[2024-01-25 17:40:20,692] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:20,694] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:20,694] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0be907c-302b-4cc9-8f4b-0787c4cc1f2e/dqc_reference
[2024-01-25 17:40:21,864] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:21,865] [INFO] Task started: Prodigal
[2024-01-25 17:40:21,865] [INFO] Running command: gunzip -c /var/lib/cwl/stga76108ad-0d61-4aa1-b42c-2f78b84996b2/GCF_900454465.1_50766_H01_genomic.fna.gz | prodigal -d GCF_900454465.1_50766_H01_genomic.fna/cds.fna -a GCF_900454465.1_50766_H01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:35,363] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:35,364] [INFO] Task started: HMMsearch
[2024-01-25 17:40:35,364] [INFO] Running command: hmmsearch --tblout GCF_900454465.1_50766_H01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0be907c-302b-4cc9-8f4b-0787c4cc1f2e/dqc_reference/reference_markers.hmm GCF_900454465.1_50766_H01_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:35,657] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:35,658] [INFO] Found 6/6 markers.
[2024-01-25 17:40:35,699] [INFO] Query marker FASTA was written to GCF_900454465.1_50766_H01_genomic.fna/markers.fasta
[2024-01-25 17:40:35,699] [INFO] Task started: Blastn
[2024-01-25 17:40:35,699] [INFO] Running command: blastn -query GCF_900454465.1_50766_H01_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0be907c-302b-4cc9-8f4b-0787c4cc1f2e/dqc_reference/reference_markers.fasta -out GCF_900454465.1_50766_H01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:36,716] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:36,719] [INFO] Selected 11 target genomes.
[2024-01-25 17:40:36,719] [INFO] Target genome list was writen to GCF_900454465.1_50766_H01_genomic.fna/target_genomes.txt
[2024-01-25 17:40:36,740] [INFO] Task started: fastANI
[2024-01-25 17:40:36,740] [INFO] Running command: fastANI --query /var/lib/cwl/stga76108ad-0d61-4aa1-b42c-2f78b84996b2/GCF_900454465.1_50766_H01_genomic.fna.gz --refList GCF_900454465.1_50766_H01_genomic.fna/target_genomes.txt --output GCF_900454465.1_50766_H01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:48,105] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:48,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0be907c-302b-4cc9-8f4b-0787c4cc1f2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:48,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0be907c-302b-4cc9-8f4b-0787c4cc1f2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:48,114] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:40:48,115] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:40:48,115] [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=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	100.0	1612	1612	95	conclusive
Pannonibacter phragmitetus	strain=DSM 14782	GCA_000382365.1	121719	121719	suspected-type	True	99.9715	1569	1612	95	conclusive
Pannonibacter indicus	strain=DSM 23407	GCA_001517385.1	466044	466044	type	True	93.5121	1277	1612	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	93.5121	1277	1612	95	below_threshold
Pannonibacter carbonis	strain=Q4.6	GCA_003012935.1	2067569	2067569	type	True	81.0619	804	1612	95	below_threshold
Roseibium suaedae	strain=DSM 22153	GCA_900142725.1	735517	735517	type	True	79.2421	580	1612	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	78.67	437	1612	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.8793	336	1612	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	77.7013	313	1612	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	77.2377	288	1612	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.3981	182	1612	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:48,116] [INFO] DFAST Taxonomy check result was written to GCF_900454465.1_50766_H01_genomic.fna/tc_result.tsv
[2024-01-25 17:40:48,117] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:48,117] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:48,117] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0be907c-302b-4cc9-8f4b-0787c4cc1f2e/dqc_reference/checkm_data
[2024-01-25 17:40:48,118] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:48,165] [INFO] Task started: CheckM
[2024-01-25 17:40:48,165] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900454465.1_50766_H01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900454465.1_50766_H01_genomic.fna/checkm_input GCF_900454465.1_50766_H01_genomic.fna/checkm_result
[2024-01-25 17:42:02,768] [INFO] Task succeeded: CheckM
[2024-01-25 17:42:02,770] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:42:02,789] [INFO] ===== Completeness check finished =====
[2024-01-25 17:42:02,789] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:42:02,790] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900454465.1_50766_H01_genomic.fna/markers.fasta)
[2024-01-25 17:42:02,790] [INFO] Task started: Blastn
[2024-01-25 17:42:02,790] [INFO] Running command: blastn -query GCF_900454465.1_50766_H01_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0be907c-302b-4cc9-8f4b-0787c4cc1f2e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900454465.1_50766_H01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:04,865] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:04,869] [INFO] Selected 8 target genomes.
[2024-01-25 17:42:04,869] [INFO] Target genome list was writen to GCF_900454465.1_50766_H01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:42:04,905] [INFO] Task started: fastANI
[2024-01-25 17:42:04,905] [INFO] Running command: fastANI --query /var/lib/cwl/stga76108ad-0d61-4aa1-b42c-2f78b84996b2/GCF_900454465.1_50766_H01_genomic.fna.gz --refList GCF_900454465.1_50766_H01_genomic.fna/target_genomes_gtdb.txt --output GCF_900454465.1_50766_H01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:42:13,627] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:13,633] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:42:13,634] [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	99.9715	1569	1612	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	93.5121	1277	1612	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	81.3586	816	1612	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	81.0653	803	1612	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	79.8156	649	1612	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	79.2261	583	1612	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	78.946	537	1612	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	77.9775	224	1612	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudorhizobium	95.0	96.75	95.31	0.86	0.77	9	-
--------------------------------------------------------------------------------
[2024-01-25 17:42:13,636] [INFO] GTDB search result was written to GCF_900454465.1_50766_H01_genomic.fna/result_gtdb.tsv
[2024-01-25 17:42:13,636] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:42:13,639] [INFO] DFAST_QC result json was written to GCF_900454465.1_50766_H01_genomic.fna/dqc_result.json
[2024-01-25 17:42:13,640] [INFO] DFAST_QC completed!
[2024-01-25 17:42:13,640] [INFO] Total running time: 0h1m53s