[2024-01-24 13:22:42,332] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:42,333] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:42,333] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f2ceea6-8bbf-44a1-bb22-7518251361bb/dqc_reference
[2024-01-24 13:22:43,655] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:43,656] [INFO] Task started: Prodigal
[2024-01-24 13:22:43,657] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a21b7a4-ebad-4e2b-b0d9-4cde266413ee/GCF_009208555.1_ASM920855v1_genomic.fna.gz | prodigal -d GCF_009208555.1_ASM920855v1_genomic.fna/cds.fna -a GCF_009208555.1_ASM920855v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:07,158] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:07,158] [INFO] Task started: HMMsearch
[2024-01-24 13:23:07,158] [INFO] Running command: hmmsearch --tblout GCF_009208555.1_ASM920855v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f2ceea6-8bbf-44a1-bb22-7518251361bb/dqc_reference/reference_markers.hmm GCF_009208555.1_ASM920855v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:07,522] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:07,524] [INFO] Found 6/6 markers.
[2024-01-24 13:23:07,583] [INFO] Query marker FASTA was written to GCF_009208555.1_ASM920855v1_genomic.fna/markers.fasta
[2024-01-24 13:23:07,583] [INFO] Task started: Blastn
[2024-01-24 13:23:07,583] [INFO] Running command: blastn -query GCF_009208555.1_ASM920855v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f2ceea6-8bbf-44a1-bb22-7518251361bb/dqc_reference/reference_markers.fasta -out GCF_009208555.1_ASM920855v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:08,575] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:08,579] [INFO] Selected 10 target genomes.
[2024-01-24 13:23:08,580] [INFO] Target genome list was writen to GCF_009208555.1_ASM920855v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:08,588] [INFO] Task started: fastANI
[2024-01-24 13:23:08,588] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a21b7a4-ebad-4e2b-b0d9-4cde266413ee/GCF_009208555.1_ASM920855v1_genomic.fna.gz --refList GCF_009208555.1_ASM920855v1_genomic.fna/target_genomes.txt --output GCF_009208555.1_ASM920855v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:23,701] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:23,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f2ceea6-8bbf-44a1-bb22-7518251361bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:23,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f2ceea6-8bbf-44a1-bb22-7518251361bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:23,717] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:23,718] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:23,718] [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
Janthinobacterium violaceinigrum	strain=FT13W	GCA_009208555.1	2654252	2654252	type	True	100.0	2091	2096	95	conclusive
Janthinobacterium lividum	strain=NCTC9796	GCA_900451145.1	29581	29581	suspected-type	True	92.6578	1837	2096	95	below_threshold
Janthinobacterium lividum	strain=ATCC 12473	GCA_020858175.1	29581	29581	suspected-type	True	92.6577	1822	2096	95	below_threshold
Janthinobacterium lividum	strain=H-24	GCA_001758635.1	29581	29581	suspected-type	True	92.6507	1783	2096	95	below_threshold
Janthinobacterium tructae	strain=SNU WT3	GCA_006517255.1	2590869	2590869	type	True	92.0523	1768	2096	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	81.7505	1026	2096	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	81.5245	1003	2096	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	81.434	1017	2096	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	80.7318	1025	2096	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	80.1146	730	2096	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:23,720] [INFO] DFAST Taxonomy check result was written to GCF_009208555.1_ASM920855v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:23,720] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:23,720] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:23,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f2ceea6-8bbf-44a1-bb22-7518251361bb/dqc_reference/checkm_data
[2024-01-24 13:23:23,722] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:23,785] [INFO] Task started: CheckM
[2024-01-24 13:23:23,785] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009208555.1_ASM920855v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009208555.1_ASM920855v1_genomic.fna/checkm_input GCF_009208555.1_ASM920855v1_genomic.fna/checkm_result
[2024-01-24 13:24:34,181] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:34,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:34,210] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:34,211] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:34,211] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009208555.1_ASM920855v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:34,211] [INFO] Task started: Blastn
[2024-01-24 13:24:34,212] [INFO] Running command: blastn -query GCF_009208555.1_ASM920855v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f2ceea6-8bbf-44a1-bb22-7518251361bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_009208555.1_ASM920855v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:36,116] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:36,120] [INFO] Selected 12 target genomes.
[2024-01-24 13:24:36,120] [INFO] Target genome list was writen to GCF_009208555.1_ASM920855v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:36,131] [INFO] Task started: fastANI
[2024-01-24 13:24:36,132] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a21b7a4-ebad-4e2b-b0d9-4cde266413ee/GCF_009208555.1_ASM920855v1_genomic.fna.gz --refList GCF_009208555.1_ASM920855v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009208555.1_ASM920855v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:56,644] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:56,665] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:56,666] [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_009208555.1	s__Janthinobacterium violaceinigrum	100.0	2091	2096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	96.88	96.88	0.91	0.91	2	conclusive
GCF_002002885.1	s__Janthinobacterium sp002002885	93.0177	1837	2096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	96.09	96.09	0.93	0.93	2	-
GCF_900451145.1	s__Janthinobacterium lividum	92.6616	1836	2096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	97.96	97.56	0.93	0.89	12	-
GCF_009208735.1	s__Janthinobacterium sp009208735	92.6453	1764	2096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	95.70	95.70	0.90	0.90	2	-
GCF_000632025.1	s__Janthinobacterium lividum_C	92.464	1780	2096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	97.00	96.24	0.94	0.92	5	-
GCF_003667705.1	s__Janthinobacterium sp001758725	92.4003	1808	2096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0774	98.10	97.46	0.93	0.89	7	-
GCF_000745325.1	s__Janthinobacterium sp000745325	92.3322	1815	2096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	97.59	97.59	0.95	0.94	3	-
GCF_011601275.1	s__Janthinobacterium lividum_E	92.2582	1802	2096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	96.41	96.40	0.93	0.92	4	-
GCF_002127655.1	s__Janthinobacterium sp002127655	92.1806	1761	2096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0774	99.99	99.99	0.99	0.99	4	-
GCA_009923995.1	s__Janthinobacterium sp009923995	91.9945	1701	2096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156175.1	s__Janthinobacterium sp900156175	91.7227	1736	2096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001865675.1	s__Janthinobacterium sp001865675	91.6757	1827	2096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:56,668] [INFO] GTDB search result was written to GCF_009208555.1_ASM920855v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:56,668] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:56,672] [INFO] DFAST_QC result json was written to GCF_009208555.1_ASM920855v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:56,673] [INFO] DFAST_QC completed!
[2024-01-24 13:24:56,673] [INFO] Total running time: 0h2m14s