[2024-01-25 18:50:05,491] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:50:05,494] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:50:05,494] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bc687b3-42f7-47c1-b6f1-580fdb4d7de0/dqc_reference
[2024-01-25 18:50:06,632] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:50:06,633] [INFO] Task started: Prodigal
[2024-01-25 18:50:06,633] [INFO] Running command: gunzip -c /var/lib/cwl/stg8019d611-0a02-4330-8f64-081f479d3eae/GCF_000961885.1_ASM96188v1_genomic.fna.gz | prodigal -d GCF_000961885.1_ASM96188v1_genomic.fna/cds.fna -a GCF_000961885.1_ASM96188v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:50:26,544] [INFO] Task succeeded: Prodigal
[2024-01-25 18:50:26,544] [INFO] Task started: HMMsearch
[2024-01-25 18:50:26,544] [INFO] Running command: hmmsearch --tblout GCF_000961885.1_ASM96188v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bc687b3-42f7-47c1-b6f1-580fdb4d7de0/dqc_reference/reference_markers.hmm GCF_000961885.1_ASM96188v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:50:26,858] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:50:26,859] [INFO] Found 6/6 markers.
[2024-01-25 18:50:26,932] [INFO] Query marker FASTA was written to GCF_000961885.1_ASM96188v1_genomic.fna/markers.fasta
[2024-01-25 18:50:26,933] [INFO] Task started: Blastn
[2024-01-25 18:50:26,933] [INFO] Running command: blastn -query GCF_000961885.1_ASM96188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bc687b3-42f7-47c1-b6f1-580fdb4d7de0/dqc_reference/reference_markers.fasta -out GCF_000961885.1_ASM96188v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:28,289] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:28,293] [INFO] Selected 11 target genomes.
[2024-01-25 18:50:28,293] [INFO] Target genome list was writen to GCF_000961885.1_ASM96188v1_genomic.fna/target_genomes.txt
[2024-01-25 18:50:28,296] [INFO] Task started: fastANI
[2024-01-25 18:50:28,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg8019d611-0a02-4330-8f64-081f479d3eae/GCF_000961885.1_ASM96188v1_genomic.fna.gz --refList GCF_000961885.1_ASM96188v1_genomic.fna/target_genomes.txt --output GCF_000961885.1_ASM96188v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:50:55,598] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:55,599] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bc687b3-42f7-47c1-b6f1-580fdb4d7de0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:50:55,599] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bc687b3-42f7-47c1-b6f1-580fdb4d7de0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:50:55,607] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:50:55,607] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:50:55,607] [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
Streptomyces rubellomurinus	strain=ATCC 31215	GCA_000961885.1	359131	359131	type	True	100.0	2704	2716	95	conclusive
Kitasatospora aureofaciens	strain=ATCC 10762	GCA_001188955.3	1894	1894	type	True	88.6254	1912	2716	95	below_threshold
Kitasatospora aureofaciens	strain=NRRL 2209	GCA_000978515.1	1894	1894	type	True	88.5387	1625	2716	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	85.7255	1774	2716	95	below_threshold
Kitasatospora herbaricolor	strain=JCM 4138	GCA_014648975.1	68217	68217	type	True	84.1465	1638	2716	95	below_threshold
Kitasatospora indigofera	strain=JCM 4646	GCA_014655955.1	67307	67307	type	True	84.0628	1641	2716	95	below_threshold
Kitasatospora paracochleata	strain=DSM 41656	GCA_024172095.1	58354	58354	type	True	83.7014	1558	2716	95	below_threshold
Kitasatospora atroaurantiaca	strain=DSM 41649	GCA_007828955.1	285545	285545	type	True	83.5891	1453	2716	95	below_threshold
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	82.6242	1387	2716	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	79.1252	880	2716	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	78.3341	1125	2716	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:50:55,608] [INFO] DFAST Taxonomy check result was written to GCF_000961885.1_ASM96188v1_genomic.fna/tc_result.tsv
[2024-01-25 18:50:55,609] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:50:55,609] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:50:55,609] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bc687b3-42f7-47c1-b6f1-580fdb4d7de0/dqc_reference/checkm_data
[2024-01-25 18:50:55,610] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:50:55,688] [INFO] Task started: CheckM
[2024-01-25 18:50:55,688] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000961885.1_ASM96188v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000961885.1_ASM96188v1_genomic.fna/checkm_input GCF_000961885.1_ASM96188v1_genomic.fna/checkm_result
[2024-01-25 18:52:17,595] [INFO] Task succeeded: CheckM
[2024-01-25 18:52:17,596] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:52:17,617] [INFO] ===== Completeness check finished =====
[2024-01-25 18:52:17,617] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:52:17,618] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000961885.1_ASM96188v1_genomic.fna/markers.fasta)
[2024-01-25 18:52:17,618] [INFO] Task started: Blastn
[2024-01-25 18:52:17,618] [INFO] Running command: blastn -query GCF_000961885.1_ASM96188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bc687b3-42f7-47c1-b6f1-580fdb4d7de0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000961885.1_ASM96188v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:19,883] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:19,897] [INFO] Selected 11 target genomes.
[2024-01-25 18:52:19,897] [INFO] Target genome list was writen to GCF_000961885.1_ASM96188v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:52:19,898] [INFO] Task started: fastANI
[2024-01-25 18:52:19,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg8019d611-0a02-4330-8f64-081f479d3eae/GCF_000961885.1_ASM96188v1_genomic.fna.gz --refList GCF_000961885.1_ASM96188v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000961885.1_ASM96188v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:52:50,387] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:50,394] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:52:50,394] [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_000961885.1	s__Kitasatospora rubellomurina	100.0	2704	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015776785.2	s__Kitasatospora sp015776785	89.6384	1615	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716875.1	s__Kitasatospora novaecaesareae	89.4013	1738	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	99.97	99.97	0.97	0.97	2	-
GCF_000720635.1	s__Kitasatospora sp000720635	88.955	1907	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199205.1	s__Kitasatospora sp900199205	88.9436	1863	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	99.37	99.37	0.96	0.96	2	-
GCF_014596465.1	s__Kitasatospora sp014596465	88.7245	1791	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656195.1	s__Kitasatospora xanthocidica	88.6865	1980	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001188955.3	s__Kitasatospora aureofaciens	88.659	1907	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	99.54	97.86	0.95	0.85	10	-
GCF_001905545.1	s__Kitasatospora sp001905545	88.6304	1921	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	98.73	98.73	0.93	0.93	2	-
GCF_001625365.1	s__Kitasatospora sp001625365	88.5953	1860	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009569385.1	s__Kitasatospora kaniharaensis	87.9551	1759	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:52:50,396] [INFO] GTDB search result was written to GCF_000961885.1_ASM96188v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:52:50,396] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:52:50,399] [INFO] DFAST_QC result json was written to GCF_000961885.1_ASM96188v1_genomic.fna/dqc_result.json
[2024-01-25 18:52:50,400] [INFO] DFAST_QC completed!
[2024-01-25 18:52:50,400] [INFO] Total running time: 0h2m45s