[2024-01-25 20:12:05,688] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:05,689] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:05,689] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5a8aeb0-f439-4aac-875f-008394302e94/dqc_reference
[2024-01-25 20:12:06,818] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:06,819] [INFO] Task started: Prodigal
[2024-01-25 20:12:06,819] [INFO] Running command: gunzip -c /var/lib/cwl/stg14477c14-3e7a-4d86-8967-e90ec4c29518/GCF_017377855.1_ASM1737785v1_genomic.fna.gz | prodigal -d GCF_017377855.1_ASM1737785v1_genomic.fna/cds.fna -a GCF_017377855.1_ASM1737785v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:04,312] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:04,312] [INFO] Task started: HMMsearch
[2024-01-25 20:13:04,312] [INFO] Running command: hmmsearch --tblout GCF_017377855.1_ASM1737785v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5a8aeb0-f439-4aac-875f-008394302e94/dqc_reference/reference_markers.hmm GCF_017377855.1_ASM1737785v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:04,804] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:04,805] [INFO] Found 6/6 markers.
[2024-01-25 20:13:04,896] [INFO] Query marker FASTA was written to GCF_017377855.1_ASM1737785v1_genomic.fna/markers.fasta
[2024-01-25 20:13:04,896] [INFO] Task started: Blastn
[2024-01-25 20:13:04,896] [INFO] Running command: blastn -query GCF_017377855.1_ASM1737785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5a8aeb0-f439-4aac-875f-008394302e94/dqc_reference/reference_markers.fasta -out GCF_017377855.1_ASM1737785v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:05,449] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:05,457] [INFO] Selected 24 target genomes.
[2024-01-25 20:13:05,458] [INFO] Target genome list was writen to GCF_017377855.1_ASM1737785v1_genomic.fna/target_genomes.txt
[2024-01-25 20:13:05,505] [INFO] Task started: fastANI
[2024-01-25 20:13:05,506] [INFO] Running command: fastANI --query /var/lib/cwl/stg14477c14-3e7a-4d86-8967-e90ec4c29518/GCF_017377855.1_ASM1737785v1_genomic.fna.gz --refList GCF_017377855.1_ASM1737785v1_genomic.fna/target_genomes.txt --output GCF_017377855.1_ASM1737785v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:13:29,685] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:29,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5a8aeb0-f439-4aac-875f-008394302e94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:13:29,686] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5a8aeb0-f439-4aac-875f-008394302e94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:13:29,690] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:13:29,690] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:13:29,690] [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
Acanthopleuribacter pedis	strain=KCTC 12899	GCA_017377855.1	442870	442870	type	True	100.0	3512	3574	95	conclusive
Sulfidibacter corallicola	strain=M133	GCA_017498545.1	2818388	2818388	type	True	76.518	455	3574	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	75.0186	50	3574	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:13:29,693] [INFO] DFAST Taxonomy check result was written to GCF_017377855.1_ASM1737785v1_genomic.fna/tc_result.tsv
[2024-01-25 20:13:29,694] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:13:29,694] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:13:29,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5a8aeb0-f439-4aac-875f-008394302e94/dqc_reference/checkm_data
[2024-01-25 20:13:29,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:13:29,794] [INFO] Task started: CheckM
[2024-01-25 20:13:29,794] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017377855.1_ASM1737785v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017377855.1_ASM1737785v1_genomic.fna/checkm_input GCF_017377855.1_ASM1737785v1_genomic.fna/checkm_result
[2024-01-25 20:16:01,174] [INFO] Task succeeded: CheckM
[2024-01-25 20:16:01,175] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:16:01,201] [INFO] ===== Completeness check finished =====
[2024-01-25 20:16:01,201] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:16:01,202] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017377855.1_ASM1737785v1_genomic.fna/markers.fasta)
[2024-01-25 20:16:01,202] [INFO] Task started: Blastn
[2024-01-25 20:16:01,202] [INFO] Running command: blastn -query GCF_017377855.1_ASM1737785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5a8aeb0-f439-4aac-875f-008394302e94/dqc_reference/reference_markers_gtdb.fasta -out GCF_017377855.1_ASM1737785v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:02,032] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:02,036] [INFO] Selected 26 target genomes.
[2024-01-25 20:16:02,036] [INFO] Target genome list was writen to GCF_017377855.1_ASM1737785v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:16:02,049] [INFO] Task started: fastANI
[2024-01-25 20:16:02,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg14477c14-3e7a-4d86-8967-e90ec4c29518/GCF_017377855.1_ASM1737785v1_genomic.fna.gz --refList GCF_017377855.1_ASM1737785v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017377855.1_ASM1737785v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:16:28,288] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:28,293] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:16:28,293] [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_017377855.1	s__Acanthopleuribacter pedis	100.0	3523	3574	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Acanthopleuribacterales;f__Acanthopleuribacteraceae;g__Acanthopleuribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017498545.1	s__Acanthopleuribacter sp017498545	76.5166	454	3574	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Acanthopleuribacterales;f__Acanthopleuribacteraceae;g__Acanthopleuribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699025.1	s__GCA-2699025 sp002699025	74.8326	85	3574	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__GCA-2699025	95.0	99.90	99.85	0.97	0.97	3	-
GCA_013297655.1	s__JAAFHV01 sp013297655	74.7264	58	3574	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JAAFHV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009692555.1	s__SHYY01 sp009692555	74.6948	61	3574	d__Bacteria;p__Myxococcota;c__Polyangia;o__Palsa-1104;f__Palsa-1104;g__SHYY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:16:28,296] [INFO] GTDB search result was written to GCF_017377855.1_ASM1737785v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:16:28,297] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:16:28,299] [INFO] DFAST_QC result json was written to GCF_017377855.1_ASM1737785v1_genomic.fna/dqc_result.json
[2024-01-25 20:16:28,299] [INFO] DFAST_QC completed!
[2024-01-25 20:16:28,299] [INFO] Total running time: 0h4m23s