[2024-01-24 11:52:49,329] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:52:49,331] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:52:49,331] [INFO] DQC Reference Directory: /var/lib/cwl/stg20c6d59e-e678-4ebd-ab04-f83a8af9cddf/dqc_reference
[2024-01-24 11:52:50,580] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:52:50,581] [INFO] Task started: Prodigal
[2024-01-24 11:52:50,581] [INFO] Running command: gunzip -c /var/lib/cwl/stg26c81a9e-7881-43a2-8aaf-ad65443e3b0b/GCF_014042345.1_ASM1404234v1_genomic.fna.gz | prodigal -d GCF_014042345.1_ASM1404234v1_genomic.fna/cds.fna -a GCF_014042345.1_ASM1404234v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:53:10,059] [INFO] Task succeeded: Prodigal
[2024-01-24 11:53:10,060] [INFO] Task started: HMMsearch
[2024-01-24 11:53:10,060] [INFO] Running command: hmmsearch --tblout GCF_014042345.1_ASM1404234v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20c6d59e-e678-4ebd-ab04-f83a8af9cddf/dqc_reference/reference_markers.hmm GCF_014042345.1_ASM1404234v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:53:10,359] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:53:10,361] [INFO] Found 6/6 markers.
[2024-01-24 11:53:10,408] [INFO] Query marker FASTA was written to GCF_014042345.1_ASM1404234v1_genomic.fna/markers.fasta
[2024-01-24 11:53:10,408] [INFO] Task started: Blastn
[2024-01-24 11:53:10,408] [INFO] Running command: blastn -query GCF_014042345.1_ASM1404234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20c6d59e-e678-4ebd-ab04-f83a8af9cddf/dqc_reference/reference_markers.fasta -out GCF_014042345.1_ASM1404234v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:11,381] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:11,385] [INFO] Selected 13 target genomes.
[2024-01-24 11:53:11,386] [INFO] Target genome list was writen to GCF_014042345.1_ASM1404234v1_genomic.fna/target_genomes.txt
[2024-01-24 11:53:11,418] [INFO] Task started: fastANI
[2024-01-24 11:53:11,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg26c81a9e-7881-43a2-8aaf-ad65443e3b0b/GCF_014042345.1_ASM1404234v1_genomic.fna.gz --refList GCF_014042345.1_ASM1404234v1_genomic.fna/target_genomes.txt --output GCF_014042345.1_ASM1404234v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:53:31,091] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:31,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20c6d59e-e678-4ebd-ab04-f83a8af9cddf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:53:31,092] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20c6d59e-e678-4ebd-ab04-f83a8af9cddf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:53:31,106] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:53:31,106] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:53:31,106] [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
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	100.0	1889	1893	95	conclusive
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	92.5788	1623	1893	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	91.1765	1586	1893	95	below_threshold
Rugamonas rivuli	strain=FT103W	GCA_009380165.1	2743358	2743358	type	True	84.0766	1238	1893	95	below_threshold
Rugamonas aquatica	strain=FT29W	GCA_009380215.1	2743357	2743357	type	True	83.9939	1225	1893	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	83.4605	1164	1893	95	below_threshold
Duganella alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	83.1695	1134	1893	95	below_threshold
Duganella callida	strain=DN04	GCA_004614165.1	2561932	2561932	type	True	83.0178	1083	1893	95	below_threshold
Duganella radicis	strain=KCTC 22382	GCA_009720825.1	551988	551988	type	True	82.8347	1138	1893	95	below_threshold
Duganella phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	82.5442	1004	1893	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	81.7087	784	1893	95	below_threshold
Pseudoduganella albidiflava	strain=DSM 17472	GCA_004322755.1	321983	321983	type	True	81.336	1028	1893	95	below_threshold
Pseudoduganella albidiflava	strain=KCTC 12343	GCA_014651415.1	321983	321983	type	True	81.2515	1019	1893	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:53:31,108] [INFO] DFAST Taxonomy check result was written to GCF_014042345.1_ASM1404234v1_genomic.fna/tc_result.tsv
[2024-01-24 11:53:31,108] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:53:31,108] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:53:31,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20c6d59e-e678-4ebd-ab04-f83a8af9cddf/dqc_reference/checkm_data
[2024-01-24 11:53:31,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:53:31,164] [INFO] Task started: CheckM
[2024-01-24 11:53:31,164] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014042345.1_ASM1404234v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014042345.1_ASM1404234v1_genomic.fna/checkm_input GCF_014042345.1_ASM1404234v1_genomic.fna/checkm_result
[2024-01-24 11:54:28,087] [INFO] Task succeeded: CheckM
[2024-01-24 11:54:28,088] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:54:28,106] [INFO] ===== Completeness check finished =====
[2024-01-24 11:54:28,106] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:54:28,106] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014042345.1_ASM1404234v1_genomic.fna/markers.fasta)
[2024-01-24 11:54:28,107] [INFO] Task started: Blastn
[2024-01-24 11:54:28,107] [INFO] Running command: blastn -query GCF_014042345.1_ASM1404234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20c6d59e-e678-4ebd-ab04-f83a8af9cddf/dqc_reference/reference_markers_gtdb.fasta -out GCF_014042345.1_ASM1404234v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:54:30,029] [INFO] Task succeeded: Blastn
[2024-01-24 11:54:30,033] [INFO] Selected 14 target genomes.
[2024-01-24 11:54:30,033] [INFO] Target genome list was writen to GCF_014042345.1_ASM1404234v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:54:30,056] [INFO] Task started: fastANI
[2024-01-24 11:54:30,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg26c81a9e-7881-43a2-8aaf-ad65443e3b0b/GCF_014042345.1_ASM1404234v1_genomic.fna.gz --refList GCF_014042345.1_ASM1404234v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014042345.1_ASM1404234v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:54:52,850] [INFO] Task succeeded: fastANI
[2024-01-24 11:54:52,866] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:54:52,866] [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_014042345.1	s__LX47W sp014042345	100.0	1889	1893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__LX47W	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014042365.1	s__LX47W sp014042365	92.5564	1625	1893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__LX47W	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014042355.1	s__LX47W sp014042355	91.1519	1589	1893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__LX47W	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003416985.1	s__Duganella sp003416985	84.4408	1282	1893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	97.63	95.41	0.92	0.79	7	-
GCF_900114705.1	s__Rugamonas rubra	84.4227	1287	1893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	96.24	96.24	0.86	0.86	2	-
GCF_016461825.1	s__Rugamonas sp016461825	84.2304	1250	1893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000381565.1	s__Duganella sp000381565	84.1845	1295	1893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	95.03	95.03	0.82	0.82	2	-
GCF_013375995.1	s__Duganella sp013375995	84.0404	1239	1893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009380215.1	s__Duganella sp009380215	84.0013	1225	1893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425045.1	s__Pseudoduganella sp001425045	83.2551	1185	1893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674495.1	s__Duganella alba	83.1189	1140	1893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.1471	100.00	100.00	1.00	1.00	2	-
GCF_004614165.1	s__Duganella callida	82.9835	1089	1893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423125.1	s__Duganella sp001423125	82.7397	1004	1893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428015.1	s__Massilia sp002428015	81.7447	911	1893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:54:52,868] [INFO] GTDB search result was written to GCF_014042345.1_ASM1404234v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:54:52,868] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:54:52,872] [INFO] DFAST_QC result json was written to GCF_014042345.1_ASM1404234v1_genomic.fna/dqc_result.json
[2024-01-24 11:54:52,872] [INFO] DFAST_QC completed!
[2024-01-24 11:54:52,872] [INFO] Total running time: 0h2m4s