[2024-01-24 14:22:44,701] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:44,708] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:44,708] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f911af7-9a0f-4c60-b090-279e757dc722/dqc_reference
[2024-01-24 14:22:45,891] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:45,892] [INFO] Task started: Prodigal
[2024-01-24 14:22:45,892] [INFO] Running command: gunzip -c /var/lib/cwl/stg036d48aa-09bf-4a23-ab65-6ea9e3b4b6be/GCF_019397265.1_ASM1939726v1_genomic.fna.gz | prodigal -d GCF_019397265.1_ASM1939726v1_genomic.fna/cds.fna -a GCF_019397265.1_ASM1939726v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:10,660] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:10,661] [INFO] Task started: HMMsearch
[2024-01-24 14:23:10,661] [INFO] Running command: hmmsearch --tblout GCF_019397265.1_ASM1939726v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f911af7-9a0f-4c60-b090-279e757dc722/dqc_reference/reference_markers.hmm GCF_019397265.1_ASM1939726v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:11,149] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:11,152] [INFO] Found 6/6 markers.
[2024-01-24 14:23:11,228] [INFO] Query marker FASTA was written to GCF_019397265.1_ASM1939726v1_genomic.fna/markers.fasta
[2024-01-24 14:23:11,228] [INFO] Task started: Blastn
[2024-01-24 14:23:11,228] [INFO] Running command: blastn -query GCF_019397265.1_ASM1939726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f911af7-9a0f-4c60-b090-279e757dc722/dqc_reference/reference_markers.fasta -out GCF_019397265.1_ASM1939726v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:12,614] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:12,617] [INFO] Selected 16 target genomes.
[2024-01-24 14:23:12,617] [INFO] Target genome list was writen to GCF_019397265.1_ASM1939726v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:12,626] [INFO] Task started: fastANI
[2024-01-24 14:23:12,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg036d48aa-09bf-4a23-ab65-6ea9e3b4b6be/GCF_019397265.1_ASM1939726v1_genomic.fna.gz --refList GCF_019397265.1_ASM1939726v1_genomic.fna/target_genomes.txt --output GCF_019397265.1_ASM1939726v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:59,642] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:59,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f911af7-9a0f-4c60-b090-279e757dc722/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:59,643] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f911af7-9a0f-4c60-b090-279e757dc722/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:59,656] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:23:59,656] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:59,656] [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
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	100.0	3022	3024	95	conclusive
Nonomuraea coxensis	strain=DSM 45129	GCA_000379885.1	404386	404386	type	True	99.9671	2944	3024	95	conclusive
Nonomuraea wenchangensis	strain=CGMCC 4.5598	GCA_900111685.1	568860	568860	type	True	94.1618	2531	3024	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	85.3075	2010	3024	95	below_threshold
Nonomuraea polychroma	strain=DSM 43925	GCA_004011505.1	46176	46176	type	True	85.2915	2041	3024	95	below_threshold
Nonomuraea turkmeniaca	strain=DSM 43926	GCA_005889735.1	103838	103838	type	True	85.2503	1937	3024	95	below_threshold
Nonomuraea rubra	strain=DSM 43768	GCA_014207985.1	46180	46180	type	True	85.0697	2195	3024	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	84.9907	2045	3024	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	84.9698	2042	3024	95	below_threshold
Nonomuraea jabiensis	strain=DSM 45507	GCA_014204795.1	882448	882448	type	True	84.7627	2145	3024	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	84.7328	2133	3024	95	below_threshold
Nonomuraea spiralis	strain=JCM 3286	GCA_014648435.1	46182	46182	type	True	84.4635	2005	3024	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	83.7768	1193	3024	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	83.7015	1719	3024	95	below_threshold
Nonomuraea indica	strain=DRQ-2	GCA_002850745.1	1581193	1581193	type	True	83.2823	1709	3024	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	82.7927	1870	3024	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:59,658] [INFO] DFAST Taxonomy check result was written to GCF_019397265.1_ASM1939726v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:59,659] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:59,659] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:59,659] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f911af7-9a0f-4c60-b090-279e757dc722/dqc_reference/checkm_data
[2024-01-24 14:23:59,661] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:59,744] [INFO] Task started: CheckM
[2024-01-24 14:23:59,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019397265.1_ASM1939726v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019397265.1_ASM1939726v1_genomic.fna/checkm_input GCF_019397265.1_ASM1939726v1_genomic.fna/checkm_result
[2024-01-24 14:25:57,784] [INFO] Task succeeded: CheckM
[2024-01-24 14:25:57,785] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.36%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 14:25:57,815] [INFO] ===== Completeness check finished =====
[2024-01-24 14:25:57,816] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:25:57,816] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019397265.1_ASM1939726v1_genomic.fna/markers.fasta)
[2024-01-24 14:25:57,816] [INFO] Task started: Blastn
[2024-01-24 14:25:57,817] [INFO] Running command: blastn -query GCF_019397265.1_ASM1939726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f911af7-9a0f-4c60-b090-279e757dc722/dqc_reference/reference_markers_gtdb.fasta -out GCF_019397265.1_ASM1939726v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:26:00,130] [INFO] Task succeeded: Blastn
[2024-01-24 14:26:00,133] [INFO] Selected 12 target genomes.
[2024-01-24 14:26:00,133] [INFO] Target genome list was writen to GCF_019397265.1_ASM1939726v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:26:00,148] [INFO] Task started: fastANI
[2024-01-24 14:26:00,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg036d48aa-09bf-4a23-ab65-6ea9e3b4b6be/GCF_019397265.1_ASM1939726v1_genomic.fna.gz --refList GCF_019397265.1_ASM1939726v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019397265.1_ASM1939726v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:26:37,671] [INFO] Task succeeded: fastANI
[2024-01-24 14:26:37,686] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:26:37,686] [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_000379885.1	s__Nonomuraea coxensis	99.9671	2944	3024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900111685.1	s__Nonomuraea wenchangensis	94.1528	2533	3024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008065375.1	s__Nonomuraea sp008065375	85.5638	2051	3024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011505.1	s__Nonomuraea polychroma	85.373	2025	3024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005893125.1	s__Nonomuraea sp005893125	85.3321	2003	3024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207985.1	s__Nonomuraea rubra	85.088	2191	3024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001935.1	s__Nonomuraea fuscirosea	85.0289	2098	3024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873145.1	s__Nonomuraea angiospora	84.7473	2125	3024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204795.1	s__Nonomuraea jabiensis	84.735	2151	3024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648435.1	s__Nonomuraea spiralis	84.5001	1998	3024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.03	98.03	0.91	0.91	2	-
GCF_014646355.1	s__Nonomuraea cavernae	83.6495	1734	3024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002850745.1	s__Nonomuraea indica	83.2794	1709	3024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:26:37,689] [INFO] GTDB search result was written to GCF_019397265.1_ASM1939726v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:26:37,690] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:26:37,694] [INFO] DFAST_QC result json was written to GCF_019397265.1_ASM1939726v1_genomic.fna/dqc_result.json
[2024-01-24 14:26:37,694] [INFO] DFAST_QC completed!
[2024-01-24 14:26:37,694] [INFO] Total running time: 0h3m53s