[2024-01-24 14:21:50,636] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:21:50,638] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:21:50,638] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e5d7889-1994-4280-83db-2d46ec94360c/dqc_reference
[2024-01-24 14:21:52,086] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:21:52,089] [INFO] Task started: Prodigal
[2024-01-24 14:21:52,090] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1dda0c8-b9d4-4e1e-9b4c-872054cf4da6/GCF_001293565.1_ASM129356v1_genomic.fna.gz | prodigal -d GCF_001293565.1_ASM129356v1_genomic.fna/cds.fna -a GCF_001293565.1_ASM129356v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:03,173] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:03,173] [INFO] Task started: HMMsearch
[2024-01-24 14:22:03,173] [INFO] Running command: hmmsearch --tblout GCF_001293565.1_ASM129356v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e5d7889-1994-4280-83db-2d46ec94360c/dqc_reference/reference_markers.hmm GCF_001293565.1_ASM129356v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:03,499] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:03,500] [INFO] Found 6/6 markers.
[2024-01-24 14:22:03,538] [INFO] Query marker FASTA was written to GCF_001293565.1_ASM129356v1_genomic.fna/markers.fasta
[2024-01-24 14:22:03,539] [INFO] Task started: Blastn
[2024-01-24 14:22:03,539] [INFO] Running command: blastn -query GCF_001293565.1_ASM129356v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e5d7889-1994-4280-83db-2d46ec94360c/dqc_reference/reference_markers.fasta -out GCF_001293565.1_ASM129356v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:04,249] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:04,254] [INFO] Selected 24 target genomes.
[2024-01-24 14:22:04,255] [INFO] Target genome list was writen to GCF_001293565.1_ASM129356v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:04,267] [INFO] Task started: fastANI
[2024-01-24 14:22:04,267] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1dda0c8-b9d4-4e1e-9b4c-872054cf4da6/GCF_001293565.1_ASM129356v1_genomic.fna.gz --refList GCF_001293565.1_ASM129356v1_genomic.fna/target_genomes.txt --output GCF_001293565.1_ASM129356v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:23,106] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:23,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e5d7889-1994-4280-83db-2d46ec94360c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:23,107] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e5d7889-1994-4280-83db-2d46ec94360c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:23,118] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:23,118] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:23,118] [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
Ahrensia marina	strain=LZD062	GCA_001293565.1	1514904	1514904	type	True	100.0	1118	1121	95	conclusive
Ahrensia kielensis	strain=DSM 5890	GCA_000374465.1	76980	76980	type	True	80.5761	669	1121	95	below_threshold
Pseudochrobactrum algeriensis		GCA_018436245.1	2834768	2834768	type	True	76.6997	55	1121	95	below_threshold
Pseudochrobactrum algeriensis		GCA_907164595.1	2834768	2834768	type	True	76.6997	55	1121	95	below_threshold
Phyllobacterium calauticae	strain=R2-JL	GCA_019991125.1	2817027	2817027	type	True	76.6306	57	1121	95	below_threshold
Phyllobacterium zundukense	strain=Tri-48; RCAM 03910	GCA_002764115.1	1867719	1867719	type	True	76.523	58	1121	95	below_threshold
Brucella pseudogrignonensis	strain=CCUG 30717	GCA_002252525.1	419475	419475	type	True	76.2999	59	1121	95	below_threshold
Brucella tritici	strain=LMG 18957	GCA_008932295.1	94626	94626	type	True	76.1947	55	1121	95	below_threshold
Pseudochrobactrum saccharolyticum	strain=CCUG 33852	GCA_008801715.1	354352	354352	type	True	76.1939	58	1121	95	below_threshold
Phyllobacterium myrsinacearum	strain=DSM 5892	GCA_002980555.1	28101	28101	type	True	76.1481	69	1121	95	below_threshold
Pseudochrobactrum asaccharolyticum	strain=DSM 25619	GCA_003314995.1	354351	354351	type	True	76.0661	66	1121	95	below_threshold
Agrobacterium salinitolerans	strain=YIC 5082	GCA_002008225.1	1183413	1183413	type	True	75.9948	60	1121	95	below_threshold
Paenochrobactrum gallinarii	strain=DSM 22336	GCA_014205685.1	643673	643673	type	True	75.9139	64	1121	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:23,120] [INFO] DFAST Taxonomy check result was written to GCF_001293565.1_ASM129356v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:23,120] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:23,120] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:23,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e5d7889-1994-4280-83db-2d46ec94360c/dqc_reference/checkm_data
[2024-01-24 14:22:23,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:23,158] [INFO] Task started: CheckM
[2024-01-24 14:22:23,158] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001293565.1_ASM129356v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001293565.1_ASM129356v1_genomic.fna/checkm_input GCF_001293565.1_ASM129356v1_genomic.fna/checkm_result
[2024-01-24 14:22:57,953] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:57,955] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:57,974] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:57,975] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:57,975] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001293565.1_ASM129356v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:57,975] [INFO] Task started: Blastn
[2024-01-24 14:22:57,976] [INFO] Running command: blastn -query GCF_001293565.1_ASM129356v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e5d7889-1994-4280-83db-2d46ec94360c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001293565.1_ASM129356v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:59,171] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:59,175] [INFO] Selected 24 target genomes.
[2024-01-24 14:22:59,175] [INFO] Target genome list was writen to GCF_001293565.1_ASM129356v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:59,199] [INFO] Task started: fastANI
[2024-01-24 14:22:59,200] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1dda0c8-b9d4-4e1e-9b4c-872054cf4da6/GCF_001293565.1_ASM129356v1_genomic.fna.gz --refList GCF_001293565.1_ASM129356v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001293565.1_ASM129356v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:17,440] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:17,451] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:17,451] [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_001293565.1	s__Ahrensia marina	100.0	1118	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ahrensia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000374465.1	s__Ahrensia kielensis	80.6001	670	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ahrensia	95.0	95.90	95.90	0.86	0.86	2	-
GCA_017642895.1	s__Roseitalea sp017642895	76.381	69	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	99.99	99.99	1.00	1.00	3	-
GCF_018798825.1	s__Ochrobactrum_A sp018798825	76.2787	62	1121	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_014397025.1	s__Ochrobactrum_A sp014397025	76.2126	60	1121	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_008801715.1	s__Pseudochrobactrum saccharolyticum	76.1939	58	1121	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	-
GCA_900470285.1	s__Pseudochrobactrum sp900470285	76.1607	56	1121	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_002980555.1	s__Phyllobacterium myrsinacearum	76.1481	69	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	99.64	98.56	0.99	0.97	5	-
GCF_003314995.1	s__Pseudochrobactrum asaccharolyticum	76.0661	66	1121	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	75.9139	64	1121	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	-
GCA_900539805.1	s__Phyllobacterium sp900539805	75.7635	59	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	96.69	96.69	0.93	0.93	2	-
GCA_002698425.1	s__Oricola sp002698425	75.5589	62	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:17,457] [INFO] GTDB search result was written to GCF_001293565.1_ASM129356v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:17,458] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:17,464] [INFO] DFAST_QC result json was written to GCF_001293565.1_ASM129356v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:17,465] [INFO] DFAST_QC completed!
[2024-01-24 14:23:17,465] [INFO] Total running time: 0h1m27s