[2024-01-24 11:12:39,946] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:39,951] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:39,951] [INFO] DQC Reference Directory: /var/lib/cwl/stg05bfadca-0747-4ca5-9f57-407a2e0d7659/dqc_reference
[2024-01-24 11:12:41,256] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:41,257] [INFO] Task started: Prodigal
[2024-01-24 11:12:41,257] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8ec34da-5199-415f-92d4-ba63574c96f6/GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna/cds.fna -a GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:04,399] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:04,400] [INFO] Task started: HMMsearch
[2024-01-24 11:13:04,400] [INFO] Running command: hmmsearch --tblout GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05bfadca-0747-4ca5-9f57-407a2e0d7659/dqc_reference/reference_markers.hmm GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:04,692] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:04,693] [INFO] Found 6/6 markers.
[2024-01-24 11:13:04,731] [INFO] Query marker FASTA was written to GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 11:13:04,732] [INFO] Task started: Blastn
[2024-01-24 11:13:04,732] [INFO] Running command: blastn -query GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg05bfadca-0747-4ca5-9f57-407a2e0d7659/dqc_reference/reference_markers.fasta -out GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:05,352] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:05,356] [INFO] Selected 20 target genomes.
[2024-01-24 11:13:05,356] [INFO] Target genome list was writen to GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 11:13:05,367] [INFO] Task started: fastANI
[2024-01-24 11:13:05,367] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8ec34da-5199-415f-92d4-ba63574c96f6/GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna.gz --refList GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:20,999] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:20,999] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05bfadca-0747-4ca5-9f57-407a2e0d7659/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:21,000] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05bfadca-0747-4ca5-9f57-407a2e0d7659/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:21,007] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:21,007] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:21,008] [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
Rubritalea squalenifaciens	strain=DSM 18772	GCA_900141815.1	407226	407226	type	True	100.0	1433	1433	95	conclusive
Rubritalea marina	strain=DSM 17716	GCA_000378105.1	361055	361055	type	True	78.2772	119	1433	95	below_threshold
Rubritalea profundi	strain=SAORIC-165	GCA_002954445.1	1658618	1658618	type	True	76.8648	118	1433	95	below_threshold
Haloferula rosea	strain=KCTC 22201	GCA_016595525.1	490093	490093	type	True	76.124	61	1433	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	75.8733	52	1433	95	below_threshold
Persicirhabdus sediminis	strain=_KCTC 22039	GCA_016595495.1	454144	454144	type	True	75.7258	63	1433	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:21,009] [INFO] DFAST Taxonomy check result was written to GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 11:13:21,010] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:21,010] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:21,010] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05bfadca-0747-4ca5-9f57-407a2e0d7659/dqc_reference/checkm_data
[2024-01-24 11:13:21,012] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:21,058] [INFO] Task started: CheckM
[2024-01-24 11:13:21,059] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna/checkm_input GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 11:14:27,774] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:27,776] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:27,795] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:27,796] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:27,796] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 11:14:27,796] [INFO] Task started: Blastn
[2024-01-24 11:14:27,797] [INFO] Running command: blastn -query GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg05bfadca-0747-4ca5-9f57-407a2e0d7659/dqc_reference/reference_markers_gtdb.fasta -out GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:28,559] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:28,564] [INFO] Selected 24 target genomes.
[2024-01-24 11:14:28,564] [INFO] Target genome list was writen to GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:28,600] [INFO] Task started: fastANI
[2024-01-24 11:14:28,600] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8ec34da-5199-415f-92d4-ba63574c96f6/GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna.gz --refList GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:45,656] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:45,664] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:45,664] [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_900141815.1	s__Rubritalea squalenifaciens	100.0	1433	1433	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Rubritalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000378105.1	s__Rubritalea marina	78.2772	119	1433	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Rubritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954445.1	s__Rubritalea profundi	76.8648	118	1433	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Rubritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595525.1	s__Haloferula rosea	76.124	61	1433	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018137965.1	s__Luteolibacter sp018137965	75.8507	53	1433	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904755.1	s__Haloferula sp014904755	75.8037	54	1433	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595495.1	s__Persicirhabdus sediminis	75.7258	63	1433	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Persicirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000739615.1	s__Haloferula sp000739615	75.5803	54	1433	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:45,695] [INFO] GTDB search result was written to GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:45,696] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:45,700] [INFO] DFAST_QC result json was written to GCF_900141815.1_IMG-taxon_2582581871_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 11:14:45,701] [INFO] DFAST_QC completed!
[2024-01-24 11:14:45,701] [INFO] Total running time: 0h2m6s