[2024-01-24 14:21:50,903] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:21:50,904] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:21:50,904] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe4e9015-f1ca-43bd-a56d-03938884c11e/dqc_reference
[2024-01-24 14:21:52,320] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:21:52,321] [INFO] Task started: Prodigal
[2024-01-24 14:21:52,321] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a663a35-bff7-47c2-812f-e1687a09fe3e/GCF_014203735.1_ASM1420373v1_genomic.fna.gz | prodigal -d GCF_014203735.1_ASM1420373v1_genomic.fna/cds.fna -a GCF_014203735.1_ASM1420373v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:32,869] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:32,869] [INFO] Task started: HMMsearch
[2024-01-24 14:22:32,869] [INFO] Running command: hmmsearch --tblout GCF_014203735.1_ASM1420373v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe4e9015-f1ca-43bd-a56d-03938884c11e/dqc_reference/reference_markers.hmm GCF_014203735.1_ASM1420373v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:33,266] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:33,267] [INFO] Found 6/6 markers.
[2024-01-24 14:22:33,342] [INFO] Query marker FASTA was written to GCF_014203735.1_ASM1420373v1_genomic.fna/markers.fasta
[2024-01-24 14:22:33,342] [INFO] Task started: Blastn
[2024-01-24 14:22:33,343] [INFO] Running command: blastn -query GCF_014203735.1_ASM1420373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe4e9015-f1ca-43bd-a56d-03938884c11e/dqc_reference/reference_markers.fasta -out GCF_014203735.1_ASM1420373v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:34,685] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:34,688] [INFO] Selected 14 target genomes.
[2024-01-24 14:22:34,688] [INFO] Target genome list was writen to GCF_014203735.1_ASM1420373v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:34,701] [INFO] Task started: fastANI
[2024-01-24 14:22:34,701] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a663a35-bff7-47c2-812f-e1687a09fe3e/GCF_014203735.1_ASM1420373v1_genomic.fna.gz --refList GCF_014203735.1_ASM1420373v1_genomic.fna/target_genomes.txt --output GCF_014203735.1_ASM1420373v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:06,418] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:06,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe4e9015-f1ca-43bd-a56d-03938884c11e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:06,419] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe4e9015-f1ca-43bd-a56d-03938884c11e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:06,431] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:23:06,431] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:06,431] [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
Actinophytocola algeriensis	strain=CECT 8960	GCA_014203735.1	1768010	1768010	type	True	100.0	3232	3232	95	conclusive
Actinophytocola algeriensis	strain=DSM 46746	GCA_014874055.1	1768010	1768010	type	True	99.9995	3232	3232	95	conclusive
Actinophytocola oryzae	strain=DSM 45499	GCA_004364325.1	502181	502181	type	True	82.7108	1942	3232	95	below_threshold
Actinophytocola xinjiangensis	strain=CGMCC 4.4663	GCA_001921215.1	485602	485602	type	True	80.433	1615	3232	95	below_threshold
Actinophytocola xanthii	strain=11-183	GCA_001921205.1	1912961	1912961	type	True	80.401	1501	3232	95	below_threshold
Actinokineospora alba	strain=DSM 45114	GCA_004362515.1	504798	504798	type	True	79.0578	1037	3232	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.5777	1009	3232	95	below_threshold
Actinokineospora auranticolor	strain=YU 961-1	GCA_002934265.1	155976	155976	type	True	78.5378	1090	3232	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.5288	1001	3232	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	78.4525	1235	3232	95	below_threshold
Saccharothrix saharensis	strain=DSM 45456	GCA_006716745.1	571190	571190	type	True	78.4434	1199	3232	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	78.2006	967	3232	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.0273	1243	3232	95	below_threshold
Lentzea aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	78.0164	1086	3232	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:06,433] [INFO] DFAST Taxonomy check result was written to GCF_014203735.1_ASM1420373v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:06,433] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:06,433] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:06,434] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe4e9015-f1ca-43bd-a56d-03938884c11e/dqc_reference/checkm_data
[2024-01-24 14:23:06,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:06,521] [INFO] Task started: CheckM
[2024-01-24 14:23:06,522] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203735.1_ASM1420373v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203735.1_ASM1420373v1_genomic.fna/checkm_input GCF_014203735.1_ASM1420373v1_genomic.fna/checkm_result
[2024-01-24 14:25:58,687] [INFO] Task succeeded: CheckM
[2024-01-24 14:25:58,688] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:25:58,715] [INFO] ===== Completeness check finished =====
[2024-01-24 14:25:58,715] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:25:58,716] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203735.1_ASM1420373v1_genomic.fna/markers.fasta)
[2024-01-24 14:25:58,716] [INFO] Task started: Blastn
[2024-01-24 14:25:58,716] [INFO] Running command: blastn -query GCF_014203735.1_ASM1420373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe4e9015-f1ca-43bd-a56d-03938884c11e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203735.1_ASM1420373v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:26:00,820] [INFO] Task succeeded: Blastn
[2024-01-24 14:26:00,823] [INFO] Selected 16 target genomes.
[2024-01-24 14:26:00,824] [INFO] Target genome list was writen to GCF_014203735.1_ASM1420373v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:26:00,944] [INFO] Task started: fastANI
[2024-01-24 14:26:00,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a663a35-bff7-47c2-812f-e1687a09fe3e/GCF_014203735.1_ASM1420373v1_genomic.fna.gz --refList GCF_014203735.1_ASM1420373v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203735.1_ASM1420373v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:26:35,916] [INFO] Task succeeded: fastANI
[2024-01-24 14:26:35,929] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:26:35,929] [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_014203735.1	s__Actinophytocola algeriensis	100.0	3232	3232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_004364325.1	s__Actinophytocola oryzae	82.685	1951	3232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009379765.1	s__Actinophytocola sp009379765	81.3668	1509	3232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001921215.1	s__Actinophytocola xinjiangensis	80.447	1611	3232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001921205.1	s__Actinophytocola xanthii	80.4036	1500	3232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362515.1	s__Actinokineospora alba	79.0337	1043	3232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	100.00	100.00	1.00	1.00	3	-
GCF_004362825.1	s__Labedaea rhizosphaerae	78.7913	1131	3232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Labedaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934265.1	s__Actinokineospora auranticolor	78.5664	1083	3232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716745.1	s__Actinosynnema saharense	78.4464	1194	3232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752005.1	s__Actinosynnema texasense	78.4464	1236	3232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
GCF_014653945.1	s__Amycolatopsis deserti	78.4189	1068	3232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739085.1	s__Amycolatopsis methanolica	78.3665	1009	3232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	96.3446	100.00	100.00	1.00	1.00	2	-
GCF_000695625.1	s__Amycolatopsis rifamycinica	78.1195	1144	3232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202285.1	s__Saccharomonospora muralis	78.1156	988	3232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003269295.1	s__Lentzea atacamensis	78.1018	1048	3232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	98.63	98.63	0.90	0.90	2	-
GCF_018263855.1	s__Kutzneria sp018263855	77.6937	1102	3232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:26:35,931] [INFO] GTDB search result was written to GCF_014203735.1_ASM1420373v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:26:35,932] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:26:35,936] [INFO] DFAST_QC result json was written to GCF_014203735.1_ASM1420373v1_genomic.fna/dqc_result.json
[2024-01-24 14:26:35,936] [INFO] DFAST_QC completed!
[2024-01-24 14:26:35,937] [INFO] Total running time: 0h4m45s