[2023-07-01 07:37:00,883] [INFO] DFAST_QC pipeline started.
[2023-07-01 07:37:00,918] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 07:37:00,918] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d5b2c6d-da0d-4b69-ab5c-d949bf790446/dqc_reference
[2023-07-01 07:37:03,341] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 07:37:03,342] [INFO] Task started: Prodigal
[2023-07-01 07:37:03,343] [INFO] Running command: gunzip -c /var/lib/cwl/stg9072e040-e42b-45d1-b489-af3a124c90a3/GCA_024762705.1_ASM2476270v1_genomic.fna.gz | prodigal -d GCA_024762705.1_ASM2476270v1_genomic.fna/cds.fna -a GCA_024762705.1_ASM2476270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 07:37:05,570] [INFO] Task succeeded: Prodigal
[2023-07-01 07:37:05,570] [INFO] Task started: HMMsearch
[2023-07-01 07:37:05,570] [INFO] Running command: hmmsearch --tblout GCA_024762705.1_ASM2476270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d5b2c6d-da0d-4b69-ab5c-d949bf790446/dqc_reference/reference_markers.hmm GCA_024762705.1_ASM2476270v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 07:37:05,761] [INFO] Task succeeded: HMMsearch
[2023-07-01 07:37:05,763] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9072e040-e42b-45d1-b489-af3a124c90a3/GCA_024762705.1_ASM2476270v1_genomic.fna.gz]
[2023-07-01 07:37:05,780] [INFO] Query marker FASTA was written to GCA_024762705.1_ASM2476270v1_genomic.fna/markers.fasta
[2023-07-01 07:37:05,781] [INFO] Task started: Blastn
[2023-07-01 07:37:05,781] [INFO] Running command: blastn -query GCA_024762705.1_ASM2476270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d5b2c6d-da0d-4b69-ab5c-d949bf790446/dqc_reference/reference_markers.fasta -out GCA_024762705.1_ASM2476270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 07:37:08,221] [INFO] Task succeeded: Blastn
[2023-07-01 07:37:08,225] [INFO] Selected 9 target genomes.
[2023-07-01 07:37:08,225] [INFO] Target genome list was writen to GCA_024762705.1_ASM2476270v1_genomic.fna/target_genomes.txt
[2023-07-01 07:37:08,231] [INFO] Task started: fastANI
[2023-07-01 07:37:08,231] [INFO] Running command: fastANI --query /var/lib/cwl/stg9072e040-e42b-45d1-b489-af3a124c90a3/GCA_024762705.1_ASM2476270v1_genomic.fna.gz --refList GCA_024762705.1_ASM2476270v1_genomic.fna/target_genomes.txt --output GCA_024762705.1_ASM2476270v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 07:37:11,546] [INFO] Task succeeded: fastANI
[2023-07-01 07:37:11,546] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d5b2c6d-da0d-4b69-ab5c-d949bf790446/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 07:37:11,547] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d5b2c6d-da0d-4b69-ab5c-d949bf790446/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 07:37:11,557] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 07:37:11,557] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 07:37:11,557] [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	81.8594	227	297	95	below_threshold
Sulfurimonas hydrogeniphila	strain=NW10	GCA_009068765.1	2509341	2509341	type	True	80.3535	198	297	95	below_threshold
Sulfurimonas sediminis	strain=S2-6	GCA_014905115.1	2590020	2590020	type	True	80.3161	195	297	95	below_threshold
Sulfurimonas paralvinellae	strain=GO25	GCA_014905135.1	317658	317658	type	True	78.4641	131	297	95	below_threshold
Sulfurimonas indica	strain=NW8N	GCA_009192995.1	2508707	2508707	type	True	78.1656	126	297	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	77.5517	76	297	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 07:37:11,560] [INFO] DFAST Taxonomy check result was written to GCA_024762705.1_ASM2476270v1_genomic.fna/tc_result.tsv
[2023-07-01 07:37:11,560] [INFO] ===== Taxonomy check completed =====
[2023-07-01 07:37:11,561] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 07:37:11,561] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d5b2c6d-da0d-4b69-ab5c-d949bf790446/dqc_reference/checkm_data
[2023-07-01 07:37:11,562] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 07:37:11,578] [INFO] Task started: CheckM
[2023-07-01 07:37:11,578] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024762705.1_ASM2476270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024762705.1_ASM2476270v1_genomic.fna/checkm_input GCA_024762705.1_ASM2476270v1_genomic.fna/checkm_result
[2023-07-01 07:37:27,606] [INFO] Task succeeded: CheckM
[2023-07-01 07:37:27,608] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 40.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 07:37:27,628] [INFO] ===== Completeness check finished =====
[2023-07-01 07:37:27,628] [INFO] ===== Start GTDB Search =====
[2023-07-01 07:37:27,629] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024762705.1_ASM2476270v1_genomic.fna/markers.fasta)
[2023-07-01 07:37:27,629] [INFO] Task started: Blastn
[2023-07-01 07:37:27,629] [INFO] Running command: blastn -query GCA_024762705.1_ASM2476270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d5b2c6d-da0d-4b69-ab5c-d949bf790446/dqc_reference/reference_markers_gtdb.fasta -out GCA_024762705.1_ASM2476270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 07:37:28,069] [INFO] Task succeeded: Blastn
[2023-07-01 07:37:28,087] [INFO] Selected 9 target genomes.
[2023-07-01 07:37:28,087] [INFO] Target genome list was writen to GCA_024762705.1_ASM2476270v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 07:37:28,095] [INFO] Task started: fastANI
[2023-07-01 07:37:28,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg9072e040-e42b-45d1-b489-af3a124c90a3/GCA_024762705.1_ASM2476270v1_genomic.fna.gz --refList GCA_024762705.1_ASM2476270v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024762705.1_ASM2476270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 07:37:31,728] [INFO] Task succeeded: fastANI
[2023-07-01 07:37:31,741] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 07:37:31,741] [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	81.8594	227	297	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	80.3535	198	297	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014905115.1	s__Sulfurimonas sediminis	80.3161	195	297	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	79.7581	134	297	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	78.4641	131	297	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	78.1656	126	297	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018822665.1	s__Sulfurimonas sp018822665	77.478	57	297	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.95	99.95	0.96	0.96	2	-
GCF_017357825.1	s__Sulfurimonas sp017357825	77.1775	75	297	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001829625.1	s__Sulfurimonas sp001829625	77.1622	56	297	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.76	99.76	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-07-01 07:37:31,754] [INFO] GTDB search result was written to GCA_024762705.1_ASM2476270v1_genomic.fna/result_gtdb.tsv
[2023-07-01 07:37:31,755] [INFO] ===== GTDB Search completed =====
[2023-07-01 07:37:31,759] [INFO] DFAST_QC result json was written to GCA_024762705.1_ASM2476270v1_genomic.fna/dqc_result.json
[2023-07-01 07:37:31,759] [INFO] DFAST_QC completed!
[2023-07-01 07:37:31,759] [INFO] Total running time: 0h0m31s