[2023-06-19 08:30:07,254] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:30:07,258] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:30:07,259] [INFO] DQC Reference Directory: /var/lib/cwl/stg133e5f7c-570e-4abc-a63c-9326e0ceae7b/dqc_reference
[2023-06-19 08:30:08,555] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:30:08,556] [INFO] Task started: Prodigal
[2023-06-19 08:30:08,556] [INFO] Running command: gunzip -c /var/lib/cwl/stg68d2d60b-2be8-4f00-aa61-873033f300f0/GCA_018970285.1_ASM1897028v1_genomic.fna.gz | prodigal -d GCA_018970285.1_ASM1897028v1_genomic.fna/cds.fna -a GCA_018970285.1_ASM1897028v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:30:19,932] [INFO] Task succeeded: Prodigal
[2023-06-19 08:30:19,933] [INFO] Task started: HMMsearch
[2023-06-19 08:30:19,933] [INFO] Running command: hmmsearch --tblout GCA_018970285.1_ASM1897028v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg133e5f7c-570e-4abc-a63c-9326e0ceae7b/dqc_reference/reference_markers.hmm GCA_018970285.1_ASM1897028v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:30:20,174] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:30:20,176] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg68d2d60b-2be8-4f00-aa61-873033f300f0/GCA_018970285.1_ASM1897028v1_genomic.fna.gz]
[2023-06-19 08:30:20,209] [INFO] Query marker FASTA was written to GCA_018970285.1_ASM1897028v1_genomic.fna/markers.fasta
[2023-06-19 08:30:20,210] [INFO] Task started: Blastn
[2023-06-19 08:30:20,210] [INFO] Running command: blastn -query GCA_018970285.1_ASM1897028v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg133e5f7c-570e-4abc-a63c-9326e0ceae7b/dqc_reference/reference_markers.fasta -out GCA_018970285.1_ASM1897028v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:30:20,957] [INFO] Task succeeded: Blastn
[2023-06-19 08:30:20,964] [INFO] Selected 22 target genomes.
[2023-06-19 08:30:20,965] [INFO] Target genome list was writen to GCA_018970285.1_ASM1897028v1_genomic.fna/target_genomes.txt
[2023-06-19 08:30:20,972] [INFO] Task started: fastANI
[2023-06-19 08:30:20,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg68d2d60b-2be8-4f00-aa61-873033f300f0/GCA_018970285.1_ASM1897028v1_genomic.fna.gz --refList GCA_018970285.1_ASM1897028v1_genomic.fna/target_genomes.txt --output GCA_018970285.1_ASM1897028v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:30:37,254] [INFO] Task succeeded: fastANI
[2023-06-19 08:30:37,254] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg133e5f7c-570e-4abc-a63c-9326e0ceae7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:30:37,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg133e5f7c-570e-4abc-a63c-9326e0ceae7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:30:37,267] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:30:37,267] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 08:30:37,268] [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
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.6446	57	258	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.4992	74	258	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.4075	81	258	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	74.9292	55	258	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	74.8855	67	258	95	below_threshold
Pseudonocardia ammonioxydans	strain=CGMCC 4.1877	GCA_900115005.1	260086	260086	type	True	74.8806	63	258	95	below_threshold
Micromonospora terminaliae	strain=TMS7	GCA_010671825.1	1914461	1914461	type	True	74.774	55	258	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:30:37,269] [INFO] DFAST Taxonomy check result was written to GCA_018970285.1_ASM1897028v1_genomic.fna/tc_result.tsv
[2023-06-19 08:30:37,270] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:30:37,270] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:30:37,270] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg133e5f7c-570e-4abc-a63c-9326e0ceae7b/dqc_reference/checkm_data
[2023-06-19 08:30:37,271] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:30:37,302] [INFO] Task started: CheckM
[2023-06-19 08:30:37,302] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018970285.1_ASM1897028v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018970285.1_ASM1897028v1_genomic.fna/checkm_input GCA_018970285.1_ASM1897028v1_genomic.fna/checkm_result
[2023-06-19 08:31:11,471] [INFO] Task succeeded: CheckM
[2023-06-19 08:31:11,473] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.70%
Contamintation: 1.56%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:31:11,501] [INFO] ===== Completeness check finished =====
[2023-06-19 08:31:11,501] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:31:11,501] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018970285.1_ASM1897028v1_genomic.fna/markers.fasta)
[2023-06-19 08:31:11,502] [INFO] Task started: Blastn
[2023-06-19 08:31:11,502] [INFO] Running command: blastn -query GCA_018970285.1_ASM1897028v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg133e5f7c-570e-4abc-a63c-9326e0ceae7b/dqc_reference/reference_markers_gtdb.fasta -out GCA_018970285.1_ASM1897028v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:31:12,442] [INFO] Task succeeded: Blastn
[2023-06-19 08:31:12,446] [INFO] Selected 12 target genomes.
[2023-06-19 08:31:12,447] [INFO] Target genome list was writen to GCA_018970285.1_ASM1897028v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:31:12,480] [INFO] Task started: fastANI
[2023-06-19 08:31:12,480] [INFO] Running command: fastANI --query /var/lib/cwl/stg68d2d60b-2be8-4f00-aa61-873033f300f0/GCA_018970285.1_ASM1897028v1_genomic.fna.gz --refList GCA_018970285.1_ASM1897028v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018970285.1_ASM1897028v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:31:21,272] [INFO] Task succeeded: fastANI
[2023-06-19 08:31:21,284] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:31:21,284] [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
GCA_005777415.1	s__SXMI01 sp005777415	96.8878	230	258	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	99.41	99.40	0.88	0.87	3	conclusive
GCA_903925745.1	s__SXMI01 sp903925745	82.0381	205	258	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873135.1	s__SXMI01 sp903873135	81.1131	190	258	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	99.54	99.49	0.91	0.89	9	-
GCA_903852755.1	s__SXMI01 sp903852755	80.5194	182	258	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	99.71	99.61	0.93	0.92	10	-
GCA_903868545.1	s__CAIPVR01 sp903868545	79.8565	147	258	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAIPVR01	95.0	99.51	99.50	0.87	0.86	3	-
GCA_903953195.1	s__SXMI01 sp903953195	79.1948	154	258	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	98.58	98.55	0.81	0.80	3	-
GCF_004349235.1	s__Spirillospora darangshiensis	74.8941	50	258	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115005.1	s__Pseudonocardia ammonioxydans	74.8891	62	258	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002904295.1	s__Amycolatopsis sp002904295	74.5942	58	258	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:31:21,286] [INFO] GTDB search result was written to GCA_018970285.1_ASM1897028v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:31:21,287] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:31:21,290] [INFO] DFAST_QC result json was written to GCA_018970285.1_ASM1897028v1_genomic.fna/dqc_result.json
[2023-06-19 08:31:21,290] [INFO] DFAST_QC completed!
[2023-06-19 08:31:21,290] [INFO] Total running time: 0h1m14s