB search result was written to GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 11:38:15,395] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:38:15,398] [INFO] DFAST_QC result json was written to GCF_900090265.1_IMG-taxon_2623620551_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 11:38:15,398] [INFO] DFAST_QC completed!
[2024-01-24 11:38:15,398] [INFO] Total running time: 0h3m5s