[2024-01-25 20:23:05,781] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:23:05,783] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:23:05,783] [INFO] DQC Reference Directory: /var/lib/cwl/stge7910bfa-1b6f-48f1-ac8e-78ba120ac5bb/dqc_reference
[2024-01-25 20:23:06,976] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:23:06,977] [INFO] Task started: Prodigal
[2024-01-25 20:23:06,977] [INFO] Running command: gunzip -c /var/lib/cwl/stgf6138ebf-ea36-49d2-8579-dc2005364ba2/GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna/cds.fna -a GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:23:22,242] [INFO] Task succeeded: Prodigal
[2024-01-25 20:23:22,243] [INFO] Task started: HMMsearch
[2024-01-25 20:23:22,243] [INFO] Running command: hmmsearch --tblout GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7910bfa-1b6f-48f1-ac8e-78ba120ac5bb/dqc_reference/reference_markers.hmm GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:23:22,511] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:23:22,512] [INFO] Found 6/6 markers.
[2024-01-25 20:23:22,557] [INFO] Query marker FASTA was written to GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:23:22,557] [INFO] Task started: Blastn
[2024-01-25 20:23:22,557] [INFO] Running command: blastn -query GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge7910bfa-1b6f-48f1-ac8e-78ba120ac5bb/dqc_reference/reference_markers.fasta -out GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:23,583] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:23,586] [INFO] Selected 17 target genomes.
[2024-01-25 20:23:23,586] [INFO] Target genome list was writen to GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:23:23,597] [INFO] Task started: fastANI
[2024-01-25 20:23:23,597] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6138ebf-ea36-49d2-8579-dc2005364ba2/GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna.gz --refList GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:23:52,803] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:52,803] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7910bfa-1b6f-48f1-ac8e-78ba120ac5bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:23:52,804] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7910bfa-1b6f-48f1-ac8e-78ba120ac5bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:23:52,814] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:23:52,814] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:23:52,814] [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
Pseudomonas jinjuensis	strain=JCM 21621	GCA_900103845.1	198616	198616	type	True	100.0	1937	1939	95	conclusive
Pseudomonas jinjuensis	strain=NBRC 103047	GCA_002091655.1	198616	198616	type	True	99.9897	1913	1939	95	conclusive
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	87.21	1323	1939	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	87.114	1327	1939	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	87.0752	1349	1939	95	below_threshold
Pseudomonas citronellolis	strain=DSM 50332	GCA_004745455.1	53408	53408	type	True	87.0336	1362	1939	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	86.9917	1365	1939	95	below_threshold
Pseudomonas knackmussii	strain=B13	GCA_000689415.1	65741	65741	type	True	86.0773	1254	1939	95	below_threshold
Pseudomonas nitroreducens	strain=DSM 14399	GCA_012986245.1	46680	46680	suspected-type	True	85.783	1224	1939	95	below_threshold
Pseudomonas nitroreducens	strain=NBRC 12694	GCA_002091755.1	46680	46680	suspected-type	True	85.7795	1231	1939	95	below_threshold
Pseudomonas panipatensis	strain=CCM 7469	GCA_900099785.1	428992	428992	type	True	85.7655	1184	1939	95	below_threshold
Pseudomonas nicosulfuronedens	strain=LAM1902	GCA_005877905.1	2571105	2571105	type	True	85.4939	1221	1939	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	83.6284	1028	1939	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	83.3493	964	1939	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	83.2881	1043	1939	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	83.1963	807	1939	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	82.6749	912	1939	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:23:52,817] [INFO] DFAST Taxonomy check result was written to GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:23:52,817] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:23:52,818] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:23:52,818] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7910bfa-1b6f-48f1-ac8e-78ba120ac5bb/dqc_reference/checkm_data
[2024-01-25 20:23:52,818] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:23:52,877] [INFO] Task started: CheckM
[2024-01-25 20:23:52,878] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna/checkm_input GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:24:39,841] [INFO] Task succeeded: CheckM
[2024-01-25 20:24:39,842] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:24:39,866] [INFO] ===== Completeness check finished =====
[2024-01-25 20:24:39,866] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:24:39,867] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:24:39,868] [INFO] Task started: Blastn
[2024-01-25 20:24:39,868] [INFO] Running command: blastn -query GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge7910bfa-1b6f-48f1-ac8e-78ba120ac5bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:41,978] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:41,980] [INFO] Selected 12 target genomes.
[2024-01-25 20:24:41,981] [INFO] Target genome list was writen to GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:24:41,997] [INFO] Task started: fastANI
[2024-01-25 20:24:41,997] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6138ebf-ea36-49d2-8579-dc2005364ba2/GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna.gz --refList GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:25:03,327] [INFO] Task succeeded: fastANI
[2024-01-25 20:25:03,336] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:25:03,336] [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_900103845.1	s__Pseudomonas jinjuensis	100.0	1937	1939	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_017589465.1	s__Pseudomonas sp017589465	89.3902	1418	1939	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187975.1	s__Pseudomonas delhiensis	87.089	1330	1939	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	98.79	97.59	0.94	0.89	3	-
GCF_900112375.1	s__Pseudomonas citronellolis	87.0435	1354	1939	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	97.44	97.08	0.86	0.82	26	-
GCF_000349845.1	s__Pseudomonas sp000349845	86.5146	1259	1939	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017491605.1	s__Pseudomonas sp017491605	86.3602	1224	1939	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204515.1	s__Pseudomonas nitritireducens_A	86.2149	1286	1939	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000689415.1	s__Pseudomonas knackmussii	86.0897	1252	1939	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	98.27	98.27	0.91	0.91	2	-
GCF_009189165.1	s__Pseudomonas sp009189165	85.9552	1226	1939	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002091755.1	s__Pseudomonas nitroreducens	85.7704	1231	1939	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	98.47	95.19	0.93	0.83	16	-
GCF_900099785.1	s__Pseudomonas panipatensis	85.7421	1188	1939	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919445.1	s__Pseudomonas sp016919445	85.5105	1250	1939	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:25:03,338] [INFO] GTDB search result was written to GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:25:03,338] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:25:03,341] [INFO] DFAST_QC result json was written to GCF_900103845.1_IMG-taxon_2663762768_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:25:03,341] [INFO] DFAST_QC completed!
[2024-01-25 20:25:03,342] [INFO] Total running time: 0h1m58s