[2024-01-25 18:06:35,666] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:35,667] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:35,668] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a8cb5c2-3250-4718-b44b-b571696e3c51/dqc_reference
[2024-01-25 18:06:36,767] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:36,768] [INFO] Task started: Prodigal
[2024-01-25 18:06:36,768] [INFO] Running command: gunzip -c /var/lib/cwl/stge026c798-d0b1-4cd5-94c6-aeb45e219de7/GCF_015732285.1_ASM1573228v1_genomic.fna.gz | prodigal -d GCF_015732285.1_ASM1573228v1_genomic.fna/cds.fna -a GCF_015732285.1_ASM1573228v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:42,340] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:42,341] [INFO] Task started: HMMsearch
[2024-01-25 18:06:42,341] [INFO] Running command: hmmsearch --tblout GCF_015732285.1_ASM1573228v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a8cb5c2-3250-4718-b44b-b571696e3c51/dqc_reference/reference_markers.hmm GCF_015732285.1_ASM1573228v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:42,552] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:42,553] [INFO] Found 6/6 markers.
[2024-01-25 18:06:42,576] [INFO] Query marker FASTA was written to GCF_015732285.1_ASM1573228v1_genomic.fna/markers.fasta
[2024-01-25 18:06:42,576] [INFO] Task started: Blastn
[2024-01-25 18:06:42,576] [INFO] Running command: blastn -query GCF_015732285.1_ASM1573228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a8cb5c2-3250-4718-b44b-b571696e3c51/dqc_reference/reference_markers.fasta -out GCF_015732285.1_ASM1573228v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:43,094] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:43,097] [INFO] Selected 13 target genomes.
[2024-01-25 18:06:43,097] [INFO] Target genome list was writen to GCF_015732285.1_ASM1573228v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:43,111] [INFO] Task started: fastANI
[2024-01-25 18:06:43,111] [INFO] Running command: fastANI --query /var/lib/cwl/stge026c798-d0b1-4cd5-94c6-aeb45e219de7/GCF_015732285.1_ASM1573228v1_genomic.fna.gz --refList GCF_015732285.1_ASM1573228v1_genomic.fna/target_genomes.txt --output GCF_015732285.1_ASM1573228v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:49,680] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:49,680] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a8cb5c2-3250-4718-b44b-b571696e3c51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:49,681] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a8cb5c2-3250-4718-b44b-b571696e3c51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:49,685] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:06:49,685] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:06:49,685] [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 frisingensis	strain=MB174	GCA_015732285.1	865	865	type	True	100.0	935	941	95	conclusive
Pectinatus cerevisiiphilus	strain=MB134	GCA_015732175.1	86956	86956	type	True	77.9936	191	941	95	below_threshold
Pectinatus cerevisiiphilus	strain=DSM 20467	GCA_004341685.1	86956	86956	type	True	77.8725	185	941	95	below_threshold
Pectinatus sottacetonis	strain=MB620	GCA_015732155.1	1002795	1002795	type	True	77.6839	226	941	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:49,687] [INFO] DFAST Taxonomy check result was written to GCF_015732285.1_ASM1573228v1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:49,687] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:49,687] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:49,687] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a8cb5c2-3250-4718-b44b-b571696e3c51/dqc_reference/checkm_data
[2024-01-25 18:06:49,688] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:49,719] [INFO] Task started: CheckM
[2024-01-25 18:06:49,719] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015732285.1_ASM1573228v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015732285.1_ASM1573228v1_genomic.fna/checkm_input GCF_015732285.1_ASM1573228v1_genomic.fna/checkm_result
[2024-01-25 18:07:11,860] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:11,861] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:11,877] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:11,877] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:11,877] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015732285.1_ASM1573228v1_genomic.fna/markers.fasta)
[2024-01-25 18:07:11,877] [INFO] Task started: Blastn
[2024-01-25 18:07:11,877] [INFO] Running command: blastn -query GCF_015732285.1_ASM1573228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a8cb5c2-3250-4718-b44b-b571696e3c51/dqc_reference/reference_markers_gtdb.fasta -out GCF_015732285.1_ASM1573228v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:12,676] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:12,681] [INFO] Selected 22 target genomes.
[2024-01-25 18:07:12,681] [INFO] Target genome list was writen to GCF_015732285.1_ASM1573228v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:12,700] [INFO] Task started: fastANI
[2024-01-25 18:07:12,700] [INFO] Running command: fastANI --query /var/lib/cwl/stge026c798-d0b1-4cd5-94c6-aeb45e219de7/GCF_015732285.1_ASM1573228v1_genomic.fna.gz --refList GCF_015732285.1_ASM1573228v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015732285.1_ASM1573228v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:22,981] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:22,986] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:22,986] [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_015732285.1	s__Pectinatus frisingensis	100.0	935	941	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	98.00	97.22	0.85	0.81	9	conclusive
GCF_015732185.1	s__Pectinatus haikarae	78.4944	210	941	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_004341685.1	s__Pectinatus cerevisiiphilus	77.8546	186	941	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	99.98	99.98	0.99	0.99	2	-
GCF_015732155.1	s__Pectinatus sottacetonis	77.6935	227	941	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:22,987] [INFO] GTDB search result was written to GCF_015732285.1_ASM1573228v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:22,988] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:22,990] [INFO] DFAST_QC result json was written to GCF_015732285.1_ASM1573228v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:22,991] [INFO] DFAST_QC completed!
[2024-01-25 18:07:22,991] [INFO] Total running time: 0h0m47s