[2024-01-24 10:47:06,592] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,601] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb635bf6-c713-46ec-a194-f1bb3ecbd2ff/dqc_reference
[2024-01-24 10:47:12,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,815] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,815] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ea44e64-aba2-43b4-a644-ee8db8743a12/GCF_019396345.1_ASM1939634v1_genomic.fna.gz | prodigal -d GCF_019396345.1_ASM1939634v1_genomic.fna/cds.fna -a GCF_019396345.1_ASM1939634v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:55,248] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:55,248] [INFO] Task started: HMMsearch
[2024-01-24 10:47:55,248] [INFO] Running command: hmmsearch --tblout GCF_019396345.1_ASM1939634v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb635bf6-c713-46ec-a194-f1bb3ecbd2ff/dqc_reference/reference_markers.hmm GCF_019396345.1_ASM1939634v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:55,773] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:55,775] [INFO] Found 6/6 markers.
[2024-01-24 10:47:55,888] [INFO] Query marker FASTA was written to GCF_019396345.1_ASM1939634v1_genomic.fna/markers.fasta
[2024-01-24 10:47:55,889] [INFO] Task started: Blastn
[2024-01-24 10:47:55,889] [INFO] Running command: blastn -query GCF_019396345.1_ASM1939634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb635bf6-c713-46ec-a194-f1bb3ecbd2ff/dqc_reference/reference_markers.fasta -out GCF_019396345.1_ASM1939634v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:57,261] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:57,265] [INFO] Selected 14 target genomes.
[2024-01-24 10:47:57,266] [INFO] Target genome list was writen to GCF_019396345.1_ASM1939634v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:57,279] [INFO] Task started: fastANI
[2024-01-24 10:47:57,279] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ea44e64-aba2-43b4-a644-ee8db8743a12/GCF_019396345.1_ASM1939634v1_genomic.fna.gz --refList GCF_019396345.1_ASM1939634v1_genomic.fna/target_genomes.txt --output GCF_019396345.1_ASM1939634v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:34,505] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:34,506] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb635bf6-c713-46ec-a194-f1bb3ecbd2ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:34,507] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb635bf6-c713-46ec-a194-f1bb3ecbd2ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:34,522] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:34,523] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:34,523] [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 guangzhouensis	strain=CGMCC 4.7101	GCA_019396345.1	1291555	1291555	type	True	100.0	4496	4497	95	conclusive
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	90.5729	2945	4497	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	86.6362	1384	4497	95	below_threshold
Nonomuraea cavernae	strain=CGMCC 4.7368	GCA_014646355.1	2045107	2045107	type	True	84.1061	1770	4497	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	83.9788	1803	4497	95	below_threshold
Nonomuraea lactucae	strain=NEAU-YG30	GCA_003313395.1	2249762	2249762	type	True	83.7795	1478	4497	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	83.7651	2425	4497	95	below_threshold
Nonomuraea muscovyensis	strain=DSM 45913	GCA_014207745.1	1124761	1124761	type	True	83.5751	2057	4497	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	83.2559	2168	4497	95	below_threshold
Nonomuraea montanisoli	strain=SMC 257	GCA_013363975.1	2741721	2741721	type	True	83.2197	2190	4497	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	83.1874	2133	4497	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	83.1684	2135	4497	95	below_threshold
Nonomuraea indica	strain=DRQ-2	GCA_002850745.1	1581193	1581193	type	True	83.1525	1915	4497	95	below_threshold
Nonomuraea maritima	strain=CGMCC 4.5681	GCA_900100395.1	683260	683260	type	True	82.2077	1720	4497	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:34,525] [INFO] DFAST Taxonomy check result was written to GCF_019396345.1_ASM1939634v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:34,526] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:34,526] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:34,526] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb635bf6-c713-46ec-a194-f1bb3ecbd2ff/dqc_reference/checkm_data
[2024-01-24 10:48:34,527] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:34,646] [INFO] Task started: CheckM
[2024-01-24 10:48:34,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019396345.1_ASM1939634v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019396345.1_ASM1939634v1_genomic.fna/checkm_input GCF_019396345.1_ASM1939634v1_genomic.fna/checkm_result
[2024-01-24 10:50:42,070] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:42,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.60%
Strain heterogeneity: 60.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:42,112] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:42,112] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:42,113] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019396345.1_ASM1939634v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:42,113] [INFO] Task started: Blastn
[2024-01-24 10:50:42,113] [INFO] Running command: blastn -query GCF_019396345.1_ASM1939634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb635bf6-c713-46ec-a194-f1bb3ecbd2ff/dqc_reference/reference_markers_gtdb.fasta -out GCF_019396345.1_ASM1939634v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:44,222] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:44,227] [INFO] Selected 14 target genomes.
[2024-01-24 10:50:44,227] [INFO] Target genome list was writen to GCF_019396345.1_ASM1939634v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:44,233] [INFO] Task started: fastANI
[2024-01-24 10:50:44,234] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ea44e64-aba2-43b4-a644-ee8db8743a12/GCF_019396345.1_ASM1939634v1_genomic.fna.gz --refList GCF_019396345.1_ASM1939634v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019396345.1_ASM1939634v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:51:22,327] [INFO] Task succeeded: fastANI
[2024-01-24 10:51:22,343] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:51:22,343] [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_018603905.1	s__Nonomuraea sp018603905	93.931	3299	4497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646355.1	s__Nonomuraea cavernae	84.0731	1777	4497	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	83.7988	2416	4497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207745.1	s__Nonomuraea muscovyensis	83.621	2047	4497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108335.1	s__Nonomuraea solani	83.4321	2527	4497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013363975.1	s__Nonomuraea montanisoli	83.2439	2181	4497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013363995.1	s__Nonomuraea rhodomycinica	83.1514	2130	4497	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	83.1504	1915	4497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283785.1	s__Nonomuraea sp013283785	82.8459	1968	4497	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	82.7953	2250	4497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086045.1	s__Nonomuraea sp008086045	82.7545	2301	4497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531495.1	s__Nonomuraea sp018531495	82.5635	2185	4497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100395.1	s__Nonomuraea maritima	82.2062	1721	4497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017896165.1	s__Microbispora sp017896165	79.0709	1194	4497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:51:22,346] [INFO] GTDB search result was written to GCF_019396345.1_ASM1939634v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:51:22,347] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:51:22,350] [INFO] DFAST_QC result json was written to GCF_019396345.1_ASM1939634v1_genomic.fna/dqc_result.json
[2024-01-24 10:51:22,351] [INFO] DFAST_QC completed!
[2024-01-24 10:51:22,351] [INFO] Total running time: 0h4m16s