[2024-01-24 13:18:33,576] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:33,577] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:33,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg70cc04c4-f482-432c-b310-3a69bdf745b7/dqc_reference
[2024-01-24 13:18:34,994] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:34,995] [INFO] Task started: Prodigal
[2024-01-24 13:18:34,995] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e5194c8-9669-4af7-9c67-f7f8d68a6df9/GCF_014905115.1_ASM1490511v1_genomic.fna.gz | prodigal -d GCF_014905115.1_ASM1490511v1_genomic.fna/cds.fna -a GCF_014905115.1_ASM1490511v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:40,682] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:40,682] [INFO] Task started: HMMsearch
[2024-01-24 13:18:40,682] [INFO] Running command: hmmsearch --tblout GCF_014905115.1_ASM1490511v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70cc04c4-f482-432c-b310-3a69bdf745b7/dqc_reference/reference_markers.hmm GCF_014905115.1_ASM1490511v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:40,979] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:40,980] [INFO] Found 6/6 markers.
[2024-01-24 13:18:41,004] [INFO] Query marker FASTA was written to GCF_014905115.1_ASM1490511v1_genomic.fna/markers.fasta
[2024-01-24 13:18:41,004] [INFO] Task started: Blastn
[2024-01-24 13:18:41,005] [INFO] Running command: blastn -query GCF_014905115.1_ASM1490511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70cc04c4-f482-432c-b310-3a69bdf745b7/dqc_reference/reference_markers.fasta -out GCF_014905115.1_ASM1490511v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:41,603] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:41,606] [INFO] Selected 8 target genomes.
[2024-01-24 13:18:41,606] [INFO] Target genome list was writen to GCF_014905115.1_ASM1490511v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:41,611] [INFO] Task started: fastANI
[2024-01-24 13:18:41,611] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e5194c8-9669-4af7-9c67-f7f8d68a6df9/GCF_014905115.1_ASM1490511v1_genomic.fna.gz --refList GCF_014905115.1_ASM1490511v1_genomic.fna/target_genomes.txt --output GCF_014905115.1_ASM1490511v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:46,395] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:46,395] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70cc04c4-f482-432c-b310-3a69bdf745b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:46,396] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70cc04c4-f482-432c-b310-3a69bdf745b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:46,403] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:46,404] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:46,404] [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 sediminis	strain=S2-6	GCA_014905115.1	2590020	2590020	type	True	100.0	773	773	95	conclusive
Sulfurimonas hydrogeniphila	strain=NW10	GCA_009068765.1	2509341	2509341	type	True	92.276	645	773	95	below_threshold
Sulfurimonas autotrophica	strain=DSM 16294	GCA_000147355.1	202747	202747	type	True	81.9669	497	773	95	below_threshold
Sulfurimonas paralvinellae	strain=GO25	GCA_014905135.1	317658	317658	type	True	78.9025	261	773	95	below_threshold
Sulfurimonas indica	strain=NW8N	GCA_009192995.1	2508707	2508707	type	True	78.5002	259	773	95	below_threshold
Sulfurimonas xiamenensis	strain=1-1N	GCA_009258045.1	2590021	2590021	type	True	78.1079	125	773	95	below_threshold
Candidatus Sulfurimonas baltica	strain=GD2	GCA_015265455.1	2740404	2740404	type	True	77.7845	134	773	95	below_threshold
Candidatus Sulfurimonas marisnigri	strain=SoZ1	GCA_015265475.1	2740405	2740405	type	True	77.6323	137	773	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:46,405] [INFO] DFAST Taxonomy check result was written to GCF_014905115.1_ASM1490511v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:46,406] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:46,406] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:46,406] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70cc04c4-f482-432c-b310-3a69bdf745b7/dqc_reference/checkm_data
[2024-01-24 13:18:46,407] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:46,442] [INFO] Task started: CheckM
[2024-01-24 13:18:46,442] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014905115.1_ASM1490511v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014905115.1_ASM1490511v1_genomic.fna/checkm_input GCF_014905115.1_ASM1490511v1_genomic.fna/checkm_result
[2024-01-24 13:19:11,179] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:11,180] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:11,196] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:11,196] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:11,197] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014905115.1_ASM1490511v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:11,197] [INFO] Task started: Blastn
[2024-01-24 13:19:11,198] [INFO] Running command: blastn -query GCF_014905115.1_ASM1490511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70cc04c4-f482-432c-b310-3a69bdf745b7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014905115.1_ASM1490511v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:12,007] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:12,011] [INFO] Selected 10 target genomes.
[2024-01-24 13:19:12,011] [INFO] Target genome list was writen to GCF_014905115.1_ASM1490511v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:12,045] [INFO] Task started: fastANI
[2024-01-24 13:19:12,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e5194c8-9669-4af7-9c67-f7f8d68a6df9/GCF_014905115.1_ASM1490511v1_genomic.fna.gz --refList GCF_014905115.1_ASM1490511v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014905115.1_ASM1490511v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:17,252] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:17,269] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:17,270] [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_014905115.1	s__Sulfurimonas sediminis	100.0	773	773	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_009068765.1	s__Sulfurimonas sp009068765	92.2854	646	773	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000147355.1	s__Sulfurimonas autotrophica	81.9762	496	773	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	80.5631	262	773	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	78.8867	262	773	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	78.7596	208	773	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	78.5011	259	773	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733945.2	s__Sulfurimonas sp002733945	77.5368	137	773	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	77.4305	132	773	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.68	99.68	0.82	0.82	2	-
GCA_018825665.1	s__Sulfurimonas sp018825665	77.2191	138	773	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.99	99.99	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:17,272] [INFO] GTDB search result was written to GCF_014905115.1_ASM1490511v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:17,272] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:17,276] [INFO] DFAST_QC result json was written to GCF_014905115.1_ASM1490511v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:17,276] [INFO] DFAST_QC completed!
[2024-01-24 13:19:17,277] [INFO] Total running time: 0h0m44s