[2024-01-24 12:06:34,248] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:34,250] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:34,251] [INFO] DQC Reference Directory: /var/lib/cwl/stg63e5fc6c-431f-4ecd-a46c-b235d2e6d351/dqc_reference
[2024-01-24 12:06:35,579] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:35,580] [INFO] Task started: Prodigal
[2024-01-24 12:06:35,580] [INFO] Running command: gunzip -c /var/lib/cwl/stg4e50f7b1-1aa8-4ac6-836b-81546464943b/GCF_002278035.1_ASM227803v1_genomic.fna.gz | prodigal -d GCF_002278035.1_ASM227803v1_genomic.fna/cds.fna -a GCF_002278035.1_ASM227803v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:52,805] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:52,806] [INFO] Task started: HMMsearch
[2024-01-24 12:06:52,806] [INFO] Running command: hmmsearch --tblout GCF_002278035.1_ASM227803v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63e5fc6c-431f-4ecd-a46c-b235d2e6d351/dqc_reference/reference_markers.hmm GCF_002278035.1_ASM227803v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:53,113] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:53,114] [INFO] Found 6/6 markers.
[2024-01-24 12:06:53,162] [INFO] Query marker FASTA was written to GCF_002278035.1_ASM227803v1_genomic.fna/markers.fasta
[2024-01-24 12:06:53,163] [INFO] Task started: Blastn
[2024-01-24 12:06:53,163] [INFO] Running command: blastn -query GCF_002278035.1_ASM227803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63e5fc6c-431f-4ecd-a46c-b235d2e6d351/dqc_reference/reference_markers.fasta -out GCF_002278035.1_ASM227803v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:53,854] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:53,859] [INFO] Selected 11 target genomes.
[2024-01-24 12:06:53,860] [INFO] Target genome list was writen to GCF_002278035.1_ASM227803v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:53,864] [INFO] Task started: fastANI
[2024-01-24 12:06:53,864] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e50f7b1-1aa8-4ac6-836b-81546464943b/GCF_002278035.1_ASM227803v1_genomic.fna.gz --refList GCF_002278035.1_ASM227803v1_genomic.fna/target_genomes.txt --output GCF_002278035.1_ASM227803v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:06,280] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:06,281] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63e5fc6c-431f-4ecd-a46c-b235d2e6d351/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:06,282] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63e5fc6c-431f-4ecd-a46c-b235d2e6d351/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:06,296] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:06,297] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:06,297] [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
[Ochrobactrum] quorumnocens	strain=A44	GCA_002278035.1	271865	271865	type	True	100.0	1878	1880	95	conclusive
Brucella pituitosa	strain=CCUG 50899	GCA_008801705.1	571256	571256	type	True	88.7567	1309	1880	95	below_threshold
Brucella pituitosa	strain=CCUG 50899	GCA_003049685.2	571256	571256	type	True	88.6763	1320	1880	95	below_threshold
Brucella rhizosphaerae	strain=PR17	GCA_002252475.1	571254	571254	type	True	88.1627	1287	1880	95	below_threshold
Brucella grignonensis	strain=OgA9a	GCA_002252505.1	94627	94627	type	True	87.6499	1178	1880	95	below_threshold
Brucella pseudogrignonensis	strain=CCUG 30717	GCA_002252525.1	419475	419475	type	True	84.439	1178	1880	95	below_threshold
Pseudochrobactrum algeriensis		GCA_907164595.1	2834768	2834768	type	True	78.1019	275	1880	95	below_threshold
Pseudochrobactrum algeriensis		GCA_018436245.1	2834768	2834768	type	True	78.0042	274	1880	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	76.4959	144	1880	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	76.4844	159	1880	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	75.9851	104	1880	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:06,300] [INFO] DFAST Taxonomy check result was written to GCF_002278035.1_ASM227803v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:06,301] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:06,301] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:06,301] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63e5fc6c-431f-4ecd-a46c-b235d2e6d351/dqc_reference/checkm_data
[2024-01-24 12:07:06,302] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:06,357] [INFO] Task started: CheckM
[2024-01-24 12:07:06,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002278035.1_ASM227803v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002278035.1_ASM227803v1_genomic.fna/checkm_input GCF_002278035.1_ASM227803v1_genomic.fna/checkm_result
[2024-01-24 12:07:57,807] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:57,809] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:57,836] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:57,836] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:57,836] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002278035.1_ASM227803v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:57,837] [INFO] Task started: Blastn
[2024-01-24 12:07:57,837] [INFO] Running command: blastn -query GCF_002278035.1_ASM227803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63e5fc6c-431f-4ecd-a46c-b235d2e6d351/dqc_reference/reference_markers_gtdb.fasta -out GCF_002278035.1_ASM227803v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:58,860] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:58,865] [INFO] Selected 8 target genomes.
[2024-01-24 12:07:58,865] [INFO] Target genome list was writen to GCF_002278035.1_ASM227803v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:58,870] [INFO] Task started: fastANI
[2024-01-24 12:07:58,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e50f7b1-1aa8-4ac6-836b-81546464943b/GCF_002278035.1_ASM227803v1_genomic.fna.gz --refList GCF_002278035.1_ASM227803v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002278035.1_ASM227803v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:09,210] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:09,224] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:09,225] [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_002278035.1	s__Ochrobactrum_A quorumnocens	100.0	1878	1880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	97.19	96.78	0.85	0.82	5	conclusive
GCF_003049685.1	s__Ochrobactrum_A pituitosa	88.6814	1321	1880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	98.27	97.05	0.91	0.82	14	-
GCF_004368705.1	s__Ochrobactrum_A sp004368705	88.5718	1329	1880	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_002252475.1	s__Ochrobactrum_A rhizosphaerae	88.1627	1287	1880	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_002252505.1	s__Ochrobactrum_A grignonensis	87.6499	1178	1880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	99.78	99.78	1.00	1.00	2	-
GCF_002252525.1	s__Ochrobactrum_A pseudogrignonensis	84.4453	1177	1880	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	-
GCF_018798825.1	s__Ochrobactrum_A sp018798825	84.4041	1169	1880	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_014253075.1	s__JACLZJ01 sp014253075	79.7719	697	1880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__JACLZJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:09,226] [INFO] GTDB search result was written to GCF_002278035.1_ASM227803v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:09,227] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:09,231] [INFO] DFAST_QC result json was written to GCF_002278035.1_ASM227803v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:09,231] [INFO] DFAST_QC completed!
[2024-01-24 12:08:09,231] [INFO] Total running time: 0h1m35s