[2024-01-24 13:37:13,506] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:13,508] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:13,508] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d362dd1-5874-44e4-8ac0-0d80a9208f22/dqc_reference
[2024-01-24 13:37:14,717] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:14,718] [INFO] Task started: Prodigal
[2024-01-24 13:37:14,718] [INFO] Running command: gunzip -c /var/lib/cwl/stgd449cbe8-93e9-49e0-b595-3365d3464409/GCF_011764425.1_ASM1176442v1_genomic.fna.gz | prodigal -d GCF_011764425.1_ASM1176442v1_genomic.fna/cds.fna -a GCF_011764425.1_ASM1176442v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:52,524] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:52,525] [INFO] Task started: HMMsearch
[2024-01-24 13:37:52,525] [INFO] Running command: hmmsearch --tblout GCF_011764425.1_ASM1176442v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d362dd1-5874-44e4-8ac0-0d80a9208f22/dqc_reference/reference_markers.hmm GCF_011764425.1_ASM1176442v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:53,028] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:53,032] [INFO] Found 6/6 markers.
[2024-01-24 13:37:53,121] [INFO] Query marker FASTA was written to GCF_011764425.1_ASM1176442v1_genomic.fna/markers.fasta
[2024-01-24 13:37:53,122] [INFO] Task started: Blastn
[2024-01-24 13:37:53,122] [INFO] Running command: blastn -query GCF_011764425.1_ASM1176442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d362dd1-5874-44e4-8ac0-0d80a9208f22/dqc_reference/reference_markers.fasta -out GCF_011764425.1_ASM1176442v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:54,479] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:54,483] [INFO] Selected 23 target genomes.
[2024-01-24 13:37:54,484] [INFO] Target genome list was writen to GCF_011764425.1_ASM1176442v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:54,505] [INFO] Task started: fastANI
[2024-01-24 13:37:54,505] [INFO] Running command: fastANI --query /var/lib/cwl/stgd449cbe8-93e9-49e0-b595-3365d3464409/GCF_011764425.1_ASM1176442v1_genomic.fna.gz --refList GCF_011764425.1_ASM1176442v1_genomic.fna/target_genomes.txt --output GCF_011764425.1_ASM1176442v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:44,979] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:44,980] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d362dd1-5874-44e4-8ac0-0d80a9208f22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:44,981] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d362dd1-5874-44e4-8ac0-0d80a9208f22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:45,001] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:38:45,002] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:38:45,002] [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
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	100.0	3778	3778	95	conclusive
Phytohabitans suffuscus	strain=NBRC 105367	GCA_011764565.1	624315	624315	type	True	87.8835	2236	3778	95	below_threshold
Phytohabitans flavus	strain=NBRC 107702	GCA_011764545.1	1076124	1076124	type	True	87.1914	2135	3778	95	below_threshold
Phytohabitans rumicis	strain=NBRC 108638	GCA_011764445.1	1076125	1076125	type	True	82.4599	1976	3778	95	below_threshold
Micromonospora pattaloongensis	strain=DSM 45245	GCA_900107255.1	405436	405436	type	True	79.8839	1098	3778	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	79.6778	936	3778	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	79.4036	1271	3778	95	below_threshold
Micromonospora citrea	strain=DSM 43903	GCA_900090315.1	47855	47855	type	True	79.3036	1325	3778	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	79.2632	1121	3778	95	below_threshold
Micromonospora veneta	strain=CAP181	GCA_016598485.1	2796464	2796464	type	True	79.2011	1176	3778	95	below_threshold
Micromonospora eburnea	strain=DSM 44814	GCA_900090225.1	227316	227316	type	True	79.1998	1178	3778	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	79.1565	1115	3778	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	79.084	1330	3778	95	below_threshold
Asanoa ishikariensis	strain=DSM 44718	GCA_900107455.1	137265	137265	type	True	79.0601	1402	3778	95	below_threshold
Asanoa ishikariensis	strain=NBRC 14551	GCA_016862535.1	137265	137265	type	True	79.0267	1406	3778	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	78.9522	1286	3778	95	below_threshold
Actinoplanes teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	78.046	1190	3778	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	78.0412	1231	3778	95	below_threshold
Actinoplanes teichomyceticus	strain=DSM 43866	GCA_007829915.1	1867	1867	type	True	78.0316	1236	3778	95	below_threshold
Catellatospora sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	78.0105	1293	3778	95	below_threshold
Actinoplanes subtropicus	strain=NRRL B-24665	GCA_000721705.1	543632	543632	type	True	77.9894	1390	3778	95	below_threshold
Actinoplanes octamycinicus	strain=NBRC 14524	GCA_016862295.1	135948	135948	type	True	77.9516	1360	3778	95	below_threshold
Actinoplanes cyaneus	strain=NBRC 14990	GCA_016862095.1	52696	52696	type	True	77.8804	1294	3778	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:45,004] [INFO] DFAST Taxonomy check result was written to GCF_011764425.1_ASM1176442v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:45,004] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:45,004] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:45,004] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d362dd1-5874-44e4-8ac0-0d80a9208f22/dqc_reference/checkm_data
[2024-01-24 13:38:45,005] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:45,114] [INFO] Task started: CheckM
[2024-01-24 13:38:45,114] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011764425.1_ASM1176442v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011764425.1_ASM1176442v1_genomic.fna/checkm_input GCF_011764425.1_ASM1176442v1_genomic.fna/checkm_result
[2024-01-24 13:40:56,740] [INFO] Task succeeded: CheckM
[2024-01-24 13:40:56,743] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:40:56,783] [INFO] ===== Completeness check finished =====
[2024-01-24 13:40:56,783] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:40:56,784] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011764425.1_ASM1176442v1_genomic.fna/markers.fasta)
[2024-01-24 13:40:56,784] [INFO] Task started: Blastn
[2024-01-24 13:40:56,784] [INFO] Running command: blastn -query GCF_011764425.1_ASM1176442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d362dd1-5874-44e4-8ac0-0d80a9208f22/dqc_reference/reference_markers_gtdb.fasta -out GCF_011764425.1_ASM1176442v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:58,819] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:58,822] [INFO] Selected 19 target genomes.
[2024-01-24 13:40:58,823] [INFO] Target genome list was writen to GCF_011764425.1_ASM1176442v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:40:58,838] [INFO] Task started: fastANI
[2024-01-24 13:40:58,839] [INFO] Running command: fastANI --query /var/lib/cwl/stgd449cbe8-93e9-49e0-b595-3365d3464409/GCF_011764425.1_ASM1176442v1_genomic.fna.gz --refList GCF_011764425.1_ASM1176442v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011764425.1_ASM1176442v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:45,059] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:45,085] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:45,085] [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_011764425.1	s__Phytohabitans houttuyneae	100.0	3778	3778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011764565.1	s__Phytohabitans suffuscus	87.8637	2239	3778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764545.1	s__Phytohabitans flavus	87.1673	2138	3778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764445.1	s__Phytohabitans rumicis	82.4994	1964	3778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107255.1	s__Micromonospora_E pattaloongensis	79.8904	1098	3778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648395.1	s__Micromonospora fulviviridis	79.3494	1286	3778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.01	95.01	0.74	0.74	2	-
GCF_900091515.1	s__Micromonospora purpureochromogenes	79.3312	1231	3778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.27	95.68	0.85	0.81	4	-
GCF_900090315.1	s__Micromonospora citrea	79.3086	1329	3778	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	79.2011	1176	3778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862515.1	s__Asanoa iriomotensis	79.1804	1381	3778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070045.1	s__Micromonospora sp018070045	79.1226	1236	3778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348525.1	s__Micromonospora sp004348525	79.0989	1094	3778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107455.1	s__Asanoa ishikariensis	79.0808	1395	3778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008119785.1	s__Micromonospora sp008119785	78.9122	1317	3778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863475.1	s__Spirilliplanes yamanashiensis	78.3911	1266	3778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Spirilliplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862635.1	s__Catellatospora coxensis	78.1156	1314	3778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711105.1	s__Actinoplanes teichomyceticus	78.0138	1245	3778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	99.99	1.00	1.00	4	-
GCF_000721705.1	s__Actinoplanes subtropicus	77.974	1397	3778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862095.1	s__Actinoplanes cyaneus	77.8747	1294	3778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:45,087] [INFO] GTDB search result was written to GCF_011764425.1_ASM1176442v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:45,087] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:45,094] [INFO] DFAST_QC result json was written to GCF_011764425.1_ASM1176442v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:45,094] [INFO] DFAST_QC completed!
[2024-01-24 13:41:45,095] [INFO] Total running time: 0h4m32s