[2024-01-24 13:22:55,301] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:55,303] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:55,303] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c2b1eb8-3165-47a7-b604-6890b3fa0f4c/dqc_reference
[2024-01-24 13:22:56,590] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:56,591] [INFO] Task started: Prodigal
[2024-01-24 13:22:56,591] [INFO] Running command: gunzip -c /var/lib/cwl/stgb04e331c-ecec-4e8b-998f-aab6dcdfbbed/GCF_000747155.1_ASM74715v1_genomic.fna.gz | prodigal -d GCF_000747155.1_ASM74715v1_genomic.fna/cds.fna -a GCF_000747155.1_ASM74715v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:05,369] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:05,370] [INFO] Task started: HMMsearch
[2024-01-24 13:23:05,370] [INFO] Running command: hmmsearch --tblout GCF_000747155.1_ASM74715v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c2b1eb8-3165-47a7-b604-6890b3fa0f4c/dqc_reference/reference_markers.hmm GCF_000747155.1_ASM74715v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:05,686] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:05,688] [INFO] Found 6/6 markers.
[2024-01-24 13:23:05,719] [INFO] Query marker FASTA was written to GCF_000747155.1_ASM74715v1_genomic.fna/markers.fasta
[2024-01-24 13:23:05,720] [INFO] Task started: Blastn
[2024-01-24 13:23:05,720] [INFO] Running command: blastn -query GCF_000747155.1_ASM74715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c2b1eb8-3165-47a7-b604-6890b3fa0f4c/dqc_reference/reference_markers.fasta -out GCF_000747155.1_ASM74715v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:06,691] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:06,695] [INFO] Selected 15 target genomes.
[2024-01-24 13:23:06,696] [INFO] Target genome list was writen to GCF_000747155.1_ASM74715v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:06,699] [INFO] Task started: fastANI
[2024-01-24 13:23:06,700] [INFO] Running command: fastANI --query /var/lib/cwl/stgb04e331c-ecec-4e8b-998f-aab6dcdfbbed/GCF_000747155.1_ASM74715v1_genomic.fna.gz --refList GCF_000747155.1_ASM74715v1_genomic.fna/target_genomes.txt --output GCF_000747155.1_ASM74715v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:17,233] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:17,234] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c2b1eb8-3165-47a7-b604-6890b3fa0f4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:17,234] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c2b1eb8-3165-47a7-b604-6890b3fa0f4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:17,246] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:17,246] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:17,246] [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
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	100.0	988	989	95	conclusive
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	87.2482	695	989	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	86.7894	761	989	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	86.2906	733	989	95	below_threshold
Arenimonas soli	strain=CGMCC 1.15905	GCA_014643775.1	2269504	2269504	type	True	84.9491	725	989	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	83.7359	673	989	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	83.7354	659	989	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	80.8878	470	989	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	80.6277	550	989	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	80.5909	495	989	95	below_threshold
Pseudoxanthomonas suwonensis	strain=DSM 17175	GCA_010093235.1	314722	314722	suspected-type	True	80.5667	502	989	95	below_threshold
Arenimonas oryziterrae	strain=DSM 21050	GCA_000420545.1	498055	498055	type	True	80.5346	539	989	95	below_threshold
Arenimonas oryziterrae	strain=YC6267	GCA_000747135.1	498055	498055	type	True	80.5014	540	989	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	80.0256	460	989	95	below_threshold
Pseudoxanthomonas kalamensis	strain=DSM 18571	GCA_010211745.1	289483	289483	type	True	79.7469	446	989	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:17,248] [INFO] DFAST Taxonomy check result was written to GCF_000747155.1_ASM74715v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:17,248] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:17,248] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:17,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c2b1eb8-3165-47a7-b604-6890b3fa0f4c/dqc_reference/checkm_data
[2024-01-24 13:23:17,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:17,279] [INFO] Task started: CheckM
[2024-01-24 13:23:17,279] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000747155.1_ASM74715v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000747155.1_ASM74715v1_genomic.fna/checkm_input GCF_000747155.1_ASM74715v1_genomic.fna/checkm_result
[2024-01-24 13:23:47,136] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:47,137] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:47,154] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:47,154] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:47,155] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000747155.1_ASM74715v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:47,155] [INFO] Task started: Blastn
[2024-01-24 13:23:47,155] [INFO] Running command: blastn -query GCF_000747155.1_ASM74715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c2b1eb8-3165-47a7-b604-6890b3fa0f4c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000747155.1_ASM74715v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:48,901] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:48,907] [INFO] Selected 10 target genomes.
[2024-01-24 13:23:48,907] [INFO] Target genome list was writen to GCF_000747155.1_ASM74715v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:48,917] [INFO] Task started: fastANI
[2024-01-24 13:23:48,917] [INFO] Running command: fastANI --query /var/lib/cwl/stgb04e331c-ecec-4e8b-998f-aab6dcdfbbed/GCF_000747155.1_ASM74715v1_genomic.fna.gz --refList GCF_000747155.1_ASM74715v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000747155.1_ASM74715v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:56,499] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:56,514] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:56,514] [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_000747155.1	s__Arenimonas metalli	100.0	988	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000747075.1	s__Arenimonas malthae	87.2544	694	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265115.1	s__Arenimonas terrae	86.8143	760	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724815.1	s__Arenimonas sp001724815	86.7563	748	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024235.1	s__Arenimonas caeni	86.3261	731	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993735.1	s__Arenimonas daejeonensis	86.209	735	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003497545.1	s__Arenimonas sp003497545	85.9067	538	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.43	99.43	0.81	0.81	2	-
GCA_003241895.1	s__Arenimonas sp003241895	85.7238	720	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426365.1	s__Arenimonas composti	83.6951	676	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.98	99.98	1.00	1.00	2	-
GCF_007667275.1	s__Stenotrophomonas maltophilia_AE	79.5015	455	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.01	98.01	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:56,516] [INFO] GTDB search result was written to GCF_000747155.1_ASM74715v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:56,517] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:56,520] [INFO] DFAST_QC result json was written to GCF_000747155.1_ASM74715v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:56,520] [INFO] DFAST_QC completed!
[2024-01-24 13:23:56,521] [INFO] Total running time: 0h1m1s