[2023-06-19 13:30:58,791] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:30:58,797] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:30:58,797] [INFO] DQC Reference Directory: /var/lib/cwl/stg878874f8-3f20-4f71-bbd9-f46f15bf7a41/dqc_reference
[2023-06-19 13:31:00,277] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:31:00,278] [INFO] Task started: Prodigal
[2023-06-19 13:31:00,278] [INFO] Running command: gunzip -c /var/lib/cwl/stgb22ed22a-97c6-47c5-a527-d9d075bc0477/GCA_013213745.1_ASM1321374v1_genomic.fna.gz | prodigal -d GCA_013213745.1_ASM1321374v1_genomic.fna/cds.fna -a GCA_013213745.1_ASM1321374v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:31:11,597] [INFO] Task succeeded: Prodigal
[2023-06-19 13:31:11,598] [INFO] Task started: HMMsearch
[2023-06-19 13:31:11,598] [INFO] Running command: hmmsearch --tblout GCA_013213745.1_ASM1321374v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg878874f8-3f20-4f71-bbd9-f46f15bf7a41/dqc_reference/reference_markers.hmm GCA_013213745.1_ASM1321374v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:31:11,918] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:31:11,920] [INFO] Found 6/6 markers.
[2023-06-19 13:31:11,955] [INFO] Query marker FASTA was written to GCA_013213745.1_ASM1321374v1_genomic.fna/markers.fasta
[2023-06-19 13:31:11,956] [INFO] Task started: Blastn
[2023-06-19 13:31:11,956] [INFO] Running command: blastn -query GCA_013213745.1_ASM1321374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg878874f8-3f20-4f71-bbd9-f46f15bf7a41/dqc_reference/reference_markers.fasta -out GCA_013213745.1_ASM1321374v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:31:12,788] [INFO] Task succeeded: Blastn
[2023-06-19 13:31:12,801] [INFO] Selected 12 target genomes.
[2023-06-19 13:31:12,801] [INFO] Target genome list was writen to GCA_013213745.1_ASM1321374v1_genomic.fna/target_genomes.txt
[2023-06-19 13:31:12,804] [INFO] Task started: fastANI
[2023-06-19 13:31:12,804] [INFO] Running command: fastANI --query /var/lib/cwl/stgb22ed22a-97c6-47c5-a527-d9d075bc0477/GCA_013213745.1_ASM1321374v1_genomic.fna.gz --refList GCA_013213745.1_ASM1321374v1_genomic.fna/target_genomes.txt --output GCA_013213745.1_ASM1321374v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:31:23,205] [INFO] Task succeeded: fastANI
[2023-06-19 13:31:23,206] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg878874f8-3f20-4f71-bbd9-f46f15bf7a41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:31:23,206] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg878874f8-3f20-4f71-bbd9-f46f15bf7a41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:31:23,216] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 13:31:23,216] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 13:31:23,216] [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
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	77.9287	293	1090	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	77.7738	374	1090	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	77.6151	317	1090	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	77.3743	311	1090	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.4658	153	1090	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.4088	173	1090	95	below_threshold
Nocardioides terrae	strain=CGMCC 1.7056	GCA_900112345.1	574651	574651	type	True	75.4083	84	1090	95	below_threshold
Propioniciclava soli	strain=YIM S02567	GCA_014858005.1	2775081	2775081	type	True	75.3715	69	1090	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	75.2168	81	1090	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	75.0364	129	1090	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 13:31:23,218] [INFO] DFAST Taxonomy check result was written to GCA_013213745.1_ASM1321374v1_genomic.fna/tc_result.tsv
[2023-06-19 13:31:23,219] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:31:23,219] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:31:23,219] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg878874f8-3f20-4f71-bbd9-f46f15bf7a41/dqc_reference/checkm_data
[2023-06-19 13:31:23,221] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:31:23,270] [INFO] Task started: CheckM
[2023-06-19 13:31:23,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013213745.1_ASM1321374v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013213745.1_ASM1321374v1_genomic.fna/checkm_input GCA_013213745.1_ASM1321374v1_genomic.fna/checkm_result
[2023-06-19 13:32:05,988] [INFO] Task succeeded: CheckM
[2023-06-19 13:32:05,990] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 13:32:06,011] [INFO] ===== Completeness check finished =====
[2023-06-19 13:32:06,011] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:32:06,012] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013213745.1_ASM1321374v1_genomic.fna/markers.fasta)
[2023-06-19 13:32:06,012] [INFO] Task started: Blastn
[2023-06-19 13:32:06,012] [INFO] Running command: blastn -query GCA_013213745.1_ASM1321374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg878874f8-3f20-4f71-bbd9-f46f15bf7a41/dqc_reference/reference_markers_gtdb.fasta -out GCA_013213745.1_ASM1321374v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:32:07,245] [INFO] Task succeeded: Blastn
[2023-06-19 13:32:07,250] [INFO] Selected 13 target genomes.
[2023-06-19 13:32:07,250] [INFO] Target genome list was writen to GCA_013213745.1_ASM1321374v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:32:07,255] [INFO] Task started: fastANI
[2023-06-19 13:32:07,255] [INFO] Running command: fastANI --query /var/lib/cwl/stgb22ed22a-97c6-47c5-a527-d9d075bc0477/GCA_013213745.1_ASM1321374v1_genomic.fna.gz --refList GCA_013213745.1_ASM1321374v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013213745.1_ASM1321374v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:32:16,118] [INFO] Task succeeded: fastANI
[2023-06-19 13:32:16,134] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 13:32:16,134] [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_013213745.1	s__JABSQH01 sp013213745	100.0	1086	1090	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JABSQH01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000350145.1	s__Ilumatobacter_A nonamiensis	77.9173	294	1090	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002175.1	s__Ilumatobacter_A sp013002175	77.8951	319	1090	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000348785.1	s__Ilumatobacter_A coccineus	77.7979	372	1090	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693335.1	s__SKSP01 sp007693335	77.7164	266	1090	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364865.1	s__Ilumatobacter fluminis	77.6038	318	1090	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007122945.1	s__SKSP01 sp007122945	77.5092	278	1090	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	99.05	99.05	0.83	0.83	2	-
GCF_003426815.1	s__Desertimonas flava	77.3506	313	1090	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Desertimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018666235.1	s__Ilumatobacter_A sp018666235	77.1894	219	1090	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	99.79	99.78	0.94	0.93	4	-
GCA_010024485.1	s__Casp-actino5 sp010024485	77.0567	100	1090	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	98.53	98.53	0.77	0.77	2	-
GCA_018969405.1	s__F1-20-MAGs160 sp018969405	76.5709	99	1090	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	76.2626	150	1090	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005787035.1	s__Casp-actino8 sp005787035	76.2179	85	1090	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 13:32:16,136] [INFO] GTDB search result was written to GCA_013213745.1_ASM1321374v1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:32:16,137] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:32:16,141] [INFO] DFAST_QC result json was written to GCA_013213745.1_ASM1321374v1_genomic.fna/dqc_result.json
[2023-06-19 13:32:16,142] [INFO] DFAST_QC completed!
[2023-06-19 13:32:16,142] [INFO] Total running time: 0h1m17s