[2024-01-24 13:31:44,529] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,531] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,531] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf2e1203-2e2b-462b-9ae4-215070efcdab/dqc_reference
[2024-01-24 13:31:45,831] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,832] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,832] [INFO] Running command: gunzip -c /var/lib/cwl/stg05613fb8-406f-4542-9f73-abc4da354ddf/GCF_014203195.1_ASM1420319v1_genomic.fna.gz | prodigal -d GCF_014203195.1_ASM1420319v1_genomic.fna/cds.fna -a GCF_014203195.1_ASM1420319v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:56,798] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:56,798] [INFO] Task started: HMMsearch
[2024-01-24 13:31:56,798] [INFO] Running command: hmmsearch --tblout GCF_014203195.1_ASM1420319v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf2e1203-2e2b-462b-9ae4-215070efcdab/dqc_reference/reference_markers.hmm GCF_014203195.1_ASM1420319v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:57,094] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:57,096] [INFO] Found 6/6 markers.
[2024-01-24 13:31:57,136] [INFO] Query marker FASTA was written to GCF_014203195.1_ASM1420319v1_genomic.fna/markers.fasta
[2024-01-24 13:31:57,137] [INFO] Task started: Blastn
[2024-01-24 13:31:57,137] [INFO] Running command: blastn -query GCF_014203195.1_ASM1420319v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf2e1203-2e2b-462b-9ae4-215070efcdab/dqc_reference/reference_markers.fasta -out GCF_014203195.1_ASM1420319v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:57,907] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:57,911] [INFO] Selected 8 target genomes.
[2024-01-24 13:31:57,911] [INFO] Target genome list was writen to GCF_014203195.1_ASM1420319v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:57,921] [INFO] Task started: fastANI
[2024-01-24 13:31:57,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg05613fb8-406f-4542-9f73-abc4da354ddf/GCF_014203195.1_ASM1420319v1_genomic.fna.gz --refList GCF_014203195.1_ASM1420319v1_genomic.fna/target_genomes.txt --output GCF_014203195.1_ASM1420319v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:06,172] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:06,173] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf2e1203-2e2b-462b-9ae4-215070efcdab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:06,173] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf2e1203-2e2b-462b-9ae4-215070efcdab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:06,183] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:32:06,183] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:32:06,183] [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
Pseudochrobactrum saccharolyticum	strain=DSM 25620	GCA_014203195.1	354352	354352	type	True	100.0	1243	1243	95	inconclusive
Pseudochrobactrum saccharolyticum	strain=CCUG 33852	GCA_008801715.1	354352	354352	type	True	99.9992	1243	1243	95	inconclusive
Pseudochrobactrum algeriensis		GCA_907164595.1	2834768	2834768	type	True	96.2512	1169	1243	95	inconclusive
Pseudochrobactrum algeriensis		GCA_018436245.1	2834768	2834768	type	True	96.2512	1169	1243	95	inconclusive
Pseudochrobactrum asaccharolyticum	strain=DSM 25619	GCA_003314995.1	354351	354351	type	True	86.9679	998	1243	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	76.5702	148	1243	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	76.0795	75	1243	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	75.8867	66	1243	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:06,186] [INFO] DFAST Taxonomy check result was written to GCF_014203195.1_ASM1420319v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:06,186] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:06,186] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:06,187] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf2e1203-2e2b-462b-9ae4-215070efcdab/dqc_reference/checkm_data
[2024-01-24 13:32:06,188] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:06,236] [INFO] Task started: CheckM
[2024-01-24 13:32:06,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203195.1_ASM1420319v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203195.1_ASM1420319v1_genomic.fna/checkm_input GCF_014203195.1_ASM1420319v1_genomic.fna/checkm_result
[2024-01-24 13:32:44,621] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:44,623] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:44,646] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:44,646] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:44,647] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203195.1_ASM1420319v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:44,647] [INFO] Task started: Blastn
[2024-01-24 13:32:44,648] [INFO] Running command: blastn -query GCF_014203195.1_ASM1420319v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf2e1203-2e2b-462b-9ae4-215070efcdab/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203195.1_ASM1420319v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:45,933] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:45,937] [INFO] Selected 14 target genomes.
[2024-01-24 13:32:45,937] [INFO] Target genome list was writen to GCF_014203195.1_ASM1420319v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:45,946] [INFO] Task started: fastANI
[2024-01-24 13:32:45,946] [INFO] Running command: fastANI --query /var/lib/cwl/stg05613fb8-406f-4542-9f73-abc4da354ddf/GCF_014203195.1_ASM1420319v1_genomic.fna.gz --refList GCF_014203195.1_ASM1420319v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203195.1_ASM1420319v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:58,659] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:58,675] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:58,675] [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_008801715.1	s__Pseudochrobactrum saccharolyticum	99.9992	1243	1243	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Pseudochrobactrum	95.0	96.83	96.24	0.94	0.92	10	conclusive
GCA_900470285.1	s__Pseudochrobactrum sp900470285	93.3083	1101	1243	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Pseudochrobactrum	95.0	97.83	97.83	0.89	0.89	2	-
GCF_003314995.1	s__Pseudochrobactrum asaccharolyticum	86.9679	998	1243	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Pseudochrobactrum	95.0	95.18	95.14	0.85	0.85	3	-
GCF_014205685.1	s__Paenochrobactrum gallinarii	78.7472	337	1243	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paenochrobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006476605.1	s__Ochrobactrum_A gallinifaecis	77.6887	254	1243	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252525.1	s__Ochrobactrum_A pseudogrignonensis	77.6186	301	1243	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	97.50	96.15	0.90	0.81	34	-
GCA_900465685.1	s__Ochrobactrum_B sp900465685	77.4489	322	1243	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B	95.0	99.22	99.21	0.91	0.91	3	-
GCF_003149535.1	s__Falsochrobactrum shanghaiense	77.3726	243	1243	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Falsochrobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008932435.1	s__Ochrobactrum pseudintermedium	77.3364	249	1243	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	98.90	97.85	0.90	0.89	7	-
GCF_014199265.1	s__Ochrobactrum_C daejeonensis	77.3025	251	1243	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_C	95.0	99.74	99.74	0.99	0.99	2	-
GCF_900104355.1	s__Phyllobacterium sp900104355	77.0912	208	1243	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640615.1	s__Paramesorhizobium endophyticum	76.6936	173	1243	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002980495.1	s__Paramesorhizobium phragmitis	76.593	208	1243	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001704765.1	s__Sinorhizobium shofinae	75.8891	77	1243	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:58,677] [INFO] GTDB search result was written to GCF_014203195.1_ASM1420319v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:58,678] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:58,682] [INFO] DFAST_QC result json was written to GCF_014203195.1_ASM1420319v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:58,682] [INFO] DFAST_QC completed!
[2024-01-24 13:32:58,682] [INFO] Total running time: 0h1m14s