[2024-01-25 19:07:20,910] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:07:20,911] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:07:20,912] [INFO] DQC Reference Directory: /var/lib/cwl/stg83a751fd-e833-4687-839b-cd2dc7f83be2/dqc_reference
[2024-01-25 19:07:22,042] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:07:22,042] [INFO] Task started: Prodigal
[2024-01-25 19:07:22,043] [INFO] Running command: gunzip -c /var/lib/cwl/stgf083d7a6-e23f-4209-bb5f-1f964118e491/GCF_007829925.1_ASM782992v1_genomic.fna.gz | prodigal -d GCF_007829925.1_ASM782992v1_genomic.fna/cds.fna -a GCF_007829925.1_ASM782992v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:07:40,093] [INFO] Task succeeded: Prodigal
[2024-01-25 19:07:40,093] [INFO] Task started: HMMsearch
[2024-01-25 19:07:40,093] [INFO] Running command: hmmsearch --tblout GCF_007829925.1_ASM782992v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83a751fd-e833-4687-839b-cd2dc7f83be2/dqc_reference/reference_markers.hmm GCF_007829925.1_ASM782992v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:07:40,355] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:07:40,356] [INFO] Found 6/6 markers.
[2024-01-25 19:07:40,407] [INFO] Query marker FASTA was written to GCF_007829925.1_ASM782992v1_genomic.fna/markers.fasta
[2024-01-25 19:07:40,407] [INFO] Task started: Blastn
[2024-01-25 19:07:40,407] [INFO] Running command: blastn -query GCF_007829925.1_ASM782992v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83a751fd-e833-4687-839b-cd2dc7f83be2/dqc_reference/reference_markers.fasta -out GCF_007829925.1_ASM782992v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:41,606] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:41,608] [INFO] Selected 19 target genomes.
[2024-01-25 19:07:41,609] [INFO] Target genome list was writen to GCF_007829925.1_ASM782992v1_genomic.fna/target_genomes.txt
[2024-01-25 19:07:41,634] [INFO] Task started: fastANI
[2024-01-25 19:07:41,635] [INFO] Running command: fastANI --query /var/lib/cwl/stgf083d7a6-e23f-4209-bb5f-1f964118e491/GCF_007829925.1_ASM782992v1_genomic.fna.gz --refList GCF_007829925.1_ASM782992v1_genomic.fna/target_genomes.txt --output GCF_007829925.1_ASM782992v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:08:19,609] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:19,610] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83a751fd-e833-4687-839b-cd2dc7f83be2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:08:19,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83a751fd-e833-4687-839b-cd2dc7f83be2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:08:19,622] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:08:19,623] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:08:19,623] [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 palomenae	strain=DSM 102131	GCA_007829925.1	1461247	1461247	type	True	100.0	2210	2215	95	inconclusive
Micromonospora purpureochromogenes	strain=DSM 43821	GCA_900091515.1	47872	47872	type	True	95.9891	1886	2215	95	inconclusive
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	89.2918	1608	2215	95	below_threshold
Micromonospora halophytica	strain=DSM 43171	GCA_900090245.1	47864	47864	type	True	89.1458	1467	2215	95	below_threshold
Micromonospora kangleipakensis	strain=DSM 45612	GCA_004217615.1	1077942	1077942	type	True	87.8509	1589	2215	95	below_threshold
Micromonospora veneta	strain=CAP181	GCA_016598485.1	2796464	2796464	type	True	87.5382	1557	2215	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	87.4123	1272	2215	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	87.0288	1618	2215	95	below_threshold
Micromonospora chersina	strain=DSM 44151	GCA_900091475.1	47854	47854	type	True	86.8526	1613	2215	95	below_threshold
Micromonospora auratinigra	strain=DSM 44815	GCA_900089595.1	261654	261654	type	True	86.7852	1534	2215	95	below_threshold
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	86.7246	1616	2215	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	86.7155	1597	2215	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	86.6799	1457	2215	95	below_threshold
Micromonospora viridifaciens	strain=DSM 43909	GCA_900091545.1	1881	1881	type	True	86.3212	1420	2215	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	86.147	1331	2215	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	86.1424	1454	2215	95	below_threshold
Micromonospora eburnea	strain=DSM 44814	GCA_900090225.1	227316	227316	type	True	85.9482	1399	2215	95	below_threshold
Micromonospora haikouensis	strain=DSM 45626	GCA_900091595.1	686309	686309	type	True	85.9433	1403	2215	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	84.1359	1337	2215	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:08:19,624] [INFO] DFAST Taxonomy check result was written to GCF_007829925.1_ASM782992v1_genomic.fna/tc_result.tsv
[2024-01-25 19:08:19,624] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:08:19,625] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:08:19,625] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83a751fd-e833-4687-839b-cd2dc7f83be2/dqc_reference/checkm_data
[2024-01-25 19:08:19,626] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:08:19,686] [INFO] Task started: CheckM
[2024-01-25 19:08:19,686] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007829925.1_ASM782992v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007829925.1_ASM782992v1_genomic.fna/checkm_input GCF_007829925.1_ASM782992v1_genomic.fna/checkm_result
[2024-01-25 19:09:40,857] [INFO] Task succeeded: CheckM
[2024-01-25 19:09:40,858] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 19:09:40,892] [INFO] ===== Completeness check finished =====
[2024-01-25 19:09:40,892] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:09:40,893] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007829925.1_ASM782992v1_genomic.fna/markers.fasta)
[2024-01-25 19:09:40,893] [INFO] Task started: Blastn
[2024-01-25 19:09:40,893] [INFO] Running command: blastn -query GCF_007829925.1_ASM782992v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83a751fd-e833-4687-839b-cd2dc7f83be2/dqc_reference/reference_markers_gtdb.fasta -out GCF_007829925.1_ASM782992v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:42,806] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:42,808] [INFO] Selected 19 target genomes.
[2024-01-25 19:09:42,809] [INFO] Target genome list was writen to GCF_007829925.1_ASM782992v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:09:42,828] [INFO] Task started: fastANI
[2024-01-25 19:09:42,828] [INFO] Running command: fastANI --query /var/lib/cwl/stgf083d7a6-e23f-4209-bb5f-1f964118e491/GCF_007829925.1_ASM782992v1_genomic.fna.gz --refList GCF_007829925.1_ASM782992v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007829925.1_ASM782992v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:10:21,528] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:21,553] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:10:21,553] [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_900091515.1	s__Micromonospora purpureochromogenes	95.9728	1886	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.27	95.68	0.85	0.81	4	conclusive
GCF_900090295.1	s__Micromonospora coxensis	89.2735	1613	2215	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	89.0904	1473	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217615.1	s__Micromonospora kangleipakensis	87.8644	1586	2215	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	87.5492	1450	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.27	99.27	0.87	0.87	2	-
GCF_004348595.1	s__Micromonospora sp004348595	87.5359	1252	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598485.1	s__Micromonospora veneta	87.5027	1561	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348325.1	s__Micromonospora sp004348325	87.045	1216	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.89	97.89	0.85	0.85	2	-
GCF_014648395.1	s__Micromonospora fulviviridis	87.0184	1619	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.01	95.01	0.74	0.74	2	-
GCF_008868175.1	s__Micromonospora sp008868175	86.9292	1442	2215	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	86.8426	1614	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.87	95.82	0.87	0.87	3	-
GCF_900089595.1	s__Micromonospora auratinigra	86.8422	1531	2215	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	86.7429	1593	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.16	95.15	0.86	0.86	3	-
GCF_900090235.1	s__Micromonospora echinaurantiaca	86.7387	1617	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.93	95.22	0.84	0.83	3	-
GCF_900090265.1	s__Micromonospora rifamycinica	86.6819	1413	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000982955.1	s__Micromonospora sp000982955	86.3357	1437	2215	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	86.3334	1420	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205165.1	s__Micromonospora carbonacea	85.9723	1434	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	-
GCF_900091595.1	s__Micromonospora haikouensis	85.9525	1401	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	97.81	97.42	0.87	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:10:21,557] [INFO] GTDB search result was written to GCF_007829925.1_ASM782992v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:10:21,559] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:10:21,563] [INFO] DFAST_QC result json was written to GCF_007829925.1_ASM782992v1_genomic.fna/dqc_result.json
[2024-01-25 19:10:21,563] [INFO] DFAST_QC completed!
[2024-01-25 19:10:21,563] [INFO] Total running time: 0h3m1s