[2024-01-25 20:19:20,578] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:19:20,579] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:19:20,579] [INFO] DQC Reference Directory: /var/lib/cwl/stg20c63073-fada-4e43-83ec-e6501d11b4f2/dqc_reference
[2024-01-25 20:19:21,735] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:19:21,738] [INFO] Task started: Prodigal
[2024-01-25 20:19:21,738] [INFO] Running command: gunzip -c /var/lib/cwl/stga1844624-aedd-4477-b550-a8bedbfb20e0/GCF_016595495.1_ASM1659549v1_genomic.fna.gz | prodigal -d GCF_016595495.1_ASM1659549v1_genomic.fna/cds.fna -a GCF_016595495.1_ASM1659549v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:19:38,918] [INFO] Task succeeded: Prodigal
[2024-01-25 20:19:38,918] [INFO] Task started: HMMsearch
[2024-01-25 20:19:38,918] [INFO] Running command: hmmsearch --tblout GCF_016595495.1_ASM1659549v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20c63073-fada-4e43-83ec-e6501d11b4f2/dqc_reference/reference_markers.hmm GCF_016595495.1_ASM1659549v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:19:39,167] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:19:39,168] [INFO] Found 6/6 markers.
[2024-01-25 20:19:39,200] [INFO] Query marker FASTA was written to GCF_016595495.1_ASM1659549v1_genomic.fna/markers.fasta
[2024-01-25 20:19:39,200] [INFO] Task started: Blastn
[2024-01-25 20:19:39,200] [INFO] Running command: blastn -query GCF_016595495.1_ASM1659549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20c63073-fada-4e43-83ec-e6501d11b4f2/dqc_reference/reference_markers.fasta -out GCF_016595495.1_ASM1659549v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:39,757] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:39,760] [INFO] Selected 20 target genomes.
[2024-01-25 20:19:39,760] [INFO] Target genome list was writen to GCF_016595495.1_ASM1659549v1_genomic.fna/target_genomes.txt
[2024-01-25 20:19:39,793] [INFO] Task started: fastANI
[2024-01-25 20:19:39,793] [INFO] Running command: fastANI --query /var/lib/cwl/stga1844624-aedd-4477-b550-a8bedbfb20e0/GCF_016595495.1_ASM1659549v1_genomic.fna.gz --refList GCF_016595495.1_ASM1659549v1_genomic.fna/target_genomes.txt --output GCF_016595495.1_ASM1659549v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:19:56,521] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:56,521] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20c63073-fada-4e43-83ec-e6501d11b4f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:19:56,521] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20c63073-fada-4e43-83ec-e6501d11b4f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:19:56,527] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:19:56,527] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:19:56,527] [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
Persicirhabdus sediminis	strain=_KCTC 22039	GCA_016595495.1	454144	454144	type	True	100.0	1367	1368	95	conclusive
Rubritalea profundi	strain=SAORIC-165	GCA_002954445.1	1658618	1658618	type	True	76.4739	65	1368	95	below_threshold
Rubritalea marina	strain=DSM 17716	GCA_000378105.1	361055	361055	type	True	76.3064	57	1368	95	below_threshold
Oceaniferula marina	strain=N1E253	GCA_013391475.1	2748318	2748318	type	True	75.9357	53	1368	95	below_threshold
Rubritalea squalenifaciens	strain=DSM 18772	GCA_900141815.1	407226	407226	type	True	75.7156	58	1368	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:19:56,529] [INFO] DFAST Taxonomy check result was written to GCF_016595495.1_ASM1659549v1_genomic.fna/tc_result.tsv
[2024-01-25 20:19:56,529] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:19:56,529] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:19:56,530] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20c63073-fada-4e43-83ec-e6501d11b4f2/dqc_reference/checkm_data
[2024-01-25 20:19:56,530] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:19:56,570] [INFO] Task started: CheckM
[2024-01-25 20:19:56,571] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016595495.1_ASM1659549v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016595495.1_ASM1659549v1_genomic.fna/checkm_input GCF_016595495.1_ASM1659549v1_genomic.fna/checkm_result
[2024-01-25 20:20:46,639] [INFO] Task succeeded: CheckM
[2024-01-25 20:20:46,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:20:46,664] [INFO] ===== Completeness check finished =====
[2024-01-25 20:20:46,664] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:20:46,665] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016595495.1_ASM1659549v1_genomic.fna/markers.fasta)
[2024-01-25 20:20:46,665] [INFO] Task started: Blastn
[2024-01-25 20:20:46,665] [INFO] Running command: blastn -query GCF_016595495.1_ASM1659549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20c63073-fada-4e43-83ec-e6501d11b4f2/dqc_reference/reference_markers_gtdb.fasta -out GCF_016595495.1_ASM1659549v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:47,403] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:47,406] [INFO] Selected 23 target genomes.
[2024-01-25 20:20:47,407] [INFO] Target genome list was writen to GCF_016595495.1_ASM1659549v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:20:47,438] [INFO] Task started: fastANI
[2024-01-25 20:20:47,438] [INFO] Running command: fastANI --query /var/lib/cwl/stga1844624-aedd-4477-b550-a8bedbfb20e0/GCF_016595495.1_ASM1659549v1_genomic.fna.gz --refList GCF_016595495.1_ASM1659549v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016595495.1_ASM1659549v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:03,643] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:03,648] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:03,648] [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_016595495.1	s__Persicirhabdus sediminis	100.0	1367	1368	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Persicirhabdus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016811075.1	s__UBA985 sp016811075	76.9248	74	1368	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	99.37	98.74	0.97	0.95	3	-
GCF_002954445.1	s__Rubritalea profundi	76.5065	64	1368	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Rubritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378105.1	s__Rubritalea marina	76.2764	58	1368	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Rubritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013391475.1	s__UBA985 sp013391475	75.9357	53	1368	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141815.1	s__Rubritalea squalenifaciens	75.7309	57	1368	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Rubritalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:03,649] [INFO] GTDB search result was written to GCF_016595495.1_ASM1659549v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:03,650] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:03,652] [INFO] DFAST_QC result json was written to GCF_016595495.1_ASM1659549v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:03,652] [INFO] DFAST_QC completed!
[2024-01-25 20:21:03,652] [INFO] Total running time: 0h1m43s