[2024-01-24 13:58:10,607] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,609] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,609] [INFO] DQC Reference Directory: /var/lib/cwl/stg7be215ff-1184-4c5a-b874-bafa94ee8283/dqc_reference
[2024-01-24 13:58:11,961] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:11,962] [INFO] Task started: Prodigal
[2024-01-24 13:58:11,962] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4a0633d-da96-46c5-a6e9-e7e44d9e442c/GCF_009380165.1_ASM938016v1_genomic.fna.gz | prodigal -d GCF_009380165.1_ASM938016v1_genomic.fna/cds.fna -a GCF_009380165.1_ASM938016v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:35,143] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:35,144] [INFO] Task started: HMMsearch
[2024-01-24 13:58:35,144] [INFO] Running command: hmmsearch --tblout GCF_009380165.1_ASM938016v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7be215ff-1184-4c5a-b874-bafa94ee8283/dqc_reference/reference_markers.hmm GCF_009380165.1_ASM938016v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:35,509] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:35,511] [INFO] Found 6/6 markers.
[2024-01-24 13:58:35,568] [INFO] Query marker FASTA was written to GCF_009380165.1_ASM938016v1_genomic.fna/markers.fasta
[2024-01-24 13:58:35,569] [INFO] Task started: Blastn
[2024-01-24 13:58:35,569] [INFO] Running command: blastn -query GCF_009380165.1_ASM938016v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7be215ff-1184-4c5a-b874-bafa94ee8283/dqc_reference/reference_markers.fasta -out GCF_009380165.1_ASM938016v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:36,617] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:36,620] [INFO] Selected 11 target genomes.
[2024-01-24 13:58:36,620] [INFO] Target genome list was writen to GCF_009380165.1_ASM938016v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:36,678] [INFO] Task started: fastANI
[2024-01-24 13:58:36,679] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4a0633d-da96-46c5-a6e9-e7e44d9e442c/GCF_009380165.1_ASM938016v1_genomic.fna.gz --refList GCF_009380165.1_ASM938016v1_genomic.fna/target_genomes.txt --output GCF_009380165.1_ASM938016v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:56,236] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:56,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7be215ff-1184-4c5a-b874-bafa94ee8283/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:56,237] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7be215ff-1184-4c5a-b874-bafa94ee8283/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:56,246] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:56,246] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:58:56,246] [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
Rugamonas rivuli	strain=FT103W	GCA_009380165.1	2743358	2743358	type	True	100.0	2265	2266	95	inconclusive
Rugamonas aquatica	strain=FT29W	GCA_009380215.1	2743357	2743357	type	True	95.1919	2035	2266	95	inconclusive
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	86.9861	1566	2266	95	below_threshold
Duganella aquatilis	strain=FT26W	GCA_009674565.1	2666082	2666082	type	True	86.3849	1472	2266	95	below_threshold
Duganella alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	86.2757	1477	2266	95	below_threshold
Duganella radicis	strain=KCTC 22382	GCA_009720825.1	551988	551988	type	True	85.4516	1496	2266	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	85.2088	1462	2266	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	84.1778	1239	2266	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	83.6984	1221	2266	95	below_threshold
Duganella phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	83.6283	1222	2266	95	below_threshold
Pseudoduganella aquatica	strain=FT127W	GCA_009857595.1	2660641	2660641	type	True	83.2385	1284	2266	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:56,248] [INFO] DFAST Taxonomy check result was written to GCF_009380165.1_ASM938016v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:56,248] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:56,248] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:56,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7be215ff-1184-4c5a-b874-bafa94ee8283/dqc_reference/checkm_data
[2024-01-24 13:58:56,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:56,314] [INFO] Task started: CheckM
[2024-01-24 13:58:56,314] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009380165.1_ASM938016v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009380165.1_ASM938016v1_genomic.fna/checkm_input GCF_009380165.1_ASM938016v1_genomic.fna/checkm_result
[2024-01-24 14:00:00,162] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:00,163] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:00,206] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:00,206] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:00,207] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009380165.1_ASM938016v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:00,207] [INFO] Task started: Blastn
[2024-01-24 14:00:00,207] [INFO] Running command: blastn -query GCF_009380165.1_ASM938016v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7be215ff-1184-4c5a-b874-bafa94ee8283/dqc_reference/reference_markers_gtdb.fasta -out GCF_009380165.1_ASM938016v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:02,225] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:02,230] [INFO] Selected 7 target genomes.
[2024-01-24 14:00:02,230] [INFO] Target genome list was writen to GCF_009380165.1_ASM938016v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:02,262] [INFO] Task started: fastANI
[2024-01-24 14:00:02,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4a0633d-da96-46c5-a6e9-e7e44d9e442c/GCF_009380165.1_ASM938016v1_genomic.fna.gz --refList GCF_009380165.1_ASM938016v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009380165.1_ASM938016v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:18,061] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:18,068] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 14:00:18,069] [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_000335815.1	s__Duganella sp000335815	95.6644	2015	2266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	95.81	95.66	0.89	0.89	4	inconclusive
GCF_009380215.1	s__Duganella sp009380215	95.1919	2035	2266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_003416895.1	s__Duganella sp003416895	91.3847	1873	2266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	99.92	99.92	0.99	0.99	2	-
GCA_000381565.1	s__Duganella sp000381565	90.766	1777	2266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	95.03	95.03	0.82	0.82	2	-
GCF_003416985.1	s__Duganella sp003416985	90.7627	1810	2266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	97.63	95.41	0.92	0.79	7	-
GCF_013375995.1	s__Duganella sp013375995	88.9222	1683	2266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017833525.1	s__Duganella sp017833525	86.1337	1537	2266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:18,070] [INFO] GTDB search result was written to GCF_009380165.1_ASM938016v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:18,071] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:18,074] [INFO] DFAST_QC result json was written to GCF_009380165.1_ASM938016v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:18,074] [INFO] DFAST_QC completed!
[2024-01-24 14:00:18,074] [INFO] Total running time: 0h2m7s