[2024-01-24 12:23:03,764] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,767] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,767] [INFO] DQC Reference Directory: /var/lib/cwl/stg20200f8e-f136-4cb7-a881-9c89a9033a3d/dqc_reference
[2024-01-24 12:23:05,067] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,068] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,068] [INFO] Running command: gunzip -c /var/lib/cwl/stge89829eb-2400-4c79-9a09-e3b9883a2f7d/GCF_014489595.1_ASM1448959v1_genomic.fna.gz | prodigal -d GCF_014489595.1_ASM1448959v1_genomic.fna/cds.fna -a GCF_014489595.1_ASM1448959v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:21,638] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:21,638] [INFO] Task started: HMMsearch
[2024-01-24 12:23:21,639] [INFO] Running command: hmmsearch --tblout GCF_014489595.1_ASM1448959v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20200f8e-f136-4cb7-a881-9c89a9033a3d/dqc_reference/reference_markers.hmm GCF_014489595.1_ASM1448959v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:21,941] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:21,942] [INFO] Found 6/6 markers.
[2024-01-24 12:23:21,992] [INFO] Query marker FASTA was written to GCF_014489595.1_ASM1448959v1_genomic.fna/markers.fasta
[2024-01-24 12:23:21,992] [INFO] Task started: Blastn
[2024-01-24 12:23:21,992] [INFO] Running command: blastn -query GCF_014489595.1_ASM1448959v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20200f8e-f136-4cb7-a881-9c89a9033a3d/dqc_reference/reference_markers.fasta -out GCF_014489595.1_ASM1448959v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:23,069] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:23,072] [INFO] Selected 21 target genomes.
[2024-01-24 12:23:23,072] [INFO] Target genome list was writen to GCF_014489595.1_ASM1448959v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:23,080] [INFO] Task started: fastANI
[2024-01-24 12:23:23,080] [INFO] Running command: fastANI --query /var/lib/cwl/stge89829eb-2400-4c79-9a09-e3b9883a2f7d/GCF_014489595.1_ASM1448959v1_genomic.fna.gz --refList GCF_014489595.1_ASM1448959v1_genomic.fna/target_genomes.txt --output GCF_014489595.1_ASM1448959v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:46,142] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:46,142] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20200f8e-f136-4cb7-a881-9c89a9033a3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:46,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20200f8e-f136-4cb7-a881-9c89a9033a3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:46,162] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:46,162] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:46,162] [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 wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	83.9363	913	1559	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	83.8663	919	1559	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	83.671	808	1559	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	83.555	809	1559	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	83.354	899	1559	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	83.3128	997	1559	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	83.3051	929	1559	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	83.2507	942	1559	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	83.1339	823	1559	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	82.9967	934	1559	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	82.8596	907	1559	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	82.7865	955	1559	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	82.6614	1002	1559	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	82.6581	851	1559	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	82.6351	947	1559	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	82.6015	857	1559	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	82.4916	768	1559	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	81.509	749	1559	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	80.5667	625	1559	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	80.3035	682	1559	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	80.1358	761	1559	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:46,164] [INFO] DFAST Taxonomy check result was written to GCF_014489595.1_ASM1448959v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:46,164] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:46,164] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:46,165] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20200f8e-f136-4cb7-a881-9c89a9033a3d/dqc_reference/checkm_data
[2024-01-24 12:23:46,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:46,213] [INFO] Task started: CheckM
[2024-01-24 12:23:46,213] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014489595.1_ASM1448959v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014489595.1_ASM1448959v1_genomic.fna/checkm_input GCF_014489595.1_ASM1448959v1_genomic.fna/checkm_result
[2024-01-24 12:25:01,935] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:01,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:01,955] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:01,956] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:01,956] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014489595.1_ASM1448959v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:01,956] [INFO] Task started: Blastn
[2024-01-24 12:25:01,956] [INFO] Running command: blastn -query GCF_014489595.1_ASM1448959v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20200f8e-f136-4cb7-a881-9c89a9033a3d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014489595.1_ASM1448959v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:04,234] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:04,238] [INFO] Selected 18 target genomes.
[2024-01-24 12:25:04,238] [INFO] Target genome list was writen to GCF_014489595.1_ASM1448959v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:04,258] [INFO] Task started: fastANI
[2024-01-24 12:25:04,258] [INFO] Running command: fastANI --query /var/lib/cwl/stge89829eb-2400-4c79-9a09-e3b9883a2f7d/GCF_014489595.1_ASM1448959v1_genomic.fna.gz --refList GCF_014489595.1_ASM1448959v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014489595.1_ASM1448959v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:25,205] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:25,227] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:25,228] [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_014489595.1	s__Acidovorax_F monticola	100.0	1559	1559	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_F	95.0	97.51	97.51	0.93	0.93	2	conclusive
GCF_000204645.1	s__Alicycliphilus denitrificans	84.8137	931	1559	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	97.26	95.80	0.83	0.76	8	-
GCA_001725235.1	s__Acidovorax_C sp001725235	84.8003	891	1559	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_C	95.0	98.36	96.90	0.87	0.83	3	-
GCF_003604195.1	s__Giesbergeria lacusdiani	84.3212	844	1559	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053545.1	s__Acidovorax sp003053545	84.0232	1057	1559	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.66	97.32	0.95	0.90	3	-
GCF_900113035.1	s__Acidovorax_A wautersii	83.9696	909	1559	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_003269065.1	s__Acidovorax_A anthurii	83.8683	917	1559	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_014207955.1	s__Acidovorax soli_A	83.8468	1080	1559	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003755025.1	s__Diaphorobacter nitroreducens	83.7409	865	1559	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter	95.0	98.11	97.62	0.91	0.81	15	-
GCF_001298675.1	s__Acidovorax_C caeni	83.6734	806	1559	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_C	95.0	99.98	99.98	0.98	0.98	2	-
GCF_001428665.1	s__Acidovorax sp001428665	83.5798	1064	1559	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.34	97.34	0.92	0.92	2	-
GCA_002397315.1	s__Acidovorax_A sp002397315	83.542	920	1559	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	83.4012	894	1559	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	83.2727	933	1559	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	83.2458	939	1559	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_900102625.1	s__Acidovorax_A valerianellae	82.8281	912	1559	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_001544075.1	s__Comamonas terrae	82.6449	853	1559	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017998575.1	s__JAGOCV01 sp017998575	80.4696	557	1559	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAGOCV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:25,230] [INFO] GTDB search result was written to GCF_014489595.1_ASM1448959v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:25,231] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:25,235] [INFO] DFAST_QC result json was written to GCF_014489595.1_ASM1448959v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:25,235] [INFO] DFAST_QC completed!
[2024-01-24 12:25:25,235] [INFO] Total running time: 0h2m21s