[2024-01-25 20:26:35,817] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:26:35,819] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:26:35,819] [INFO] DQC Reference Directory: /var/lib/cwl/stge6513e73-1725-4e07-b12b-8cc0afa63a1f/dqc_reference
[2024-01-25 20:26:37,001] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:26:37,001] [INFO] Task started: Prodigal
[2024-01-25 20:26:37,002] [INFO] Running command: gunzip -c /var/lib/cwl/stg04b95b0f-e1f1-4232-8f0f-0fc5e37c7fb2/GCF_016598485.1_ASM1659848v1_genomic.fna.gz | prodigal -d GCF_016598485.1_ASM1659848v1_genomic.fna/cds.fna -a GCF_016598485.1_ASM1659848v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:26:53,477] [INFO] Task succeeded: Prodigal
[2024-01-25 20:26:53,478] [INFO] Task started: HMMsearch
[2024-01-25 20:26:53,478] [INFO] Running command: hmmsearch --tblout GCF_016598485.1_ASM1659848v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6513e73-1725-4e07-b12b-8cc0afa63a1f/dqc_reference/reference_markers.hmm GCF_016598485.1_ASM1659848v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:26:53,747] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:26:53,748] [INFO] Found 6/6 markers.
[2024-01-25 20:26:53,815] [INFO] Query marker FASTA was written to GCF_016598485.1_ASM1659848v1_genomic.fna/markers.fasta
[2024-01-25 20:26:53,815] [INFO] Task started: Blastn
[2024-01-25 20:26:53,815] [INFO] Running command: blastn -query GCF_016598485.1_ASM1659848v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6513e73-1725-4e07-b12b-8cc0afa63a1f/dqc_reference/reference_markers.fasta -out GCF_016598485.1_ASM1659848v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:26:54,990] [INFO] Task succeeded: Blastn
[2024-01-25 20:26:54,993] [INFO] Selected 17 target genomes.
[2024-01-25 20:26:54,994] [INFO] Target genome list was writen to GCF_016598485.1_ASM1659848v1_genomic.fna/target_genomes.txt
[2024-01-25 20:26:54,999] [INFO] Task started: fastANI
[2024-01-25 20:26:55,000] [INFO] Running command: fastANI --query /var/lib/cwl/stg04b95b0f-e1f1-4232-8f0f-0fc5e37c7fb2/GCF_016598485.1_ASM1659848v1_genomic.fna.gz --refList GCF_016598485.1_ASM1659848v1_genomic.fna/target_genomes.txt --output GCF_016598485.1_ASM1659848v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:27:27,308] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:27,308] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6513e73-1725-4e07-b12b-8cc0afa63a1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:27:27,309] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6513e73-1725-4e07-b12b-8cc0afa63a1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:27:27,319] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:27:27,319] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:27:27,320] [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 veneta	strain=CAP181	GCA_016598485.1	2796464	2796464	type	True	100.0	2206	2210	95	conclusive
Micromonospora kangleipakensis	strain=DSM 45612	GCA_004217615.1	1077942	1077942	type	True	91.4089	1734	2210	95	below_threshold
Micromonospora inositola	strain=DSM 43819	GCA_900090285.1	47865	47865	type	True	91.098	1650	2210	95	below_threshold
Micromonospora rhizosphaerae	strain=DSM 45431	GCA_900091465.1	568872	568872	type	True	88.637	1581	2210	95	below_threshold
Micromonospora globispora	strain=S2901	GCA_003857015.1	1450148	1450148	type	True	88.5213	1270	2210	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	87.7373	1564	2210	95	below_threshold
Micromonospora palomenae	strain=DSM 102131	GCA_007829925.1	1461247	1461247	type	True	87.5937	1528	2210	95	below_threshold
Micromonospora purpureochromogenes	strain=DSM 43821	GCA_900091515.1	47872	47872	type	True	87.476	1561	2210	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	86.6654	1445	2210	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	86.6555	1226	2210	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	86.558	1411	2210	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	85.7354	1268	2210	95	below_threshold
Micromonospora haikouensis	strain=DSM 45626	GCA_900091595.1	686309	686309	type	True	85.5614	1338	2210	95	below_threshold
Micromonospora carbonacea	strain=DSM 43168	GCA_900091535.1	47853	47853	type	True	85.4197	1358	2210	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	85.4172	1371	2210	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	85.2656	1305	2210	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.8254	1215	2210	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:27:27,321] [INFO] DFAST Taxonomy check result was written to GCF_016598485.1_ASM1659848v1_genomic.fna/tc_result.tsv
[2024-01-25 20:27:27,322] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:27:27,322] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:27:27,322] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6513e73-1725-4e07-b12b-8cc0afa63a1f/dqc_reference/checkm_data
[2024-01-25 20:27:27,323] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:27:27,386] [INFO] Task started: CheckM
[2024-01-25 20:27:27,387] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016598485.1_ASM1659848v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016598485.1_ASM1659848v1_genomic.fna/checkm_input GCF_016598485.1_ASM1659848v1_genomic.fna/checkm_result
[2024-01-25 20:28:29,641] [INFO] Task succeeded: CheckM
[2024-01-25 20:28:29,644] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:28:29,665] [INFO] ===== Completeness check finished =====
[2024-01-25 20:28:29,665] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:28:29,667] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016598485.1_ASM1659848v1_genomic.fna/markers.fasta)
[2024-01-25 20:28:29,667] [INFO] Task started: Blastn
[2024-01-25 20:28:29,667] [INFO] Running command: blastn -query GCF_016598485.1_ASM1659848v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6513e73-1725-4e07-b12b-8cc0afa63a1f/dqc_reference/reference_markers_gtdb.fasta -out GCF_016598485.1_ASM1659848v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:28:31,576] [INFO] Task succeeded: Blastn
[2024-01-25 20:28:31,580] [INFO] Selected 10 target genomes.
[2024-01-25 20:28:31,580] [INFO] Target genome list was writen to GCF_016598485.1_ASM1659848v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:28:31,608] [INFO] Task started: fastANI
[2024-01-25 20:28:31,608] [INFO] Running command: fastANI --query /var/lib/cwl/stg04b95b0f-e1f1-4232-8f0f-0fc5e37c7fb2/GCF_016598485.1_ASM1659848v1_genomic.fna.gz --refList GCF_016598485.1_ASM1659848v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016598485.1_ASM1659848v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:28:52,038] [INFO] Task succeeded: fastANI
[2024-01-25 20:28:52,045] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:28:52,045] [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_016598485.1	s__Micromonospora veneta	100.0	2206	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004217615.1	s__Micromonospora kangleipakensis	91.4199	1733	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003172935.1	s__Micromonospora sp003172935	91.415	1629	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.27	99.27	0.87	0.87	2	-
GCF_900090285.1	s__Micromonospora inositola	91.0493	1655	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003857015.1	s__Micromonospora globispora	88.5133	1271	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.52	99.52	0.89	0.89	2	-
GCF_900091435.1	s__Micromonospora chaiyaphumensis	87.7288	1565	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.16	95.15	0.86	0.86	3	-
GCF_900091515.1	s__Micromonospora purpureochromogenes	87.459	1562	2210	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	86.6669	1444	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091595.1	s__Micromonospora haikouensis	85.512	1344	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	97.81	97.42	0.87	0.87	3	-
GCF_014205165.1	s__Micromonospora carbonacea	85.419	1363	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:28:52,047] [INFO] GTDB search result was written to GCF_016598485.1_ASM1659848v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:28:52,048] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:28:52,054] [INFO] DFAST_QC result json was written to GCF_016598485.1_ASM1659848v1_genomic.fna/dqc_result.json
[2024-01-25 20:28:52,054] [INFO] DFAST_QC completed!
[2024-01-25 20:28:52,054] [INFO] Total running time: 0h2m16s