[2024-01-24 10:57:13,026] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:13,035] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:13,035] [INFO] DQC Reference Directory: /var/lib/cwl/stgbaa78bd6-6ad8-432a-a520-29a652e7ec84/dqc_reference
[2024-01-24 10:57:14,431] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,432] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,432] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5d6d4a2-e577-46a0-8315-feb15ef27b11/GCF_013155545.1_ASM1315554v1_genomic.fna.gz | prodigal -d GCF_013155545.1_ASM1315554v1_genomic.fna/cds.fna -a GCF_013155545.1_ASM1315554v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:33,910] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:33,910] [INFO] Task started: HMMsearch
[2024-01-24 10:57:33,910] [INFO] Running command: hmmsearch --tblout GCF_013155545.1_ASM1315554v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbaa78bd6-6ad8-432a-a520-29a652e7ec84/dqc_reference/reference_markers.hmm GCF_013155545.1_ASM1315554v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:34,292] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:34,293] [INFO] Found 6/6 markers.
[2024-01-24 10:57:34,345] [INFO] Query marker FASTA was written to GCF_013155545.1_ASM1315554v1_genomic.fna/markers.fasta
[2024-01-24 10:57:34,345] [INFO] Task started: Blastn
[2024-01-24 10:57:34,345] [INFO] Running command: blastn -query GCF_013155545.1_ASM1315554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaa78bd6-6ad8-432a-a520-29a652e7ec84/dqc_reference/reference_markers.fasta -out GCF_013155545.1_ASM1315554v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:35,566] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:35,570] [INFO] Selected 17 target genomes.
[2024-01-24 10:57:35,570] [INFO] Target genome list was writen to GCF_013155545.1_ASM1315554v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:35,577] [INFO] Task started: fastANI
[2024-01-24 10:57:35,577] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5d6d4a2-e577-46a0-8315-feb15ef27b11/GCF_013155545.1_ASM1315554v1_genomic.fna.gz --refList GCF_013155545.1_ASM1315554v1_genomic.fna/target_genomes.txt --output GCF_013155545.1_ASM1315554v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:54,821] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:54,822] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbaa78bd6-6ad8-432a-a520-29a652e7ec84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:54,822] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbaa78bd6-6ad8-432a-a520-29a652e7ec84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:54,837] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:57:54,838] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:57:54,838] [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 tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	82.7502	785	1852	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	81.9818	691	1852	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	81.8244	807	1852	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	81.7139	848	1852	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	81.5115	812	1852	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	81.1678	814	1852	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	81.1527	866	1852	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	81.1242	692	1852	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	81.0713	807	1852	95	below_threshold
Ramlibacter monticola	strain=KACC 19175	GCA_016722785.1	1926872	1926872	type	True	81.0295	818	1852	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	80.9603	740	1852	95	below_threshold
Caenimonas koreensis	strain=EMB320	GCA_009646335.1	367474	367474	type	True	80.3202	675	1852	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.2721	641	1852	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	80.1398	639	1852	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	79.816	353	1852	95	below_threshold
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	79.7375	498	1852	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	79.3473	479	1852	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:54,840] [INFO] DFAST Taxonomy check result was written to GCF_013155545.1_ASM1315554v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:54,840] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:54,841] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:54,841] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbaa78bd6-6ad8-432a-a520-29a652e7ec84/dqc_reference/checkm_data
[2024-01-24 10:57:54,842] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:54,900] [INFO] Task started: CheckM
[2024-01-24 10:57:54,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013155545.1_ASM1315554v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013155545.1_ASM1315554v1_genomic.fna/checkm_input GCF_013155545.1_ASM1315554v1_genomic.fna/checkm_result
[2024-01-24 10:58:52,015] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:52,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:52,039] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:52,040] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:52,040] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013155545.1_ASM1315554v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:52,041] [INFO] Task started: Blastn
[2024-01-24 10:58:52,041] [INFO] Running command: blastn -query GCF_013155545.1_ASM1315554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaa78bd6-6ad8-432a-a520-29a652e7ec84/dqc_reference/reference_markers_gtdb.fasta -out GCF_013155545.1_ASM1315554v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:54,223] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:54,227] [INFO] Selected 18 target genomes.
[2024-01-24 10:58:54,227] [INFO] Target genome list was writen to GCF_013155545.1_ASM1315554v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:54,242] [INFO] Task started: fastANI
[2024-01-24 10:58:54,243] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5d6d4a2-e577-46a0-8315-feb15ef27b11/GCF_013155545.1_ASM1315554v1_genomic.fna.gz --refList GCF_013155545.1_ASM1315554v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013155545.1_ASM1315554v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:14,824] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:14,840] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:14,841] [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_013155545.1	s__Ramlibacter soli	100.0	1849	1852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013815685.1	s__Ramlibacter sp013815685	83.6848	835	1852	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	82.7407	786	1852	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	82.7164	978	1852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191525.1	s__Ramlibacter sp016191525	82.6022	852	1852	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	82.1805	883	1852	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	82.0608	762	1852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	99.97	99.97	0.98	0.97	3	-
GCF_001580455.1	s__Ramlibacter tataouinensis_B	82.0089	837	1852	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	81.9771	848	1852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015831345.1	s__Ramlibacter sp015831345	81.8529	807	1852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004681975.1	s__Ramlibacter sp004681975	81.8335	806	1852	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	81.5581	577	1852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005503335.1	s__SCMQ01 sp005503335	81.3862	719	1852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCMQ01	95.0	99.99	99.99	1.00	1.00	3	-
GCA_014376915.1	s__Ramlibacter sp014376915	81.3746	498	1852	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	81.2138	841	1852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012184415.1	s__Ramlibacter lithotrophicus	81.1966	811	1852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113035.1	s__Acidovorax_A wautersii	80.1408	637	1852	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_001424265.1	s__Acidovorax_A sp001424265	79.8528	633	1852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:14,842] [INFO] GTDB search result was written to GCF_013155545.1_ASM1315554v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:14,843] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:14,847] [INFO] DFAST_QC result json was written to GCF_013155545.1_ASM1315554v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:14,847] [INFO] DFAST_QC completed!
[2024-01-24 10:59:14,847] [INFO] Total running time: 0h2m2s