[2024-01-25 17:40:35,518] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:35,520] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:35,520] [INFO] DQC Reference Directory: /var/lib/cwl/stgebcfc0d7-70cc-4386-ace8-96e733cfc28d/dqc_reference
[2024-01-25 17:40:36,671] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:36,672] [INFO] Task started: Prodigal
[2024-01-25 17:40:36,672] [INFO] Running command: gunzip -c /var/lib/cwl/stgceb8c09a-77cb-43a0-a4dd-4114fe5574c9/GCF_000147355.1_ASM14735v1_genomic.fna.gz | prodigal -d GCF_000147355.1_ASM14735v1_genomic.fna/cds.fna -a GCF_000147355.1_ASM14735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:40,701] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:40,702] [INFO] Task started: HMMsearch
[2024-01-25 17:40:40,702] [INFO] Running command: hmmsearch --tblout GCF_000147355.1_ASM14735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebcfc0d7-70cc-4386-ace8-96e733cfc28d/dqc_reference/reference_markers.hmm GCF_000147355.1_ASM14735v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:40,884] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:40,885] [INFO] Found 6/6 markers.
[2024-01-25 17:40:40,904] [INFO] Query marker FASTA was written to GCF_000147355.1_ASM14735v1_genomic.fna/markers.fasta
[2024-01-25 17:40:40,905] [INFO] Task started: Blastn
[2024-01-25 17:40:40,905] [INFO] Running command: blastn -query GCF_000147355.1_ASM14735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebcfc0d7-70cc-4386-ace8-96e733cfc28d/dqc_reference/reference_markers.fasta -out GCF_000147355.1_ASM14735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:41,445] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:41,448] [INFO] Selected 9 target genomes.
[2024-01-25 17:40:41,448] [INFO] Target genome list was writen to GCF_000147355.1_ASM14735v1_genomic.fna/target_genomes.txt
[2024-01-25 17:40:41,453] [INFO] Task started: fastANI
[2024-01-25 17:40:41,453] [INFO] Running command: fastANI --query /var/lib/cwl/stgceb8c09a-77cb-43a0-a4dd-4114fe5574c9/GCF_000147355.1_ASM14735v1_genomic.fna.gz --refList GCF_000147355.1_ASM14735v1_genomic.fna/target_genomes.txt --output GCF_000147355.1_ASM14735v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:45,852] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:45,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebcfc0d7-70cc-4386-ace8-96e733cfc28d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:45,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebcfc0d7-70cc-4386-ace8-96e733cfc28d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:45,859] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:40:45,859] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:40:45,859] [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
Sulfurimonas autotrophica	strain=DSM 16294	GCA_000147355.1	202747	202747	type	True	100.0	717	717	95	conclusive
Sulfurimonas sediminis	strain=S2-6	GCA_014905115.1	2590020	2590020	type	True	81.9187	492	717	95	below_threshold
Sulfurimonas hydrogeniphila	strain=NW10	GCA_009068765.1	2509341	2509341	type	True	81.8213	507	717	95	below_threshold
Sulfurimonas paralvinellae	strain=GO25	GCA_014905135.1	317658	317658	type	True	79.6377	284	717	95	below_threshold
Sulfurimonas indica	strain=NW8N	GCA_009192995.1	2508707	2508707	type	True	78.9618	278	717	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	78.5199	192	717	95	below_threshold
Candidatus Sulfurimonas marisnigri	strain=SoZ1	GCA_015265475.1	2740405	2740405	type	True	78.29	167	717	95	below_threshold
Sulfurimonas crateris	strain=SN118	GCA_005217605.1	2574727	2574727	type	True	77.2853	116	717	95	below_threshold
Sulfurospirillum arcachonense	strain=DSM 9755	GCA_000597725.1	57666	57666	type	True	76.171	53	717	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:45,861] [INFO] DFAST Taxonomy check result was written to GCF_000147355.1_ASM14735v1_genomic.fna/tc_result.tsv
[2024-01-25 17:40:45,861] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:45,861] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:45,862] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebcfc0d7-70cc-4386-ace8-96e733cfc28d/dqc_reference/checkm_data
[2024-01-25 17:40:45,862] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:45,886] [INFO] Task started: CheckM
[2024-01-25 17:40:45,886] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000147355.1_ASM14735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000147355.1_ASM14735v1_genomic.fna/checkm_input GCF_000147355.1_ASM14735v1_genomic.fna/checkm_result
[2024-01-25 17:41:04,283] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:04,284] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:04,301] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:04,302] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:04,302] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000147355.1_ASM14735v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:04,302] [INFO] Task started: Blastn
[2024-01-25 17:41:04,302] [INFO] Running command: blastn -query GCF_000147355.1_ASM14735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebcfc0d7-70cc-4386-ace8-96e733cfc28d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000147355.1_ASM14735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:05,184] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:05,186] [INFO] Selected 10 target genomes.
[2024-01-25 17:41:05,186] [INFO] Target genome list was writen to GCF_000147355.1_ASM14735v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:05,202] [INFO] Task started: fastANI
[2024-01-25 17:41:05,203] [INFO] Running command: fastANI --query /var/lib/cwl/stgceb8c09a-77cb-43a0-a4dd-4114fe5574c9/GCF_000147355.1_ASM14735v1_genomic.fna.gz --refList GCF_000147355.1_ASM14735v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000147355.1_ASM14735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:41:09,451] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:09,458] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:41:09,458] [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_000147355.1	s__Sulfurimonas autotrophica	100.0	716	717	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014905115.1	s__Sulfurimonas sediminis	81.9388	494	717	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009068765.1	s__Sulfurimonas sp009068765	81.8274	506	717	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015662405.1	s__Sulfurimonas autotrophica_A	81.2266	257	717	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014905135.1	s__Sulfurimonas paralvinellae	79.6612	284	717	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013607665.1	s__Sulfurimonas sp013607665	79.1755	221	717	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009192995.1	s__Sulfurimonas indica	78.9703	278	717	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015488615.1	s__Sulfurimonas sp015488615	77.6695	152	717	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.68	99.68	0.82	0.82	2	-
GCA_015488855.1	s__Sulfurimonas sp015488855	77.3985	101	717	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.17	99.17	0.76	0.76	2	-
GCA_001829785.1	s__Sulfurimonas sp001829785	77.3086	175	717	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.93	99.89	1.00	1.00	4	-
--------------------------------------------------------------------------------
[2024-01-25 17:41:09,459] [INFO] GTDB search result was written to GCF_000147355.1_ASM14735v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:41:09,460] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:41:09,462] [INFO] DFAST_QC result json was written to GCF_000147355.1_ASM14735v1_genomic.fna/dqc_result.json
[2024-01-25 17:41:09,463] [INFO] DFAST_QC completed!
[2024-01-25 17:41:09,463] [INFO] Total running time: 0h0m34s