[2024-01-24 13:46:03,786] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:03,788] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:03,788] [INFO] DQC Reference Directory: /var/lib/cwl/stgba5e3340-20f9-4052-a2dd-23be5e44711c/dqc_reference
[2024-01-24 13:46:05,106] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:05,119] [INFO] Task started: Prodigal
[2024-01-24 13:46:05,120] [INFO] Running command: gunzip -c /var/lib/cwl/stg55d93600-7761-4a60-b497-f6d3cba7d0a3/GCF_013087525.1_ASM1308752v1_genomic.fna.gz | prodigal -d GCF_013087525.1_ASM1308752v1_genomic.fna/cds.fna -a GCF_013087525.1_ASM1308752v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:21,457] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:21,457] [INFO] Task started: HMMsearch
[2024-01-24 13:46:21,457] [INFO] Running command: hmmsearch --tblout GCF_013087525.1_ASM1308752v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba5e3340-20f9-4052-a2dd-23be5e44711c/dqc_reference/reference_markers.hmm GCF_013087525.1_ASM1308752v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:21,710] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:21,712] [INFO] Found 6/6 markers.
[2024-01-24 13:46:21,756] [INFO] Query marker FASTA was written to GCF_013087525.1_ASM1308752v1_genomic.fna/markers.fasta
[2024-01-24 13:46:21,756] [INFO] Task started: Blastn
[2024-01-24 13:46:21,757] [INFO] Running command: blastn -query GCF_013087525.1_ASM1308752v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba5e3340-20f9-4052-a2dd-23be5e44711c/dqc_reference/reference_markers.fasta -out GCF_013087525.1_ASM1308752v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:22,884] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:22,889] [INFO] Selected 12 target genomes.
[2024-01-24 13:46:22,890] [INFO] Target genome list was writen to GCF_013087525.1_ASM1308752v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:22,900] [INFO] Task started: fastANI
[2024-01-24 13:46:22,901] [INFO] Running command: fastANI --query /var/lib/cwl/stg55d93600-7761-4a60-b497-f6d3cba7d0a3/GCF_013087525.1_ASM1308752v1_genomic.fna.gz --refList GCF_013087525.1_ASM1308752v1_genomic.fna/target_genomes.txt --output GCF_013087525.1_ASM1308752v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:38,259] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:38,259] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba5e3340-20f9-4052-a2dd-23be5e44711c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:38,259] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba5e3340-20f9-4052-a2dd-23be5e44711c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:38,269] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:46:38,270] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:46:38,270] [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 monticola	strain=KACC 19175	GCA_016722785.1	1926872	1926872	type	True	85.3735	1185	1583	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	85.1981	1138	1583	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	84.6076	1059	1583	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	83.7122	885	1583	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	83.4888	890	1583	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	83.1364	956	1583	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	83.0976	902	1583	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	82.9723	897	1583	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	82.9505	787	1583	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	82.0406	927	1583	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	81.2271	729	1583	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	81.0404	397	1583	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:38,271] [INFO] DFAST Taxonomy check result was written to GCF_013087525.1_ASM1308752v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:38,272] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:38,272] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:38,272] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba5e3340-20f9-4052-a2dd-23be5e44711c/dqc_reference/checkm_data
[2024-01-24 13:46:38,273] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:38,321] [INFO] Task started: CheckM
[2024-01-24 13:46:38,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013087525.1_ASM1308752v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013087525.1_ASM1308752v1_genomic.fna/checkm_input GCF_013087525.1_ASM1308752v1_genomic.fna/checkm_result
[2024-01-24 13:47:52,910] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:52,912] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:52,930] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:52,930] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:52,931] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013087525.1_ASM1308752v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:52,931] [INFO] Task started: Blastn
[2024-01-24 13:47:52,931] [INFO] Running command: blastn -query GCF_013087525.1_ASM1308752v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba5e3340-20f9-4052-a2dd-23be5e44711c/dqc_reference/reference_markers_gtdb.fasta -out GCF_013087525.1_ASM1308752v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:54,989] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:54,994] [INFO] Selected 12 target genomes.
[2024-01-24 13:47:54,994] [INFO] Target genome list was writen to GCF_013087525.1_ASM1308752v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:55,002] [INFO] Task started: fastANI
[2024-01-24 13:47:55,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg55d93600-7761-4a60-b497-f6d3cba7d0a3/GCF_013087525.1_ASM1308752v1_genomic.fna.gz --refList GCF_013087525.1_ASM1308752v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013087525.1_ASM1308752v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:10,287] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:10,298] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:10,298] [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_013087525.1	s__Ramlibacter sp013087525	100.0	1583	1583	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_014297465.1	s__Ramlibacter sp014297465	85.8762	1163	1583	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	85.8158	1041	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004144865.1	s__Ramlibacter sp004144865	85.8128	992	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016722785.1	s__Ramlibacter monticola	85.3767	1184	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016722765.1	s__Ramlibacter alkalitolerans	85.1828	1141	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016654015.1	s__Ramlibacter ginsenosidimutans	84.7088	1078	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012927085.1	s__Ramlibacter sp012927085	84.6173	1058	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014874145.1	s__Ramlibacter sp014874145	83.7359	937	1583	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	83.1392	956	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007833165.1	s__Ramlibacter sp007833165	83.0913	990	1583	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	83.0858	903	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:10,302] [INFO] GTDB search result was written to GCF_013087525.1_ASM1308752v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:10,302] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:10,306] [INFO] DFAST_QC result json was written to GCF_013087525.1_ASM1308752v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:10,306] [INFO] DFAST_QC completed!
[2024-01-24 13:48:10,306] [INFO] Total running time: 0h2m7s