[2024-01-24 11:52:04,786] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:52:04,789] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:52:04,789] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf19c2af-66e9-487b-bd0c-d7c8384250b3/dqc_reference
[2024-01-24 11:52:05,977] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:52:05,978] [INFO] Task started: Prodigal
[2024-01-24 11:52:05,978] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d93f06b-0c9f-4c69-b582-fd97a418b18a/GCF_016862695.1_ASM1686269v1_genomic.fna.gz | prodigal -d GCF_016862695.1_ASM1686269v1_genomic.fna/cds.fna -a GCF_016862695.1_ASM1686269v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:17,044] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:17,045] [INFO] Task started: HMMsearch
[2024-01-24 11:52:17,045] [INFO] Running command: hmmsearch --tblout GCF_016862695.1_ASM1686269v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf19c2af-66e9-487b-bd0c-d7c8384250b3/dqc_reference/reference_markers.hmm GCF_016862695.1_ASM1686269v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:17,310] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:17,312] [INFO] Found 6/6 markers.
[2024-01-24 11:52:17,350] [INFO] Query marker FASTA was written to GCF_016862695.1_ASM1686269v1_genomic.fna/markers.fasta
[2024-01-24 11:52:17,350] [INFO] Task started: Blastn
[2024-01-24 11:52:17,351] [INFO] Running command: blastn -query GCF_016862695.1_ASM1686269v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf19c2af-66e9-487b-bd0c-d7c8384250b3/dqc_reference/reference_markers.fasta -out GCF_016862695.1_ASM1686269v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:18,718] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:18,722] [INFO] Selected 15 target genomes.
[2024-01-24 11:52:18,723] [INFO] Target genome list was writen to GCF_016862695.1_ASM1686269v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:18,729] [INFO] Task started: fastANI
[2024-01-24 11:52:18,730] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d93f06b-0c9f-4c69-b582-fd97a418b18a/GCF_016862695.1_ASM1686269v1_genomic.fna.gz --refList GCF_016862695.1_ASM1686269v1_genomic.fna/target_genomes.txt --output GCF_016862695.1_ASM1686269v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:31,171] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:31,172] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf19c2af-66e9-487b-bd0c-d7c8384250b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:31,173] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf19c2af-66e9-487b-bd0c-d7c8384250b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:31,189] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:31,189] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:31,190] [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
Cellulomonas denverensis	strain=ATCC BAA-788	GCA_012396125.1	264297	264297	type	True	99.9988	1297	1304	95	conclusive
Cellulomonas taurus	strain=P40-2	GCA_012931845.1	2729175	2729175	type	True	87.0442	903	1304	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	82.094	811	1304	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	82.0843	784	1304	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	79.7606	562	1304	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	79.4564	540	1304	95	below_threshold
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	79.3583	525	1304	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	79.3554	474	1304	95	below_threshold
Cellulomonas oligotrophica	strain=DSM 24482	GCA_013409875.1	931536	931536	type	True	79.0499	569	1304	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	78.9745	568	1304	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	78.8529	562	1304	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	78.8101	520	1304	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	78.4881	415	1304	95	below_threshold
Cellulomonas endophytica	strain=SYSUP0004	GCA_004123805.1	2494735	2494735	type	True	78.4318	459	1304	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	78.3082	430	1304	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:31,192] [INFO] DFAST Taxonomy check result was written to GCF_016862695.1_ASM1686269v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:31,193] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:31,193] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:31,193] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf19c2af-66e9-487b-bd0c-d7c8384250b3/dqc_reference/checkm_data
[2024-01-24 11:52:31,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:31,238] [INFO] Task started: CheckM
[2024-01-24 11:52:31,238] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862695.1_ASM1686269v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862695.1_ASM1686269v1_genomic.fna/checkm_input GCF_016862695.1_ASM1686269v1_genomic.fna/checkm_result
[2024-01-24 11:53:33,920] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:33,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:33,943] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:33,943] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:33,944] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862695.1_ASM1686269v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:33,944] [INFO] Task started: Blastn
[2024-01-24 11:53:33,944] [INFO] Running command: blastn -query GCF_016862695.1_ASM1686269v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf19c2af-66e9-487b-bd0c-d7c8384250b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862695.1_ASM1686269v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:36,084] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:36,089] [INFO] Selected 11 target genomes.
[2024-01-24 11:53:36,089] [INFO] Target genome list was writen to GCF_016862695.1_ASM1686269v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:36,097] [INFO] Task started: fastANI
[2024-01-24 11:53:36,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d93f06b-0c9f-4c69-b582-fd97a418b18a/GCF_016862695.1_ASM1686269v1_genomic.fna.gz --refList GCF_016862695.1_ASM1686269v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862695.1_ASM1686269v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:46,751] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:46,763] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:46,763] [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_012396125.1	s__Cellulomonas denverensis	99.9988	1297	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_012931845.1	s__Cellulomonas taurus	87.0302	904	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011603975.1	s__Cellulomonas sp011603975	82.4462	721	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005239125.1	s__Cellulomonas hominis_A	82.2366	747	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679345.1	s__Cellulomonas cellulans_A	82.0985	852	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201095.1	s__Cellulomonas hominis	82.0779	813	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.15	98.63	0.95	0.92	4	-
GCF_008033115.1	s__Cellulomonas sp008033115	82.0043	824	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	96.34	96.34	0.91	0.91	2	-
GCF_013409475.1	s__Cellulomonas hominis_B	81.9012	810	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862755.1	s__Cellulomonas pakistanensis	81.8874	802	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901521055.1	s__Cellulomonas hominis_C	81.6595	758	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763765.1	s__Cellulomonas sp014763765	81.4302	688	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:46,765] [INFO] GTDB search result was written to GCF_016862695.1_ASM1686269v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:46,766] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:46,769] [INFO] DFAST_QC result json was written to GCF_016862695.1_ASM1686269v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:46,769] [INFO] DFAST_QC completed!
[2024-01-24 11:53:46,769] [INFO] Total running time: 0h1m42s