[2024-01-24 13:55:15,826] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:15,829] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:15,829] [INFO] DQC Reference Directory: /var/lib/cwl/stgf68f2dd7-3050-4efc-8087-29a484f21c10/dqc_reference
[2024-01-24 13:55:17,032] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:17,033] [INFO] Task started: Prodigal
[2024-01-24 13:55:17,033] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a5392a8-e93d-4509-b13a-39dcdcdf1898/GCF_000382365.1_ASM38236v1_genomic.fna.gz | prodigal -d GCF_000382365.1_ASM38236v1_genomic.fna/cds.fna -a GCF_000382365.1_ASM38236v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:32,113] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:32,114] [INFO] Task started: HMMsearch
[2024-01-24 13:55:32,114] [INFO] Running command: hmmsearch --tblout GCF_000382365.1_ASM38236v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf68f2dd7-3050-4efc-8087-29a484f21c10/dqc_reference/reference_markers.hmm GCF_000382365.1_ASM38236v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:32,460] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:32,461] [INFO] Found 6/6 markers.
[2024-01-24 13:55:32,501] [INFO] Query marker FASTA was written to GCF_000382365.1_ASM38236v1_genomic.fna/markers.fasta
[2024-01-24 13:55:32,501] [INFO] Task started: Blastn
[2024-01-24 13:55:32,501] [INFO] Running command: blastn -query GCF_000382365.1_ASM38236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf68f2dd7-3050-4efc-8087-29a484f21c10/dqc_reference/reference_markers.fasta -out GCF_000382365.1_ASM38236v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:33,585] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:33,587] [INFO] Selected 11 target genomes.
[2024-01-24 13:55:33,588] [INFO] Target genome list was writen to GCF_000382365.1_ASM38236v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:33,598] [INFO] Task started: fastANI
[2024-01-24 13:55:33,599] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a5392a8-e93d-4509-b13a-39dcdcdf1898/GCF_000382365.1_ASM38236v1_genomic.fna.gz --refList GCF_000382365.1_ASM38236v1_genomic.fna/target_genomes.txt --output GCF_000382365.1_ASM38236v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:44,883] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:44,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf68f2dd7-3050-4efc-8087-29a484f21c10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:44,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf68f2dd7-3050-4efc-8087-29a484f21c10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:44,894] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:55:44,894] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:44,895] [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
Pannonibacter phragmitetus	strain=DSM 14782	GCA_000382365.1	121719	121719	suspected-type	True	100.0	1574	1575	95	conclusive
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	99.9887	1571	1575	95	conclusive
Pannonibacter indicus	strain=DSM 23407	GCA_001517385.1	466044	466044	type	True	93.5317	1255	1575	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	93.5317	1255	1575	95	below_threshold
Pannonibacter carbonis	strain=Q4.6	GCA_003012935.1	2067569	2067569	type	True	80.8789	814	1575	95	below_threshold
Roseibium suaedae	strain=DSM 22153	GCA_900142725.1	735517	735517	type	True	79.172	565	1575	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	78.4491	447	1575	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.6807	345	1575	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	77.5336	319	1575	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	77.1638	285	1575	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.2579	174	1575	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:44,896] [INFO] DFAST Taxonomy check result was written to GCF_000382365.1_ASM38236v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:44,897] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:44,897] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:44,898] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf68f2dd7-3050-4efc-8087-29a484f21c10/dqc_reference/checkm_data
[2024-01-24 13:55:44,899] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:44,950] [INFO] Task started: CheckM
[2024-01-24 13:55:44,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000382365.1_ASM38236v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000382365.1_ASM38236v1_genomic.fna/checkm_input GCF_000382365.1_ASM38236v1_genomic.fna/checkm_result
[2024-01-24 13:56:43,923] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:43,925] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:43,947] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:43,947] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:43,948] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000382365.1_ASM38236v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:43,948] [INFO] Task started: Blastn
[2024-01-24 13:56:43,948] [INFO] Running command: blastn -query GCF_000382365.1_ASM38236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf68f2dd7-3050-4efc-8087-29a484f21c10/dqc_reference/reference_markers_gtdb.fasta -out GCF_000382365.1_ASM38236v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:46,036] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:46,040] [INFO] Selected 8 target genomes.
[2024-01-24 13:56:46,040] [INFO] Target genome list was writen to GCF_000382365.1_ASM38236v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:46,056] [INFO] Task started: fastANI
[2024-01-24 13:56:46,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a5392a8-e93d-4509-b13a-39dcdcdf1898/GCF_000382365.1_ASM38236v1_genomic.fna.gz --refList GCF_000382365.1_ASM38236v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000382365.1_ASM38236v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:54,683] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:54,695] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:54,695] [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_000382365.1	s__Pannonibacter phragmitetus	100.0	1574	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_001418225.1	s__Pannonibacter indicus	93.5317	1255	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	96.01	95.55	0.94	0.89	12	-
GCF_009915765.1	s__Pannonibacter sp009915765	81.3033	808	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	98.76	98.76	0.96	0.96	2	-
GCF_003012935.1	s__Pannonibacter carbonis	80.8918	812	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000192745.1	s__Polymorphum gilvum	79.8082	629	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Polymorphum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142725.1	s__Roseibium suaedae	79.167	566	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610575.1	s__Stappia sp003610575	78.9451	544	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	98.18	0.97	0.97	2	-
GCF_902502825.2	s__Pseudorhizobium flavum	77.2728	227	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudorhizobium	95.0	96.75	95.31	0.86	0.77	9	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:54,697] [INFO] GTDB search result was written to GCF_000382365.1_ASM38236v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:54,697] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:54,700] [INFO] DFAST_QC result json was written to GCF_000382365.1_ASM38236v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:54,700] [INFO] DFAST_QC completed!
[2024-01-24 13:56:54,700] [INFO] Total running time: 0h1m39s