[2024-01-25 19:08:20,662] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:08:20,664] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:08:20,664] [INFO] DQC Reference Directory: /var/lib/cwl/stgc50b933f-0666-4320-a4e6-c62b35338698/dqc_reference
[2024-01-25 19:08:21,812] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:08:21,813] [INFO] Task started: Prodigal
[2024-01-25 19:08:21,813] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c62320a-a29a-4ca4-a4ec-49eeb48317e7/GCF_030813505.1_ASM3081350v1_genomic.fna.gz | prodigal -d GCF_030813505.1_ASM3081350v1_genomic.fna/cds.fna -a GCF_030813505.1_ASM3081350v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:08:27,887] [INFO] Task succeeded: Prodigal
[2024-01-25 19:08:27,888] [INFO] Task started: HMMsearch
[2024-01-25 19:08:27,888] [INFO] Running command: hmmsearch --tblout GCF_030813505.1_ASM3081350v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc50b933f-0666-4320-a4e6-c62b35338698/dqc_reference/reference_markers.hmm GCF_030813505.1_ASM3081350v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:08:28,130] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:08:28,131] [INFO] Found 6/6 markers.
[2024-01-25 19:08:28,159] [INFO] Query marker FASTA was written to GCF_030813505.1_ASM3081350v1_genomic.fna/markers.fasta
[2024-01-25 19:08:28,160] [INFO] Task started: Blastn
[2024-01-25 19:08:28,160] [INFO] Running command: blastn -query GCF_030813505.1_ASM3081350v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc50b933f-0666-4320-a4e6-c62b35338698/dqc_reference/reference_markers.fasta -out GCF_030813505.1_ASM3081350v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:28,697] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:28,700] [INFO] Selected 16 target genomes.
[2024-01-25 19:08:28,701] [INFO] Target genome list was writen to GCF_030813505.1_ASM3081350v1_genomic.fna/target_genomes.txt
[2024-01-25 19:08:28,715] [INFO] Task started: fastANI
[2024-01-25 19:08:28,715] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c62320a-a29a-4ca4-a4ec-49eeb48317e7/GCF_030813505.1_ASM3081350v1_genomic.fna.gz --refList GCF_030813505.1_ASM3081350v1_genomic.fna/target_genomes.txt --output GCF_030813505.1_ASM3081350v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:08:37,417] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:37,417] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc50b933f-0666-4320-a4e6-c62b35338698/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:08:37,417] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc50b933f-0666-4320-a4e6-c62b35338698/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:08:37,423] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:08:37,423] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:08:37,423] [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	79.2572	409	988	95	below_threshold
Pectinatus cerevisiiphilus	strain=MB134	GCA_015732175.1	86956	86956	type	True	79.1783	420	988	95	below_threshold
Pectinatus frisingensis	strain=MB174	GCA_015732285.1	865	865	type	True	77.82	195	988	95	below_threshold
Pectinatus sottacetonis	strain=MB620	GCA_015732155.1	1002795	1002795	type	True	77.6289	197	988	95	below_threshold
Pectinatus brassicae	strain=MB591	GCA_015732205.1	862415	862415	type	True	77.541	178	988	95	below_threshold
Pectinatus brassicae	strain=DSM 24661	GCA_014201835.1	862415	862415	type	True	77.5297	173	988	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:08:37,424] [INFO] DFAST Taxonomy check result was written to GCF_030813505.1_ASM3081350v1_genomic.fna/tc_result.tsv
[2024-01-25 19:08:37,425] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:08:37,425] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:08:37,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc50b933f-0666-4320-a4e6-c62b35338698/dqc_reference/checkm_data
[2024-01-25 19:08:37,426] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:08:37,456] [INFO] Task started: CheckM
[2024-01-25 19:08:37,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030813505.1_ASM3081350v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030813505.1_ASM3081350v1_genomic.fna/checkm_input GCF_030813505.1_ASM3081350v1_genomic.fna/checkm_result
[2024-01-25 19:09:00,260] [INFO] Task succeeded: CheckM
[2024-01-25 19:09:00,260] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:09:00,276] [INFO] ===== Completeness check finished =====
[2024-01-25 19:09:00,276] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:09:00,277] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030813505.1_ASM3081350v1_genomic.fna/markers.fasta)
[2024-01-25 19:09:00,277] [INFO] Task started: Blastn
[2024-01-25 19:09:00,277] [INFO] Running command: blastn -query GCF_030813505.1_ASM3081350v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc50b933f-0666-4320-a4e6-c62b35338698/dqc_reference/reference_markers_gtdb.fasta -out GCF_030813505.1_ASM3081350v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:01,000] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:01,003] [INFO] Selected 19 target genomes.
[2024-01-25 19:09:01,003] [INFO] Target genome list was writen to GCF_030813505.1_ASM3081350v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:09:01,017] [INFO] Task started: fastANI
[2024-01-25 19:09:01,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c62320a-a29a-4ca4-a4ec-49eeb48317e7/GCF_030813505.1_ASM3081350v1_genomic.fna.gz --refList GCF_030813505.1_ASM3081350v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030813505.1_ASM3081350v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:09:11,754] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:11,759] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:09:11,759] [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_015732185.1	s__Pectinatus haikarae	99.0849	888	988	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004341685.1	s__Pectinatus cerevisiiphilus	79.2806	407	988	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_015732285.1	s__Pectinatus frisingensis	77.82	195	988	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	77.6289	197	988	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_014201835.1	s__Pectinatus brassicae	77.5442	173	988	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:09:11,763] [INFO] GTDB search result was written to GCF_030813505.1_ASM3081350v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:09:11,763] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:09:11,769] [INFO] DFAST_QC result json was written to GCF_030813505.1_ASM3081350v1_genomic.fna/dqc_result.json
[2024-01-25 19:09:11,769] [INFO] DFAST_QC completed!
[2024-01-25 19:09:11,769] [INFO] Total running time: 0h0m51s