[2024-01-24 13:01:07,734] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:07,735] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:07,736] [INFO] DQC Reference Directory: /var/lib/cwl/stg56eabc8b-e0f4-444f-b064-5a3c9066863d/dqc_reference
[2024-01-24 13:01:08,923] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:08,924] [INFO] Task started: Prodigal
[2024-01-24 13:01:08,924] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5ba6183-5be0-48e6-bafe-9f1a02c6f753/GCF_009674565.1_ASM967456v1_genomic.fna.gz | prodigal -d GCF_009674565.1_ASM967456v1_genomic.fna/cds.fna -a GCF_009674565.1_ASM967456v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:29,205] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:29,206] [INFO] Task started: HMMsearch
[2024-01-24 13:01:29,206] [INFO] Running command: hmmsearch --tblout GCF_009674565.1_ASM967456v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56eabc8b-e0f4-444f-b064-5a3c9066863d/dqc_reference/reference_markers.hmm GCF_009674565.1_ASM967456v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:29,649] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:29,651] [INFO] Found 6/6 markers.
[2024-01-24 13:01:29,718] [INFO] Query marker FASTA was written to GCF_009674565.1_ASM967456v1_genomic.fna/markers.fasta
[2024-01-24 13:01:29,719] [INFO] Task started: Blastn
[2024-01-24 13:01:29,719] [INFO] Running command: blastn -query GCF_009674565.1_ASM967456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56eabc8b-e0f4-444f-b064-5a3c9066863d/dqc_reference/reference_markers.fasta -out GCF_009674565.1_ASM967456v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:30,685] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:30,689] [INFO] Selected 19 target genomes.
[2024-01-24 13:01:30,689] [INFO] Target genome list was writen to GCF_009674565.1_ASM967456v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:30,697] [INFO] Task started: fastANI
[2024-01-24 13:01:30,697] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5ba6183-5be0-48e6-bafe-9f1a02c6f753/GCF_009674565.1_ASM967456v1_genomic.fna.gz --refList GCF_009674565.1_ASM967456v1_genomic.fna/target_genomes.txt --output GCF_009674565.1_ASM967456v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:01,460] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:01,461] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56eabc8b-e0f4-444f-b064-5a3c9066863d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:01,461] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56eabc8b-e0f4-444f-b064-5a3c9066863d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:01,483] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:02:01,483] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:02:01,483] [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
Duganella aquatilis	strain=FT26W	GCA_009674565.1	2666082	2666082	type	True	100.0	2142	2144	95	inconclusive
Duganella alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	95.147	1834	2144	95	inconclusive
Duganella levis	strain=CY42W	GCA_009857605.1	2692169	2692169	type	True	89.6126	1730	2144	95	below_threshold
Duganella margarita	strain=FT109W	GCA_009857535.1	2692170	2692170	type	True	89.4889	1670	2144	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	89.1627	1755	2144	95	below_threshold
Duganella radicis	strain=KCTC 22382	GCA_009720825.1	551988	551988	type	True	87.6686	1570	2144	95	below_threshold
Duganella lactea	strain=FT50W	GCA_009857505.1	2692173	2692173	type	True	87.6622	1420	2144	95	below_threshold
Duganella guangzhouensis	strain=FT80W	GCA_009674535.1	2666084	2666084	type	True	87.0507	1610	2144	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	86.7509	1601	2144	95	below_threshold
Duganella flavida	strain=FT135W	GCA_009857445.1	2692175	2692175	type	True	86.5273	1528	2144	95	below_threshold
Duganella sacchari	strain=Sac-22	GCA_900143065.1	551987	551987	type	True	86.2968	1529	2144	95	below_threshold
Duganella phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	83.5749	1272	2144	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	83.3135	1123	2144	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	83.0206	1124	2144	95	below_threshold
Nakamurella aerolata	strain=DB0629	GCA_013002705.1	1656892	1656892	type	True	74.9032	128	2144	95	below_threshold
Actinoplanes octamycinicus	strain=DSM 45809	GCA_014205225.1	135948	135948	type	True	74.7417	285	2144	95	below_threshold
Actinoplanes octamycinicus	strain=NBRC 14524	GCA_016862295.1	135948	135948	type	True	74.7369	281	2144	95	below_threshold
Actinoplanes missouriensis	strain=431	GCA_000284295.1	1866	1866	type	True	74.6818	208	2144	95	below_threshold
Allorhizocola rhizosphaerae	strain=CPCC 204380	GCA_003426775.1	1872709	1872709	type	True	74.5907	128	2144	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:01,485] [INFO] DFAST Taxonomy check result was written to GCF_009674565.1_ASM967456v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:01,487] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:01,487] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:01,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56eabc8b-e0f4-444f-b064-5a3c9066863d/dqc_reference/checkm_data
[2024-01-24 13:02:01,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:01,554] [INFO] Task started: CheckM
[2024-01-24 13:02:01,554] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009674565.1_ASM967456v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009674565.1_ASM967456v1_genomic.fna/checkm_input GCF_009674565.1_ASM967456v1_genomic.fna/checkm_result
[2024-01-24 13:02:57,797] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:57,798] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:57,823] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:57,823] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:57,824] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009674565.1_ASM967456v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:57,824] [INFO] Task started: Blastn
[2024-01-24 13:02:57,824] [INFO] Running command: blastn -query GCF_009674565.1_ASM967456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56eabc8b-e0f4-444f-b064-5a3c9066863d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009674565.1_ASM967456v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:59,463] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:59,467] [INFO] Selected 16 target genomes.
[2024-01-24 13:02:59,467] [INFO] Target genome list was writen to GCF_009674565.1_ASM967456v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:59,478] [INFO] Task started: fastANI
[2024-01-24 13:02:59,479] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5ba6183-5be0-48e6-bafe-9f1a02c6f753/GCF_009674565.1_ASM967456v1_genomic.fna.gz --refList GCF_009674565.1_ASM967456v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009674565.1_ASM967456v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:26,092] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:26,106] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:26,106] [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_009674565.1	s__Duganella rivi	100.0	2142	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.1471	N/A	N/A	N/A	N/A	1	conclusive
GCF_009674495.1	s__Duganella alba	95.1358	1835	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.1471	100.00	100.00	1.00	1.00	2	-
GCF_009857605.1	s__Duganella levis	89.5993	1731	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857535.1	s__Duganella margarita	89.4791	1671	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	98.08	98.08	0.91	0.91	2	-
GCF_012849375.1	s__Duganella sp003217375	89.1541	1756	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	98.22	98.21	0.93	0.93	11	-
GCF_013408245.1	s__Duganella sp013408245	89.1388	1637	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376005.1	s__Duganella sp013376005	87.9339	1572	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720825.1	s__Duganella radicis	87.6743	1569	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100205.1	s__Duganella sp900100205	87.5855	1594	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900109645.1	s__Duganella sp900109645	87.5344	1549	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009857495.1	s__Duganella sp009857495	87.4886	1417	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	98.63	98.63	0.91	0.91	2	-
GCF_009857435.1	s__Duganella sp009857435	86.7664	1568	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857445.1	s__Duganella sp009857445	86.5222	1529	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114705.1	s__Rugamonas rubra	83.2439	1261	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	96.24	96.24	0.86	0.86	2	-
GCF_000723165.1	s__Janthinobacterium agaricidamnosum	80.919	997	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_013002705.1	s__Nakamurella aerolata	74.8874	132	2144	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:26,108] [INFO] GTDB search result was written to GCF_009674565.1_ASM967456v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:26,108] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:26,113] [INFO] DFAST_QC result json was written to GCF_009674565.1_ASM967456v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:26,113] [INFO] DFAST_QC completed!
[2024-01-24 13:03:26,113] [INFO] Total running time: 0h2m18s