[2024-01-25 18:55:05,649] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:55:05,651] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:55:05,651] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7a9c755-2ac6-4917-b92d-92d463353272/dqc_reference
[2024-01-25 18:55:06,821] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:55:06,822] [INFO] Task started: Prodigal
[2024-01-25 18:55:06,822] [INFO] Running command: gunzip -c /var/lib/cwl/stg90132545-ec7d-4e82-8edf-6c5c1e502b45/GCF_011064595.1_ASM1106459v1_genomic.fna.gz | prodigal -d GCF_011064595.1_ASM1106459v1_genomic.fna/cds.fna -a GCF_011064595.1_ASM1106459v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:55:23,250] [INFO] Task succeeded: Prodigal
[2024-01-25 18:55:23,250] [INFO] Task started: HMMsearch
[2024-01-25 18:55:23,250] [INFO] Running command: hmmsearch --tblout GCF_011064595.1_ASM1106459v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7a9c755-2ac6-4917-b92d-92d463353272/dqc_reference/reference_markers.hmm GCF_011064595.1_ASM1106459v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:55:23,615] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:55:23,617] [INFO] Found 6/6 markers.
[2024-01-25 18:55:23,675] [INFO] Query marker FASTA was written to GCF_011064595.1_ASM1106459v1_genomic.fna/markers.fasta
[2024-01-25 18:55:23,675] [INFO] Task started: Blastn
[2024-01-25 18:55:23,675] [INFO] Running command: blastn -query GCF_011064595.1_ASM1106459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7a9c755-2ac6-4917-b92d-92d463353272/dqc_reference/reference_markers.fasta -out GCF_011064595.1_ASM1106459v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:24,340] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:24,342] [INFO] Selected 17 target genomes.
[2024-01-25 18:55:24,343] [INFO] Target genome list was writen to GCF_011064595.1_ASM1106459v1_genomic.fna/target_genomes.txt
[2024-01-25 18:55:24,375] [INFO] Task started: fastANI
[2024-01-25 18:55:24,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg90132545-ec7d-4e82-8edf-6c5c1e502b45/GCF_011064595.1_ASM1106459v1_genomic.fna.gz --refList GCF_011064595.1_ASM1106459v1_genomic.fna/target_genomes.txt --output GCF_011064595.1_ASM1106459v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:55:50,228] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:50,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7a9c755-2ac6-4917-b92d-92d463353272/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:55:50,228] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7a9c755-2ac6-4917-b92d-92d463353272/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:55:50,239] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:55:50,239] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:55:50,239] [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
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	100.0	2578	2583	95	conclusive
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	81.4422	1485	2583	95	below_threshold
Paludisphaera borealis	strain=PX4	GCA_001956985.1	1387353	1387353	type	True	80.0618	1341	2583	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	78.7301	1186	2583	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	77.1469	889	2583	95	below_threshold
Tautonia sociabilis	strain=GM2012	GCA_003977685.1	2080755	2080755	type	True	77.0033	670	2583	95	below_threshold
Singulisphaera acidiphila	strain=DSM 18658	GCA_000255675.1	466153	466153	type	True	76.8907	532	2583	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	75.5063	162	2583	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	74.9738	109	2583	95	below_threshold
Microbispora amethystogenes	strain=NBRC 101907	GCA_016863015.1	1427754	1427754	type	True	74.9117	327	2583	95	below_threshold
Euzebya pacifica	strain=DY32-46	GCA_003344865.1	1608957	1608957	type	True	74.8714	241	2583	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	74.8616	161	2583	95	below_threshold
Microbispora cellulosiformans	strain=Gxj-6	GCA_008728085.1	2614688	2614688	type	True	74.8591	347	2583	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	74.8584	370	2583	95	below_threshold
Microbispora rosea subsp. aerata	strain=NBRC 14624	GCA_016863075.1	147065	58117	type	True	74.8478	303	2583	95	below_threshold
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	74.7718	354	2583	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:55:50,241] [INFO] DFAST Taxonomy check result was written to GCF_011064595.1_ASM1106459v1_genomic.fna/tc_result.tsv
[2024-01-25 18:55:50,241] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:55:50,242] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:55:50,242] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7a9c755-2ac6-4917-b92d-92d463353272/dqc_reference/checkm_data
[2024-01-25 18:55:50,242] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:55:50,318] [INFO] Task started: CheckM
[2024-01-25 18:55:50,318] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011064595.1_ASM1106459v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011064595.1_ASM1106459v1_genomic.fna/checkm_input GCF_011064595.1_ASM1106459v1_genomic.fna/checkm_result
[2024-01-25 18:56:40,148] [INFO] Task succeeded: CheckM
[2024-01-25 18:56:40,149] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:56:40,172] [INFO] ===== Completeness check finished =====
[2024-01-25 18:56:40,173] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:56:40,174] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011064595.1_ASM1106459v1_genomic.fna/markers.fasta)
[2024-01-25 18:56:40,174] [INFO] Task started: Blastn
[2024-01-25 18:56:40,174] [INFO] Running command: blastn -query GCF_011064595.1_ASM1106459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7a9c755-2ac6-4917-b92d-92d463353272/dqc_reference/reference_markers_gtdb.fasta -out GCF_011064595.1_ASM1106459v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:41,252] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:41,254] [INFO] Selected 6 target genomes.
[2024-01-25 18:56:41,255] [INFO] Target genome list was writen to GCF_011064595.1_ASM1106459v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:56:41,275] [INFO] Task started: fastANI
[2024-01-25 18:56:41,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg90132545-ec7d-4e82-8edf-6c5c1e502b45/GCF_011064595.1_ASM1106459v1_genomic.fna.gz --refList GCF_011064595.1_ASM1106459v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011064595.1_ASM1106459v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:56:55,451] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:55,456] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:56:55,456] [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_011064595.1	s__Paludisphaera soli	100.0	2578	2583	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001610895.1	s__Paludisphaera sp001610895	85.8189	1816	2583	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898385.1	s__Paludisphaera sp001898385	83.0782	1619	2583	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011065895.1	s__Paludisphaera sp011065895	81.4216	1489	2583	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956985.1	s__Paludisphaera borealis	80.0544	1345	2583	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008087625.1	s__Aquisphaera giovannonii	78.7494	1180	2583	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Aquisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:56:55,458] [INFO] GTDB search result was written to GCF_011064595.1_ASM1106459v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:56:55,458] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:56:55,462] [INFO] DFAST_QC result json was written to GCF_011064595.1_ASM1106459v1_genomic.fna/dqc_result.json
[2024-01-25 18:56:55,462] [INFO] DFAST_QC completed!
[2024-01-25 18:56:55,462] [INFO] Total running time: 0h1m50s