[2024-01-24 13:46:18,400] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:18,404] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:18,405] [INFO] DQC Reference Directory: /var/lib/cwl/stg44600e17-f0fd-40d5-9bc9-a450beb2eaee/dqc_reference
[2024-01-24 13:46:19,643] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:19,644] [INFO] Task started: Prodigal
[2024-01-24 13:46:19,644] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0244763-36e2-4054-84ed-bbb90d47f5c7/GCF_014042355.1_ASM1404235v1_genomic.fna.gz | prodigal -d GCF_014042355.1_ASM1404235v1_genomic.fna/cds.fna -a GCF_014042355.1_ASM1404235v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:42,929] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:42,929] [INFO] Task started: HMMsearch
[2024-01-24 13:46:42,929] [INFO] Running command: hmmsearch --tblout GCF_014042355.1_ASM1404235v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44600e17-f0fd-40d5-9bc9-a450beb2eaee/dqc_reference/reference_markers.hmm GCF_014042355.1_ASM1404235v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:43,335] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:43,336] [INFO] Found 6/6 markers.
[2024-01-24 13:46:43,386] [INFO] Query marker FASTA was written to GCF_014042355.1_ASM1404235v1_genomic.fna/markers.fasta
[2024-01-24 13:46:43,386] [INFO] Task started: Blastn
[2024-01-24 13:46:43,386] [INFO] Running command: blastn -query GCF_014042355.1_ASM1404235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44600e17-f0fd-40d5-9bc9-a450beb2eaee/dqc_reference/reference_markers.fasta -out GCF_014042355.1_ASM1404235v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:44,443] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:44,447] [INFO] Selected 11 target genomes.
[2024-01-24 13:46:44,447] [INFO] Target genome list was writen to GCF_014042355.1_ASM1404235v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:44,459] [INFO] Task started: fastANI
[2024-01-24 13:46:44,459] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0244763-36e2-4054-84ed-bbb90d47f5c7/GCF_014042355.1_ASM1404235v1_genomic.fna.gz --refList GCF_014042355.1_ASM1404235v1_genomic.fna/target_genomes.txt --output GCF_014042355.1_ASM1404235v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:02,870] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:02,870] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44600e17-f0fd-40d5-9bc9-a450beb2eaee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:02,870] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44600e17-f0fd-40d5-9bc9-a450beb2eaee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:02,880] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:02,881] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:02,881] [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 apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	100.0	2020	2022	95	conclusive
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	91.2933	1548	2022	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	91.0981	1586	2022	95	below_threshold
Rugamonas rivuli	strain=FT103W	GCA_009380165.1	2743358	2743358	type	True	83.7303	1216	2022	95	below_threshold
Rugamonas aquatica	strain=FT29W	GCA_009380215.1	2743357	2743357	type	True	83.6656	1217	2022	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	83.145	1150	2022	95	below_threshold
Duganella alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	82.9201	1128	2022	95	below_threshold
Duganella callida	strain=DN04	GCA_004614165.1	2561932	2561932	type	True	82.747	1053	2022	95	below_threshold
Duganella phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	82.124	1004	2022	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	81.4089	771	2022	95	below_threshold
Pseudoduganella dura	strain=KCTC 12342	GCA_014651395.1	321982	321982	type	True	80.824	941	2022	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:02,883] [INFO] DFAST Taxonomy check result was written to GCF_014042355.1_ASM1404235v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:02,883] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:02,883] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:02,884] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44600e17-f0fd-40d5-9bc9-a450beb2eaee/dqc_reference/checkm_data
[2024-01-24 13:47:02,885] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:02,947] [INFO] Task started: CheckM
[2024-01-24 13:47:02,948] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014042355.1_ASM1404235v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014042355.1_ASM1404235v1_genomic.fna/checkm_input GCF_014042355.1_ASM1404235v1_genomic.fna/checkm_result
[2024-01-24 13:48:04,852] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:04,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:04,873] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:04,874] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:04,874] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014042355.1_ASM1404235v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:04,874] [INFO] Task started: Blastn
[2024-01-24 13:48:04,875] [INFO] Running command: blastn -query GCF_014042355.1_ASM1404235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44600e17-f0fd-40d5-9bc9-a450beb2eaee/dqc_reference/reference_markers_gtdb.fasta -out GCF_014042355.1_ASM1404235v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:06,934] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:06,938] [INFO] Selected 13 target genomes.
[2024-01-24 13:48:06,938] [INFO] Target genome list was writen to GCF_014042355.1_ASM1404235v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:06,948] [INFO] Task started: fastANI
[2024-01-24 13:48:06,948] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0244763-36e2-4054-84ed-bbb90d47f5c7/GCF_014042355.1_ASM1404235v1_genomic.fna.gz --refList GCF_014042355.1_ASM1404235v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014042355.1_ASM1404235v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:28,689] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:28,704] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:28,705] [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_014042355.1	s__LX47W sp014042355	100.0	2020	2022	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	91.2883	1548	2022	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__LX47W	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014042345.1	s__LX47W sp014042345	91.1086	1585	2022	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__LX47W	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000381565.1	s__Duganella sp000381565	84.0118	1252	2022	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	95.03	95.03	0.82	0.82	2	-
GCF_900114705.1	s__Rugamonas rubra	83.8279	1278	2022	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	96.24	96.24	0.86	0.86	2	-
GCF_003416895.1	s__Duganella sp003416895	83.7625	1236	2022	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	99.92	99.92	0.99	0.99	2	-
GCF_016461825.1	s__Rugamonas sp016461825	83.7337	1239	2022	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375995.1	s__Duganella sp013375995	83.7025	1213	2022	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	83.664	1217	2022	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011090165.1	s__Duganella aceris	83.1594	1147	2022	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	82.9372	1206	2022	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110275.1	s__Duganella sp900110275	82.927	1146	2022	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674495.1	s__Duganella alba	82.9128	1128	2022	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.1471	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:28,706] [INFO] GTDB search result was written to GCF_014042355.1_ASM1404235v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:28,707] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:28,710] [INFO] DFAST_QC result json was written to GCF_014042355.1_ASM1404235v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:28,710] [INFO] DFAST_QC completed!
[2024-01-24 13:48:28,710] [INFO] Total running time: 0h2m10s