[2024-01-24 12:21:44,232] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:44,234] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:44,234] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c67487b-61b1-4d67-adeb-f43c733f4420/dqc_reference
[2024-01-24 12:21:45,638] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:45,639] [INFO] Task started: Prodigal
[2024-01-24 12:21:45,639] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e06a747-05d3-4258-b5d3-b4c0608f883e/GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna/cds.fna -a GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:59,727] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:59,728] [INFO] Task started: HMMsearch
[2024-01-24 12:21:59,728] [INFO] Running command: hmmsearch --tblout GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c67487b-61b1-4d67-adeb-f43c733f4420/dqc_reference/reference_markers.hmm GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:00,074] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:00,075] [INFO] Found 6/6 markers.
[2024-01-24 12:22:00,112] [INFO] Query marker FASTA was written to GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:22:00,112] [INFO] Task started: Blastn
[2024-01-24 12:22:00,112] [INFO] Running command: blastn -query GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c67487b-61b1-4d67-adeb-f43c733f4420/dqc_reference/reference_markers.fasta -out GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:01,135] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:01,139] [INFO] Selected 12 target genomes.
[2024-01-24 12:22:01,139] [INFO] Target genome list was writen to GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:22:01,153] [INFO] Task started: fastANI
[2024-01-24 12:22:01,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e06a747-05d3-4258-b5d3-b4c0608f883e/GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna.gz --refList GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:12,547] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:12,548] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c67487b-61b1-4d67-adeb-f43c733f4420/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:12,548] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c67487b-61b1-4d67-adeb-f43c733f4420/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:12,563] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:12,563] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:12,563] [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
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	100.0	1457	1461	95	conclusive
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	80.7672	742	1461	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	80.7359	701	1461	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	80.4832	694	1461	95	below_threshold
Solimonas fluminis	strain=HR-BB	GCA_002930645.1	2086571	2086571	type	True	79.8561	638	1461	95	below_threshold
Solimonas marina	strain=C16B3	GCA_012241385.1	2714601	2714601	type	True	79.6636	597	1461	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	79.582	637	1461	95	below_threshold
Flagellatimonas centrodinii	strain=R2A-3	GCA_016918765.2	2806210	2806210	type	True	78.1012	309	1461	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.4761	268	1461	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	76.3617	252	1461	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	76.2262	263	1461	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.1407	259	1461	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:12,566] [INFO] DFAST Taxonomy check result was written to GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:22:12,566] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:12,566] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:12,567] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c67487b-61b1-4d67-adeb-f43c733f4420/dqc_reference/checkm_data
[2024-01-24 12:22:12,568] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:12,609] [INFO] Task started: CheckM
[2024-01-24 12:22:12,609] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna/checkm_input GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:23:05,130] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:05,131] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:05,154] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:05,154] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:05,154] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:23:05,155] [INFO] Task started: Blastn
[2024-01-24 12:23:05,155] [INFO] Running command: blastn -query GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c67487b-61b1-4d67-adeb-f43c733f4420/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:07,000] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:07,003] [INFO] Selected 9 target genomes.
[2024-01-24 12:23:07,004] [INFO] Target genome list was writen to GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:07,037] [INFO] Task started: fastANI
[2024-01-24 12:23:07,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e06a747-05d3-4258-b5d3-b4c0608f883e/GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna.gz --refList GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:17,223] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:17,239] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:17,239] [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_900111015.1	s__Solimonas aquatica	100.0	1457	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000474945.1	s__Solimonas soli	80.7344	702	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426685.1	s__Solimonas flava	80.6942	749	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_000382285.1	s__Solimonas variicoloris	80.486	698	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_003428335.1	s__Solimonas_A sp003428335	79.8746	632	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002930645.1	s__Solimonas_A fluminis	79.8576	638	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012241385.1	s__Solimonas marina	79.6525	598	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201205.1	s__Sinimarinibacterium flocculans	79.5723	533	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Sinimarinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011067135.1	s__Solimonas terrae	79.5177	644	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:17,243] [INFO] GTDB search result was written to GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:17,244] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:17,249] [INFO] DFAST_QC result json was written to GCF_900111015.1_IMG-taxon_2616644811_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:23:17,249] [INFO] DFAST_QC completed!
[2024-01-24 12:23:17,249] [INFO] Total running time: 0h1m33s