[2024-01-25 18:57:50,607] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:57:50,608] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:57:50,609] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbe71fc0-92f6-40d2-888c-f65f9441db6a/dqc_reference
[2024-01-25 18:57:51,735] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:57:51,736] [INFO] Task started: Prodigal
[2024-01-25 18:57:51,736] [INFO] Running command: gunzip -c /var/lib/cwl/stg58194265-a23b-4c54-84ac-050410f59ee0/GCF_014192225.1_ASM1419222v1_genomic.fna.gz | prodigal -d GCF_014192225.1_ASM1419222v1_genomic.fna/cds.fna -a GCF_014192225.1_ASM1419222v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:58:12,850] [INFO] Task succeeded: Prodigal
[2024-01-25 18:58:12,850] [INFO] Task started: HMMsearch
[2024-01-25 18:58:12,850] [INFO] Running command: hmmsearch --tblout GCF_014192225.1_ASM1419222v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbe71fc0-92f6-40d2-888c-f65f9441db6a/dqc_reference/reference_markers.hmm GCF_014192225.1_ASM1419222v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:58:13,139] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:58:13,140] [INFO] Found 6/6 markers.
[2024-01-25 18:58:13,194] [INFO] Query marker FASTA was written to GCF_014192225.1_ASM1419222v1_genomic.fna/markers.fasta
[2024-01-25 18:58:13,194] [INFO] Task started: Blastn
[2024-01-25 18:58:13,194] [INFO] Running command: blastn -query GCF_014192225.1_ASM1419222v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbe71fc0-92f6-40d2-888c-f65f9441db6a/dqc_reference/reference_markers.fasta -out GCF_014192225.1_ASM1419222v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:14,192] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:14,194] [INFO] Selected 13 target genomes.
[2024-01-25 18:58:14,195] [INFO] Target genome list was writen to GCF_014192225.1_ASM1419222v1_genomic.fna/target_genomes.txt
[2024-01-25 18:58:14,202] [INFO] Task started: fastANI
[2024-01-25 18:58:14,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg58194265-a23b-4c54-84ac-050410f59ee0/GCF_014192225.1_ASM1419222v1_genomic.fna.gz --refList GCF_014192225.1_ASM1419222v1_genomic.fna/target_genomes.txt --output GCF_014192225.1_ASM1419222v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:58:37,252] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:37,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbe71fc0-92f6-40d2-888c-f65f9441db6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:58:37,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbe71fc0-92f6-40d2-888c-f65f9441db6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:58:37,261] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:58:37,262] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:58:37,262] [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
Pseudoduganella umbonata	strain=CECT 7753	GCA_014192225.1	864828	864828	type	True	100.0	2435	2437	95	conclusive
Pseudoduganella albidiflava	strain=KCTC 12343	GCA_014651415.1	321983	321983	type	True	89.7565	1929	2437	95	below_threshold
Pseudoduganella albidiflava	strain=DSM 17472	GCA_004322755.1	321983	321983	type	True	89.695	1951	2437	95	below_threshold
Pseudoduganella lutea	strain=DSM 17473	GCA_004209755.1	321985	321985	type	True	87.9784	1870	2437	95	below_threshold
Pseudoduganella dura	strain=KCTC 12342	GCA_014651395.1	321982	321982	type	True	87.4352	1754	2437	95	below_threshold
Pseudoduganella dura	strain=DSM 17513	GCA_009727155.1	321982	321982	type	True	87.3884	1806	2437	95	below_threshold
Pseudoduganella flava	strain=CGMCC 1.10685	GCA_007830495.1	871742	871742	type	True	84.9469	1564	2437	95	below_threshold
Pseudoduganella buxea	strain=KCTC 52429	GCA_009720835.1	1949069	1949069	type	True	83.2228	1343	2437	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	80.9749	971	2437	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	80.7963	1203	2437	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	80.6572	974	2437	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	80.5632	814	2437	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	80.3209	961	2437	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:58:37,263] [INFO] DFAST Taxonomy check result was written to GCF_014192225.1_ASM1419222v1_genomic.fna/tc_result.tsv
[2024-01-25 18:58:37,264] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:58:37,264] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:58:37,264] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbe71fc0-92f6-40d2-888c-f65f9441db6a/dqc_reference/checkm_data
[2024-01-25 18:58:37,265] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:58:37,331] [INFO] Task started: CheckM
[2024-01-25 18:58:37,331] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014192225.1_ASM1419222v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014192225.1_ASM1419222v1_genomic.fna/checkm_input GCF_014192225.1_ASM1419222v1_genomic.fna/checkm_result
[2024-01-25 18:59:41,773] [INFO] Task succeeded: CheckM
[2024-01-25 18:59:41,774] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:59:41,793] [INFO] ===== Completeness check finished =====
[2024-01-25 18:59:41,793] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:59:41,795] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014192225.1_ASM1419222v1_genomic.fna/markers.fasta)
[2024-01-25 18:59:41,795] [INFO] Task started: Blastn
[2024-01-25 18:59:41,795] [INFO] Running command: blastn -query GCF_014192225.1_ASM1419222v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbe71fc0-92f6-40d2-888c-f65f9441db6a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014192225.1_ASM1419222v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:43,877] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:43,880] [INFO] Selected 9 target genomes.
[2024-01-25 18:59:43,881] [INFO] Target genome list was writen to GCF_014192225.1_ASM1419222v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:59:43,892] [INFO] Task started: fastANI
[2024-01-25 18:59:43,892] [INFO] Running command: fastANI --query /var/lib/cwl/stg58194265-a23b-4c54-84ac-050410f59ee0/GCF_014192225.1_ASM1419222v1_genomic.fna.gz --refList GCF_014192225.1_ASM1419222v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014192225.1_ASM1419222v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:00:01,142] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:01,149] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:00:01,149] [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_014192225.1	s__Pseudoduganella umbonata	100.0	2435	2437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_004322755.1	s__Pseudoduganella albidiflava	89.6837	1951	2437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004209755.1	s__Pseudoduganella lutea	87.9769	1870	2437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009727155.1	s__Pseudoduganella dura	87.3942	1806	2437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_007830495.1	s__Pseudoduganella flava	84.9521	1563	2437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_007830455.1	s__Pseudoduganella lurida	84.644	1495	2437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002454505.1	s__Pseudoduganella sp002454505	84.4846	1357	2437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008011715.1	s__Pseudoduganella haloabium	83.4846	1383	2437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	98.13	98.13	0.91	0.91	2	-
GCF_009720835.1	s__Pseudoduganella buxea	83.2095	1344	2437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:00:01,150] [INFO] GTDB search result was written to GCF_014192225.1_ASM1419222v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:00:01,151] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:00:01,153] [INFO] DFAST_QC result json was written to GCF_014192225.1_ASM1419222v1_genomic.fna/dqc_result.json
[2024-01-25 19:00:01,153] [INFO] DFAST_QC completed!
[2024-01-25 19:00:01,153] [INFO] Total running time: 0h2m11s