[2024-01-24 10:57:12,845] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:12,848] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:12,849] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b6722c5-ba67-442d-b7ce-55def801dba7/dqc_reference
[2024-01-24 10:57:14,421] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,422] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,422] [INFO] Running command: gunzip -c /var/lib/cwl/stg0bf2772b-1f31-4ef2-94df-b41b6d8fd8d5/GCF_025996105.1_ASM2599610v1_genomic.fna.gz | prodigal -d GCF_025996105.1_ASM2599610v1_genomic.fna/cds.fna -a GCF_025996105.1_ASM2599610v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:23,915] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:23,915] [INFO] Task started: HMMsearch
[2024-01-24 10:57:23,916] [INFO] Running command: hmmsearch --tblout GCF_025996105.1_ASM2599610v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b6722c5-ba67-442d-b7ce-55def801dba7/dqc_reference/reference_markers.hmm GCF_025996105.1_ASM2599610v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:24,254] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:24,255] [INFO] Found 6/6 markers.
[2024-01-24 10:57:24,282] [INFO] Query marker FASTA was written to GCF_025996105.1_ASM2599610v1_genomic.fna/markers.fasta
[2024-01-24 10:57:24,282] [INFO] Task started: Blastn
[2024-01-24 10:57:24,282] [INFO] Running command: blastn -query GCF_025996105.1_ASM2599610v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b6722c5-ba67-442d-b7ce-55def801dba7/dqc_reference/reference_markers.fasta -out GCF_025996105.1_ASM2599610v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:24,982] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:24,984] [INFO] Selected 21 target genomes.
[2024-01-24 10:57:24,985] [INFO] Target genome list was writen to GCF_025996105.1_ASM2599610v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:24,992] [INFO] Task started: fastANI
[2024-01-24 10:57:24,993] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bf2772b-1f31-4ef2-94df-b41b6d8fd8d5/GCF_025996105.1_ASM2599610v1_genomic.fna.gz --refList GCF_025996105.1_ASM2599610v1_genomic.fna/target_genomes.txt --output GCF_025996105.1_ASM2599610v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:38,190] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:38,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b6722c5-ba67-442d-b7ce-55def801dba7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:38,191] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b6722c5-ba67-442d-b7ce-55def801dba7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:38,204] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:57:38,205] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:38,205] [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
Acetobacter cibinongensis	strain=NBRC 16605	GCA_007989305.1	146475	146475	type	True	99.9941	997	1014	95	conclusive
Acetobacter cibinongensis	strain=4H-1	GCA_000963925.1	146475	146475	type	True	99.9927	985	1014	95	conclusive
Acetobacter orientalis	strain=NBRC 16606	GCA_007989335.1	146474	146474	type	True	80.209	425	1014	95	below_threshold
Acetobacter orientalis	strain=21F-2	GCA_000963965.1	146474	146474	type	True	80.1432	430	1014	95	below_threshold
Acetobacter senegalensis	strain=LMG 23690	GCA_001580995.1	446692	446692	type	True	80.1248	426	1014	95	below_threshold
Acetobacter indonesiensis	strain=NBRC 16471	GCA_007991075.1	104101	104101	type	True	79.967	435	1014	95	below_threshold
Acetobacter tropicalis	strain=NBRC 16470	GCA_007989245.1	104102	104102	type	True	79.7322	422	1014	95	below_threshold
Acetobacter tropicalis	strain=LMG 19825	GCA_001580915.1	104102	104102	type	True	79.6625	422	1014	95	below_threshold
Acetobacter tropicalis	strain=NBRC 16470	GCA_000787635.2	104102	104102	type	True	79.6198	424	1014	95	below_threshold
Acetobacter cerevisiae	strain=LMG 1625	GCA_001580535.1	178900	178900	type	True	79.2084	381	1014	95	below_threshold
Acetobacter lambici	strain=LMG 27439	GCA_011516885.1	1332824	1332824	type	True	78.6221	274	1014	95	below_threshold
Acetobacter ghanensis	strain=LMG 23848T	GCA_001499675.1	431306	431306	type	True	78.3964	289	1014	95	below_threshold
Acetobacter ghanensis	strain=LMG 23848	GCA_011516865.1	431306	431306	type	True	78.3456	294	1014	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	77.9497	198	1014	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:38,206] [INFO] DFAST Taxonomy check result was written to GCF_025996105.1_ASM2599610v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:38,207] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:38,207] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:38,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b6722c5-ba67-442d-b7ce-55def801dba7/dqc_reference/checkm_data
[2024-01-24 10:57:38,209] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:38,243] [INFO] Task started: CheckM
[2024-01-24 10:57:38,243] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025996105.1_ASM2599610v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025996105.1_ASM2599610v1_genomic.fna/checkm_input GCF_025996105.1_ASM2599610v1_genomic.fna/checkm_result
[2024-01-24 10:58:11,007] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:11,008] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:11,024] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:11,024] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:11,025] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025996105.1_ASM2599610v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:11,025] [INFO] Task started: Blastn
[2024-01-24 10:58:11,025] [INFO] Running command: blastn -query GCF_025996105.1_ASM2599610v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b6722c5-ba67-442d-b7ce-55def801dba7/dqc_reference/reference_markers_gtdb.fasta -out GCF_025996105.1_ASM2599610v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:12,167] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:12,171] [INFO] Selected 15 target genomes.
[2024-01-24 10:58:12,171] [INFO] Target genome list was writen to GCF_025996105.1_ASM2599610v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:12,179] [INFO] Task started: fastANI
[2024-01-24 10:58:12,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bf2772b-1f31-4ef2-94df-b41b6d8fd8d5/GCF_025996105.1_ASM2599610v1_genomic.fna.gz --refList GCF_025996105.1_ASM2599610v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025996105.1_ASM2599610v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:21,577] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:21,594] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:21,594] [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_000963925.1	s__Acetobacter cibinongensis	99.9927	985	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.47	96.95	0.93	0.86	3	conclusive
GCF_000963965.1	s__Acetobacter orientalis	80.1481	430	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.55	97.80	0.92	0.88	7	-
GCF_001580995.1	s__Acetobacter senegalensis	80.1201	426	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.25	96.97	0.85	0.80	6	-
GCF_000963945.1	s__Acetobacter indonesiensis	79.8786	444	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.28	96.85	0.92	0.88	4	-
GCF_001580915.1	s__Acetobacter tropicalis	79.6502	423	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.32	97.71	0.90	0.87	9	-
GCF_001580535.1	s__Acetobacter cerevisiae	79.2083	381	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.52	96.47	0.88	0.86	4	-
GCF_011516935.1	s__Acetobacter farinalis	79.1045	368	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011516885.1	s__Acetobacter lambici	78.6068	275	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499675.1	s__Acetobacter ghanensis	78.3827	290	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002005445.1	s__Acetobacter aceti_B	77.3979	96	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613885.1	s__Asaia prunellae	76.7769	51	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:21,596] [INFO] GTDB search result was written to GCF_025996105.1_ASM2599610v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:21,597] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:21,600] [INFO] DFAST_QC result json was written to GCF_025996105.1_ASM2599610v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:21,600] [INFO] DFAST_QC completed!
[2024-01-24 10:58:21,600] [INFO] Total running time: 0h1m9s