[2024-01-24 12:31:34,016] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:34,018] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:34,018] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c78762f-7264-4176-9c7b-f250610f2de0/dqc_reference
[2024-01-24 12:31:35,302] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:35,303] [INFO] Task started: Prodigal
[2024-01-24 12:31:35,304] [INFO] Running command: gunzip -c /var/lib/cwl/stgeecdbe9c-d22f-4ef1-9fce-d1c4dcc375de/GCF_002954445.1_ASM295444v1_genomic.fna.gz | prodigal -d GCF_002954445.1_ASM295444v1_genomic.fna/cds.fna -a GCF_002954445.1_ASM295444v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:55,672] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:55,673] [INFO] Task started: HMMsearch
[2024-01-24 12:31:55,673] [INFO] Running command: hmmsearch --tblout GCF_002954445.1_ASM295444v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c78762f-7264-4176-9c7b-f250610f2de0/dqc_reference/reference_markers.hmm GCF_002954445.1_ASM295444v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:55,942] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:55,943] [INFO] Found 6/6 markers.
[2024-01-24 12:31:55,986] [INFO] Query marker FASTA was written to GCF_002954445.1_ASM295444v1_genomic.fna/markers.fasta
[2024-01-24 12:31:55,986] [INFO] Task started: Blastn
[2024-01-24 12:31:55,986] [INFO] Running command: blastn -query GCF_002954445.1_ASM295444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c78762f-7264-4176-9c7b-f250610f2de0/dqc_reference/reference_markers.fasta -out GCF_002954445.1_ASM295444v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:56,559] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:56,563] [INFO] Selected 19 target genomes.
[2024-01-24 12:31:56,564] [INFO] Target genome list was writen to GCF_002954445.1_ASM295444v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:56,573] [INFO] Task started: fastANI
[2024-01-24 12:31:56,573] [INFO] Running command: fastANI --query /var/lib/cwl/stgeecdbe9c-d22f-4ef1-9fce-d1c4dcc375de/GCF_002954445.1_ASM295444v1_genomic.fna.gz --refList GCF_002954445.1_ASM295444v1_genomic.fna/target_genomes.txt --output GCF_002954445.1_ASM295444v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:09,896] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:09,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c78762f-7264-4176-9c7b-f250610f2de0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:09,898] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c78762f-7264-4176-9c7b-f250610f2de0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:09,907] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:09,908] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:09,908] [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 profundi	strain=SAORIC-165	GCA_002954445.1	1658618	1658618	type	True	99.9809	1362	1387	95	conclusive
Rubritalea marina	strain=DSM 17716	GCA_000378105.1	361055	361055	type	True	78.0764	156	1387	95	below_threshold
Rubritalea squalenifaciens	strain=DSM 18772	GCA_900141815.1	407226	407226	type	True	76.9434	125	1387	95	below_threshold
Persicirhabdus sediminis	strain=_KCTC 22039	GCA_016595495.1	454144	454144	type	True	76.3412	73	1387	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:09,910] [INFO] DFAST Taxonomy check result was written to GCF_002954445.1_ASM295444v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:09,910] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:09,910] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:09,910] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c78762f-7264-4176-9c7b-f250610f2de0/dqc_reference/checkm_data
[2024-01-24 12:32:09,911] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:09,959] [INFO] Task started: CheckM
[2024-01-24 12:32:09,959] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002954445.1_ASM295444v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002954445.1_ASM295444v1_genomic.fna/checkm_input GCF_002954445.1_ASM295444v1_genomic.fna/checkm_result
[2024-01-24 12:33:09,594] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:09,596] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:09,620] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:09,620] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:09,620] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002954445.1_ASM295444v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:09,621] [INFO] Task started: Blastn
[2024-01-24 12:33:09,621] [INFO] Running command: blastn -query GCF_002954445.1_ASM295444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c78762f-7264-4176-9c7b-f250610f2de0/dqc_reference/reference_markers_gtdb.fasta -out GCF_002954445.1_ASM295444v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:10,351] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:10,355] [INFO] Selected 24 target genomes.
[2024-01-24 12:33:10,356] [INFO] Target genome list was writen to GCF_002954445.1_ASM295444v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:10,375] [INFO] Task started: fastANI
[2024-01-24 12:33:10,375] [INFO] Running command: fastANI --query /var/lib/cwl/stgeecdbe9c-d22f-4ef1-9fce-d1c4dcc375de/GCF_002954445.1_ASM295444v1_genomic.fna.gz --refList GCF_002954445.1_ASM295444v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002954445.1_ASM295444v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:23,991] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:24,000] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:24,001] [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_002954445.1	s__Rubritalea profundi	99.9809	1362	1387	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	78.0484	156	1387	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Rubritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141815.1	s__Rubritalea squalenifaciens	76.9434	125	1387	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Rubritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595495.1	s__Persicirhabdus sediminis	76.3412	73	1387	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Persicirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016811075.1	s__UBA985 sp016811075	76.0978	60	1387	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	99.37	98.74	0.97	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:24,003] [INFO] GTDB search result was written to GCF_002954445.1_ASM295444v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:24,004] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:24,006] [INFO] DFAST_QC result json was written to GCF_002954445.1_ASM295444v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:24,007] [INFO] DFAST_QC completed!
[2024-01-24 12:33:24,007] [INFO] Total running time: 0h1m50s