[2024-01-24 11:35:23,206] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:23,208] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:23,208] [INFO] DQC Reference Directory: /var/lib/cwl/stga7065880-5a36-4701-8e3d-34f1aca3a9bb/dqc_reference
[2024-01-24 11:35:26,243] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,244] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,245] [INFO] Running command: gunzip -c /var/lib/cwl/stg48052381-1fd7-484d-b4cc-8564a180be5a/GCF_004341685.1_ASM434168v1_genomic.fna.gz | prodigal -d GCF_004341685.1_ASM434168v1_genomic.fna/cds.fna -a GCF_004341685.1_ASM434168v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:32,161] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:32,162] [INFO] Task started: HMMsearch
[2024-01-24 11:35:32,162] [INFO] Running command: hmmsearch --tblout GCF_004341685.1_ASM434168v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7065880-5a36-4701-8e3d-34f1aca3a9bb/dqc_reference/reference_markers.hmm GCF_004341685.1_ASM434168v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:32,458] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:32,459] [INFO] Found 6/6 markers.
[2024-01-24 11:35:32,484] [INFO] Query marker FASTA was written to GCF_004341685.1_ASM434168v1_genomic.fna/markers.fasta
[2024-01-24 11:35:32,484] [INFO] Task started: Blastn
[2024-01-24 11:35:32,484] [INFO] Running command: blastn -query GCF_004341685.1_ASM434168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7065880-5a36-4701-8e3d-34f1aca3a9bb/dqc_reference/reference_markers.fasta -out GCF_004341685.1_ASM434168v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:33,115] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:33,118] [INFO] Selected 12 target genomes.
[2024-01-24 11:35:33,118] [INFO] Target genome list was writen to GCF_004341685.1_ASM434168v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:33,149] [INFO] Task started: fastANI
[2024-01-24 11:35:33,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg48052381-1fd7-484d-b4cc-8564a180be5a/GCF_004341685.1_ASM434168v1_genomic.fna.gz --refList GCF_004341685.1_ASM434168v1_genomic.fna/target_genomes.txt --output GCF_004341685.1_ASM434168v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:39,762] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:39,762] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7065880-5a36-4701-8e3d-34f1aca3a9bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:39,763] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7065880-5a36-4701-8e3d-34f1aca3a9bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:39,769] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:39,769] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:39,769] [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
Pectinatus cerevisiiphilus	strain=DSM 20467	GCA_004341685.1	86956	86956	type	True	100.0	852	854	95	conclusive
Pectinatus cerevisiiphilus	strain=MB134	GCA_015732175.1	86956	86956	type	True	99.978	848	854	95	conclusive
Pectinatus frisingensis	strain=MB174	GCA_015732285.1	865	865	type	True	77.8256	195	854	95	below_threshold
Pectinatus sottacetonis	strain=MB620	GCA_015732155.1	1002795	1002795	type	True	77.8203	213	854	95	below_threshold
Propionispira raffinosivorans	strain=DSM 20765	GCA_000381065.1	86959	86959	type	True	76.0179	53	854	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:39,771] [INFO] DFAST Taxonomy check result was written to GCF_004341685.1_ASM434168v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:39,772] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:39,772] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:39,772] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7065880-5a36-4701-8e3d-34f1aca3a9bb/dqc_reference/checkm_data
[2024-01-24 11:35:39,773] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:39,800] [INFO] Task started: CheckM
[2024-01-24 11:35:39,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004341685.1_ASM434168v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004341685.1_ASM434168v1_genomic.fna/checkm_input GCF_004341685.1_ASM434168v1_genomic.fna/checkm_result
[2024-01-24 11:36:03,667] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:03,669] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:03,689] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:03,689] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:03,690] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004341685.1_ASM434168v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:03,690] [INFO] Task started: Blastn
[2024-01-24 11:36:03,691] [INFO] Running command: blastn -query GCF_004341685.1_ASM434168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7065880-5a36-4701-8e3d-34f1aca3a9bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_004341685.1_ASM434168v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:04,564] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:04,568] [INFO] Selected 15 target genomes.
[2024-01-24 11:36:04,568] [INFO] Target genome list was writen to GCF_004341685.1_ASM434168v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:04,580] [INFO] Task started: fastANI
[2024-01-24 11:36:04,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg48052381-1fd7-484d-b4cc-8564a180be5a/GCF_004341685.1_ASM434168v1_genomic.fna.gz --refList GCF_004341685.1_ASM434168v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004341685.1_ASM434168v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:12,204] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:12,214] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:12,215] [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_004341685.1	s__Pectinatus cerevisiiphilus	100.0	852	854	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_015732185.1	s__Pectinatus haikarae	79.221	423	854	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015732285.1	s__Pectinatus frisingensis	77.8222	196	854	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	98.00	97.22	0.85	0.81	9	-
GCF_015732155.1	s__Pectinatus sottacetonis	77.8203	213	854	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381065.1	s__Propionispira raffinosivorans	76.0289	54	854	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Propionispira	96.4486	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:12,217] [INFO] GTDB search result was written to GCF_004341685.1_ASM434168v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:12,218] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:12,221] [INFO] DFAST_QC result json was written to GCF_004341685.1_ASM434168v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:12,222] [INFO] DFAST_QC completed!
[2024-01-24 11:36:12,222] [INFO] Total running time: 0h0m49s