[2024-01-24 13:03:20,839] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:03:20,842] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:03:20,843] [INFO] DQC Reference Directory: /var/lib/cwl/stg05d86e91-1461-46df-805c-ddcc2d5841c1/dqc_reference
[2024-01-24 13:03:22,060] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:03:22,061] [INFO] Task started: Prodigal
[2024-01-24 13:03:22,062] [INFO] Running command: gunzip -c /var/lib/cwl/stgb51f4f53-9c61-42a7-9c61-6206cf8bf2db/GCF_002245625.1_ASM224562v1_genomic.fna.gz | prodigal -d GCF_002245625.1_ASM224562v1_genomic.fna/cds.fna -a GCF_002245625.1_ASM224562v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:03:40,827] [INFO] Task succeeded: Prodigal
[2024-01-24 13:03:40,828] [INFO] Task started: HMMsearch
[2024-01-24 13:03:40,828] [INFO] Running command: hmmsearch --tblout GCF_002245625.1_ASM224562v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05d86e91-1461-46df-805c-ddcc2d5841c1/dqc_reference/reference_markers.hmm GCF_002245625.1_ASM224562v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:03:41,140] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:03:41,141] [INFO] Found 6/6 markers.
[2024-01-24 13:03:41,184] [INFO] Query marker FASTA was written to GCF_002245625.1_ASM224562v1_genomic.fna/markers.fasta
[2024-01-24 13:03:41,184] [INFO] Task started: Blastn
[2024-01-24 13:03:41,184] [INFO] Running command: blastn -query GCF_002245625.1_ASM224562v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05d86e91-1461-46df-805c-ddcc2d5841c1/dqc_reference/reference_markers.fasta -out GCF_002245625.1_ASM224562v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:42,163] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:42,167] [INFO] Selected 14 target genomes.
[2024-01-24 13:03:42,168] [INFO] Target genome list was writen to GCF_002245625.1_ASM224562v1_genomic.fna/target_genomes.txt
[2024-01-24 13:03:42,174] [INFO] Task started: fastANI
[2024-01-24 13:03:42,174] [INFO] Running command: fastANI --query /var/lib/cwl/stgb51f4f53-9c61-42a7-9c61-6206cf8bf2db/GCF_002245625.1_ASM224562v1_genomic.fna.gz --refList GCF_002245625.1_ASM224562v1_genomic.fna/target_genomes.txt --output GCF_002245625.1_ASM224562v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:03:58,189] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:58,189] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05d86e91-1461-46df-805c-ddcc2d5841c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:03:58,189] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05d86e91-1461-46df-805c-ddcc2d5841c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:03:58,204] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:03:58,205] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:03:58,205] [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
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	100.0	1694	1696	95	conclusive
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	88.5203	1327	1696	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	88.1319	1292	1696	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	87.2134	1363	1696	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	84.6834	836	1696	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	84.3807	885	1696	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	84.1724	955	1696	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	81.4687	840	1696	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	81.3854	872	1696	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	81.3759	864	1696	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.3369	688	1696	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.2185	649	1696	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	79.5411	573	1696	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	79.3196	718	1696	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:03:58,206] [INFO] DFAST Taxonomy check result was written to GCF_002245625.1_ASM224562v1_genomic.fna/tc_result.tsv
[2024-01-24 13:03:58,207] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:03:58,207] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:03:58,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05d86e91-1461-46df-805c-ddcc2d5841c1/dqc_reference/checkm_data
[2024-01-24 13:03:58,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:03:58,257] [INFO] Task started: CheckM
[2024-01-24 13:03:58,257] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002245625.1_ASM224562v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002245625.1_ASM224562v1_genomic.fna/checkm_input GCF_002245625.1_ASM224562v1_genomic.fna/checkm_result
[2024-01-24 13:05:06,284] [INFO] Task succeeded: CheckM
[2024-01-24 13:05:06,286] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:05:06,306] [INFO] ===== Completeness check finished =====
[2024-01-24 13:05:06,307] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:05:06,307] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002245625.1_ASM224562v1_genomic.fna/markers.fasta)
[2024-01-24 13:05:06,307] [INFO] Task started: Blastn
[2024-01-24 13:05:06,308] [INFO] Running command: blastn -query GCF_002245625.1_ASM224562v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05d86e91-1461-46df-805c-ddcc2d5841c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_002245625.1_ASM224562v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:05:08,271] [INFO] Task succeeded: Blastn
[2024-01-24 13:05:08,276] [INFO] Selected 9 target genomes.
[2024-01-24 13:05:08,276] [INFO] Target genome list was writen to GCF_002245625.1_ASM224562v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:05:08,284] [INFO] Task started: fastANI
[2024-01-24 13:05:08,284] [INFO] Running command: fastANI --query /var/lib/cwl/stgb51f4f53-9c61-42a7-9c61-6206cf8bf2db/GCF_002245625.1_ASM224562v1_genomic.fna.gz --refList GCF_002245625.1_ASM224562v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002245625.1_ASM224562v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:05:21,107] [INFO] Task succeeded: fastANI
[2024-01-24 13:05:21,124] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:05:21,125] [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_002245625.1	s__Acidovorax kalamii	100.0	1694	1696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001633105.1	s__Acidovorax sp001633105	93.7647	1460	1696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405905.1	s__Acidovorax sp005405905	91.5673	1448	1696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003060895.1	s__Acidovorax sp003060895	90.8734	1206	1696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003852545.1	s__Acidovorax sp003852545	90.1133	1311	1696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993815.1	s__Acidovorax delafieldii	88.5328	1325	1696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.08	96.33	0.92	0.90	8	-
GCF_000302535.1	s__Acidovorax sp000302535	88.4878	1298	1696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	95.71	95.42	0.83	0.75	7	-
GCF_001424425.1	s__Acidovorax sp001424425	86.4873	1322	1696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	99.93	99.87	0.98	0.97	3	-
GCF_014207955.1	s__Acidovorax soli_A	85.0113	1300	1696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:05:21,127] [INFO] GTDB search result was written to GCF_002245625.1_ASM224562v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:05:21,127] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:05:21,132] [INFO] DFAST_QC result json was written to GCF_002245625.1_ASM224562v1_genomic.fna/dqc_result.json
[2024-01-24 13:05:21,132] [INFO] DFAST_QC completed!
[2024-01-24 13:05:21,132] [INFO] Total running time: 0h2m0s