[2024-01-24 13:49:41,058] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:41,060] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:41,060] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c4db166-d775-4ca7-b208-839d3a66d2d2/dqc_reference
[2024-01-24 13:49:42,484] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:42,485] [INFO] Task started: Prodigal
[2024-01-24 13:49:42,486] [INFO] Running command: gunzip -c /var/lib/cwl/stg4330ed57-7c51-4a04-bb9a-6f8977933255/GCF_012184415.1_ASM1218441v1_genomic.fna.gz | prodigal -d GCF_012184415.1_ASM1218441v1_genomic.fna/cds.fna -a GCF_012184415.1_ASM1218441v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:59,686] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:59,686] [INFO] Task started: HMMsearch
[2024-01-24 13:49:59,687] [INFO] Running command: hmmsearch --tblout GCF_012184415.1_ASM1218441v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c4db166-d775-4ca7-b208-839d3a66d2d2/dqc_reference/reference_markers.hmm GCF_012184415.1_ASM1218441v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:59,992] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:59,994] [INFO] Found 6/6 markers.
[2024-01-24 13:50:00,046] [INFO] Query marker FASTA was written to GCF_012184415.1_ASM1218441v1_genomic.fna/markers.fasta
[2024-01-24 13:50:00,046] [INFO] Task started: Blastn
[2024-01-24 13:50:00,046] [INFO] Running command: blastn -query GCF_012184415.1_ASM1218441v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c4db166-d775-4ca7-b208-839d3a66d2d2/dqc_reference/reference_markers.fasta -out GCF_012184415.1_ASM1218441v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:01,169] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:01,174] [INFO] Selected 15 target genomes.
[2024-01-24 13:50:01,174] [INFO] Target genome list was writen to GCF_012184415.1_ASM1218441v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:01,176] [INFO] Task started: fastANI
[2024-01-24 13:50:01,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg4330ed57-7c51-4a04-bb9a-6f8977933255/GCF_012184415.1_ASM1218441v1_genomic.fna.gz --refList GCF_012184415.1_ASM1218441v1_genomic.fna/target_genomes.txt --output GCF_012184415.1_ASM1218441v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:17,843] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:17,843] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c4db166-d775-4ca7-b208-839d3a66d2d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:17,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c4db166-d775-4ca7-b208-839d3a66d2d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:17,859] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:17,859] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:17,859] [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
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	100.0	1741	1744	95	conclusive
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	82.0923	832	1744	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	81.9764	794	1744	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	81.9033	793	1744	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	81.8994	813	1744	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	81.8624	715	1744	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	81.7391	931	1744	95	below_threshold
Ramlibacter monticola	strain=KACC 19175	GCA_016722785.1	1926872	1926872	type	True	81.6854	932	1744	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	81.6808	877	1744	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	81.0844	925	1744	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	80.7353	749	1744	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.0602	627	1744	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.9644	559	1744	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	79.3841	630	1744	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	79.3839	765	1744	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:17,866] [INFO] DFAST Taxonomy check result was written to GCF_012184415.1_ASM1218441v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:17,867] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:17,867] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:17,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c4db166-d775-4ca7-b208-839d3a66d2d2/dqc_reference/checkm_data
[2024-01-24 13:50:17,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:17,921] [INFO] Task started: CheckM
[2024-01-24 13:50:17,921] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012184415.1_ASM1218441v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012184415.1_ASM1218441v1_genomic.fna/checkm_input GCF_012184415.1_ASM1218441v1_genomic.fna/checkm_result
[2024-01-24 13:51:22,564] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:22,565] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:22,582] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:22,583] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:22,583] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012184415.1_ASM1218441v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:22,583] [INFO] Task started: Blastn
[2024-01-24 13:51:22,583] [INFO] Running command: blastn -query GCF_012184415.1_ASM1218441v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c4db166-d775-4ca7-b208-839d3a66d2d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_012184415.1_ASM1218441v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:24,797] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:24,800] [INFO] Selected 18 target genomes.
[2024-01-24 13:51:24,800] [INFO] Target genome list was writen to GCF_012184415.1_ASM1218441v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:24,827] [INFO] Task started: fastANI
[2024-01-24 13:51:24,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg4330ed57-7c51-4a04-bb9a-6f8977933255/GCF_012184415.1_ASM1218441v1_genomic.fna.gz --refList GCF_012184415.1_ASM1218441v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012184415.1_ASM1218441v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:44,644] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:44,659] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:44,659] [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_012184415.1	s__Ramlibacter lithotrophicus	100.0	1741	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014874145.1	s__Ramlibacter sp014874145	82.2578	838	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215705.1	s__Ramlibacter tataouinensis	82.1077	830	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424545.1	s__Ramlibacter sp001424545	82.0347	848	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004682015.1	s__Ramlibacter henchirensis	81.9516	797	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002427815.1	s__Ramlibacter tataouinensis_A	81.8922	889	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	99.97	99.97	0.98	0.97	3	-
GCA_013697775.1	s__Ramlibacter sp013697775	81.8639	707	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001580455.1	s__Ramlibacter tataouinensis_B	81.7985	837	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013778345.1	s__Ramlibacter sp013778345	81.6469	880	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013127575.1	s__Ramlibacter sp013127575	81.622	876	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015070875.1	s__Ramlibacter sp015070875	81.5698	833	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012274225.1	s__Ramlibacter sp012274225	81.505	710	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297465.1	s__Ramlibacter sp014297465	81.327	898	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155545.1	s__Ramlibacter soli	81.3108	786	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927085.1	s__Ramlibacter sp012927085	81.0961	923	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797765.1	s__Ramlibacter sp003797765	80.9464	792	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007833165.1	s__Ramlibacter sp007833165	80.8787	836	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337555.1	s__Pseudorhodoferax soli	79.4263	759	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:44,661] [INFO] GTDB search result was written to GCF_012184415.1_ASM1218441v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:44,661] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:44,665] [INFO] DFAST_QC result json was written to GCF_012184415.1_ASM1218441v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:44,665] [INFO] DFAST_QC completed!
[2024-01-24 13:51:44,665] [INFO] Total running time: 0h2m4s