[2024-01-24 12:37:24,930] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:24,932] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:24,932] [INFO] DQC Reference Directory: /var/lib/cwl/stg78d0a0c7-813f-4b70-9c7a-0a89d11591fa/dqc_reference
[2024-01-24 12:37:26,269] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:26,270] [INFO] Task started: Prodigal
[2024-01-24 12:37:26,270] [INFO] Running command: gunzip -c /var/lib/cwl/stg8230d7a2-fc7c-4b9b-bec6-f4a9f1cd0bb4/GCF_003269065.1_ASM326906v1_genomic.fna.gz | prodigal -d GCF_003269065.1_ASM326906v1_genomic.fna/cds.fna -a GCF_003269065.1_ASM326906v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:44,304] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:44,305] [INFO] Task started: HMMsearch
[2024-01-24 12:37:44,305] [INFO] Running command: hmmsearch --tblout GCF_003269065.1_ASM326906v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78d0a0c7-813f-4b70-9c7a-0a89d11591fa/dqc_reference/reference_markers.hmm GCF_003269065.1_ASM326906v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:44,626] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:44,628] [INFO] Found 6/6 markers.
[2024-01-24 12:37:44,671] [INFO] Query marker FASTA was written to GCF_003269065.1_ASM326906v1_genomic.fna/markers.fasta
[2024-01-24 12:37:44,672] [INFO] Task started: Blastn
[2024-01-24 12:37:44,672] [INFO] Running command: blastn -query GCF_003269065.1_ASM326906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78d0a0c7-813f-4b70-9c7a-0a89d11591fa/dqc_reference/reference_markers.fasta -out GCF_003269065.1_ASM326906v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:45,732] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:45,736] [INFO] Selected 13 target genomes.
[2024-01-24 12:37:45,737] [INFO] Target genome list was writen to GCF_003269065.1_ASM326906v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:45,746] [INFO] Task started: fastANI
[2024-01-24 12:37:45,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg8230d7a2-fc7c-4b9b-bec6-f4a9f1cd0bb4/GCF_003269065.1_ASM326906v1_genomic.fna.gz --refList GCF_003269065.1_ASM326906v1_genomic.fna/target_genomes.txt --output GCF_003269065.1_ASM326906v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:01,273] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:01,274] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78d0a0c7-813f-4b70-9c7a-0a89d11591fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:01,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78d0a0c7-813f-4b70-9c7a-0a89d11591fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:01,291] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:38:01,291] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:38:01,291] [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
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	100.0	1748	1756	95	conclusive
Acidovorax konjaci	strain=DSM 7481	GCA_900112675.1	32040	32040	type	True	87.2852	1253	1756	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	86.085	1139	1756	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	85.9988	1189	1756	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	85.9323	1201	1756	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	85.7657	1185	1756	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	81.015	830	1756	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	81.0109	669	1756	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	80.8433	708	1756	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	80.5108	669	1756	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	80.3599	706	1756	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.1002	710	1756	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:01,295] [INFO] DFAST Taxonomy check result was written to GCF_003269065.1_ASM326906v1_genomic.fna/tc_result.tsv
[2024-01-24 12:38:01,295] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:01,295] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:01,296] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78d0a0c7-813f-4b70-9c7a-0a89d11591fa/dqc_reference/checkm_data
[2024-01-24 12:38:01,297] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:01,352] [INFO] Task started: CheckM
[2024-01-24 12:38:01,352] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003269065.1_ASM326906v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003269065.1_ASM326906v1_genomic.fna/checkm_input GCF_003269065.1_ASM326906v1_genomic.fna/checkm_result
[2024-01-24 12:39:14,023] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:14,025] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:14,047] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:14,047] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:14,048] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003269065.1_ASM326906v1_genomic.fna/markers.fasta)
[2024-01-24 12:39:14,048] [INFO] Task started: Blastn
[2024-01-24 12:39:14,048] [INFO] Running command: blastn -query GCF_003269065.1_ASM326906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78d0a0c7-813f-4b70-9c7a-0a89d11591fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_003269065.1_ASM326906v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:16,126] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:16,130] [INFO] Selected 11 target genomes.
[2024-01-24 12:39:16,130] [INFO] Target genome list was writen to GCF_003269065.1_ASM326906v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:16,143] [INFO] Task started: fastANI
[2024-01-24 12:39:16,144] [INFO] Running command: fastANI --query /var/lib/cwl/stg8230d7a2-fc7c-4b9b-bec6-f4a9f1cd0bb4/GCF_003269065.1_ASM326906v1_genomic.fna.gz --refList GCF_003269065.1_ASM326906v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003269065.1_ASM326906v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:39:29,488] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:29,503] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:39:29,503] [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_003269065.1	s__Acidovorax_A anthurii	100.0	1748	1756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900112675.1	s__Acidovorax_A konjaci	87.2938	1253	1756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002397315.1	s__Acidovorax_A sp002397315	86.3204	1121	1756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100305.1	s__Acidovorax_A citrulli	86.0744	1141	1756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	99.47	99.27	0.97	0.96	11	-
GCF_000687165.1	s__Acidovorax_A oryzae	85.9847	1190	1756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.2137	98.08	98.08	0.87	0.87	2	-
GCF_000176855.2	s__Acidovorax_A avenae	85.9076	1205	1756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.2137	96.92	95.92	0.74	0.51	18	-
GCF_900104515.1	s__Acidovorax_A cattleyae	85.7612	1185	1756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	99.69	99.69	0.82	0.82	2	-
GCF_009755665.1	s__Variovorax paradoxus_G	80.1572	680	1756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099805.1	s__Variovorax sp900099805	80.1419	710	1756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003984625.1	s__Variovorax sp003984625	80.0015	712	1756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903875275.1	s__Rhodoferax sp903875275	76.7494	157	1756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.13	98.99	0.72	0.68	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:39:29,504] [INFO] GTDB search result was written to GCF_003269065.1_ASM326906v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:39:29,505] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:39:29,508] [INFO] DFAST_QC result json was written to GCF_003269065.1_ASM326906v1_genomic.fna/dqc_result.json
[2024-01-24 12:39:29,508] [INFO] DFAST_QC completed!
[2024-01-24 12:39:29,508] [INFO] Total running time: 0h2m5s