[2023-06-16 20:29:01,631] [INFO] DFAST_QC pipeline started.
[2023-06-16 20:29:01,634] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 20:29:01,635] [INFO] DQC Reference Directory: /var/lib/cwl/stg7bd186df-4ad9-4af3-9fdc-674c74194362/dqc_reference
[2023-06-16 20:29:03,369] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 20:29:03,371] [INFO] Task started: Prodigal
[2023-06-16 20:29:03,371] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f99935e-3f55-4e15-9328-1d6bd89f5c3e/GCA_003166375.1_20110700_S2D_genomic.fna.gz | prodigal -d GCA_003166375.1_20110700_S2D_genomic.fna/cds.fna -a GCA_003166375.1_20110700_S2D_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 20:29:12,867] [INFO] Task succeeded: Prodigal
[2023-06-16 20:29:12,867] [INFO] Task started: HMMsearch
[2023-06-16 20:29:12,867] [INFO] Running command: hmmsearch --tblout GCA_003166375.1_20110700_S2D_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7bd186df-4ad9-4af3-9fdc-674c74194362/dqc_reference/reference_markers.hmm GCA_003166375.1_20110700_S2D_genomic.fna/protein.faa > /dev/null
[2023-06-16 20:29:13,123] [INFO] Task succeeded: HMMsearch
[2023-06-16 20:29:13,125] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2f99935e-3f55-4e15-9328-1d6bd89f5c3e/GCA_003166375.1_20110700_S2D_genomic.fna.gz]
[2023-06-16 20:29:13,175] [INFO] Query marker FASTA was written to GCA_003166375.1_20110700_S2D_genomic.fna/markers.fasta
[2023-06-16 20:29:13,175] [INFO] Task started: Blastn
[2023-06-16 20:29:13,175] [INFO] Running command: blastn -query GCA_003166375.1_20110700_S2D_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bd186df-4ad9-4af3-9fdc-674c74194362/dqc_reference/reference_markers.fasta -out GCA_003166375.1_20110700_S2D_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:29:13,909] [INFO] Task succeeded: Blastn
[2023-06-16 20:29:13,913] [INFO] Selected 20 target genomes.
[2023-06-16 20:29:13,914] [INFO] Target genome list was writen to GCA_003166375.1_20110700_S2D_genomic.fna/target_genomes.txt
[2023-06-16 20:29:13,918] [INFO] Task started: fastANI
[2023-06-16 20:29:13,918] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f99935e-3f55-4e15-9328-1d6bd89f5c3e/GCA_003166375.1_20110700_S2D_genomic.fna.gz --refList GCA_003166375.1_20110700_S2D_genomic.fna/target_genomes.txt --output GCA_003166375.1_20110700_S2D_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 20:29:30,219] [INFO] Task succeeded: fastANI
[2023-06-16 20:29:30,219] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7bd186df-4ad9-4af3-9fdc-674c74194362/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 20:29:30,220] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7bd186df-4ad9-4af3-9fdc-674c74194362/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 20:29:30,242] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 20:29:30,242] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 20:29:30,243] [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 salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.0236	78	1026	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	75.9139	70	1026	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	75.8862	100	1026	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.4627	94	1026	95	below_threshold
Nocardioides gansuensis	strain=WSJ-1	GCA_003076135.1	2138300	2138300	type	True	75.377	61	1026	95	below_threshold
Streptomyces smaragdinus	strain=RB5	GCA_009604385.1	2585196	2585196	type	True	75.0427	52	1026	95	below_threshold
Streptomyces griseorubiginosus	strain=DSM 40469	GCA_001514195.1	67304	67304	type	True	75.0384	81	1026	95	below_threshold
Streptomyces umbrinus	strain=JCM 4521	GCA_014650195.1	67370	67370	type	True	75.0096	73	1026	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	74.9986	55	1026	95	below_threshold
Pseudonocardia xinjiangensis	strain=JCM 11839	GCA_012911925.1	75289	75289	type	True	74.9635	79	1026	95	below_threshold
Pseudonocardia broussonetiae	strain=Gen 01	GCA_013155125.1	2736640	2736640	type	True	74.9256	91	1026	95	below_threshold
Sinomonas mesophila	strain=MPKL 26	GCA_001999765.1	1531955	1531955	type	True	74.8553	50	1026	95	below_threshold
Streptomyces antimycoticus	strain=NBRC 12839	GCA_005405925.1	68175	68175	type	True	74.6814	82	1026	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 20:29:30,248] [INFO] DFAST Taxonomy check result was written to GCA_003166375.1_20110700_S2D_genomic.fna/tc_result.tsv
[2023-06-16 20:29:30,249] [INFO] ===== Taxonomy check completed =====
[2023-06-16 20:29:30,250] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 20:29:30,250] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7bd186df-4ad9-4af3-9fdc-674c74194362/dqc_reference/checkm_data
[2023-06-16 20:29:30,251] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 20:29:30,295] [INFO] Task started: CheckM
[2023-06-16 20:29:30,296] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003166375.1_20110700_S2D_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003166375.1_20110700_S2D_genomic.fna/checkm_input GCA_003166375.1_20110700_S2D_genomic.fna/checkm_result
[2023-06-16 20:30:02,232] [INFO] Task succeeded: CheckM
[2023-06-16 20:30:02,234] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 20:30:02,258] [INFO] ===== Completeness check finished =====
[2023-06-16 20:30:02,259] [INFO] ===== Start GTDB Search =====
[2023-06-16 20:30:02,259] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003166375.1_20110700_S2D_genomic.fna/markers.fasta)
[2023-06-16 20:30:02,259] [INFO] Task started: Blastn
[2023-06-16 20:30:02,260] [INFO] Running command: blastn -query GCA_003166375.1_20110700_S2D_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bd186df-4ad9-4af3-9fdc-674c74194362/dqc_reference/reference_markers_gtdb.fasta -out GCA_003166375.1_20110700_S2D_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:30:03,373] [INFO] Task succeeded: Blastn
[2023-06-16 20:30:03,378] [INFO] Selected 10 target genomes.
[2023-06-16 20:30:03,378] [INFO] Target genome list was writen to GCA_003166375.1_20110700_S2D_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 20:30:03,380] [INFO] Task started: fastANI
[2023-06-16 20:30:03,380] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f99935e-3f55-4e15-9328-1d6bd89f5c3e/GCA_003166375.1_20110700_S2D_genomic.fna.gz --refList GCA_003166375.1_20110700_S2D_genomic.fna/target_genomes_gtdb.txt --output GCA_003166375.1_20110700_S2D_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 20:30:09,318] [INFO] Task succeeded: fastANI
[2023-06-16 20:30:09,330] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 20:30:09,330] [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_003166375.1	s__Fen-455 sp003166375	100.0	1017	1026	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bog-793;g__Fen-455	95.0	98.47	95.00	0.77	0.72	7	conclusive
GCA_003170375.1	s__Fen-455 sp003170375	89.2069	442	1026	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bog-793;g__Fen-455	95.0	98.62	98.35	0.78	0.71	12	-
GCA_003139355.1	s__Fen-455 sp003139355	85.1832	570	1026	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bog-793;g__Fen-455	95.0	99.71	99.34	0.89	0.84	20	-
GCA_003140595.1	s__Fen-455 sp003140595	83.848	622	1026	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bog-793;g__Fen-455	95.0	99.78	99.58	0.92	0.82	27	-
GCA_003159795.1	s__Bog-793 sp003159795	77.8327	130	1026	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bog-793;g__Bog-793	95.0	99.80	99.71	0.91	0.89	3	-
GCA_003136185.1	s__Palsa-601 sp003136185	76.4612	127	1026	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bog-793;g__Palsa-601	95.0	99.68	99.63	0.86	0.84	3	-
GCA_005888395.1	s__AC-25 sp005888395	76.3325	73	1026	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-25;g__AC-25	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 20:30:09,332] [INFO] GTDB search result was written to GCA_003166375.1_20110700_S2D_genomic.fna/result_gtdb.tsv
[2023-06-16 20:30:09,333] [INFO] ===== GTDB Search completed =====
[2023-06-16 20:30:09,336] [INFO] DFAST_QC result json was written to GCA_003166375.1_20110700_S2D_genomic.fna/dqc_result.json
[2023-06-16 20:30:09,336] [INFO] DFAST_QC completed!
[2023-06-16 20:30:09,336] [INFO] Total running time: 0h1m8s