[2024-01-25 17:45:35,343] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:45:35,344] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:45:35,345] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf92b057-0079-4cab-ba8b-f4c65ba1af10/dqc_reference
[2024-01-25 17:45:36,475] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:45:36,476] [INFO] Task started: Prodigal
[2024-01-25 17:45:36,476] [INFO] Running command: gunzip -c /var/lib/cwl/stg9151cbbe-c7eb-4385-b205-31a2da66712d/GCF_014905095.1_ASM1490509v1_genomic.fna.gz | prodigal -d GCF_014905095.1_ASM1490509v1_genomic.fna/cds.fna -a GCF_014905095.1_ASM1490509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:45:40,369] [INFO] Task succeeded: Prodigal
[2024-01-25 17:45:40,370] [INFO] Task started: HMMsearch
[2024-01-25 17:45:40,370] [INFO] Running command: hmmsearch --tblout GCF_014905095.1_ASM1490509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf92b057-0079-4cab-ba8b-f4c65ba1af10/dqc_reference/reference_markers.hmm GCF_014905095.1_ASM1490509v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:45:40,546] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:45:40,547] [INFO] Found 6/6 markers.
[2024-01-25 17:45:40,568] [INFO] Query marker FASTA was written to GCF_014905095.1_ASM1490509v1_genomic.fna/markers.fasta
[2024-01-25 17:45:40,568] [INFO] Task started: Blastn
[2024-01-25 17:45:40,568] [INFO] Running command: blastn -query GCF_014905095.1_ASM1490509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf92b057-0079-4cab-ba8b-f4c65ba1af10/dqc_reference/reference_markers.fasta -out GCF_014905095.1_ASM1490509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:41,119] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:41,122] [INFO] Selected 19 target genomes.
[2024-01-25 17:45:41,123] [INFO] Target genome list was writen to GCF_014905095.1_ASM1490509v1_genomic.fna/target_genomes.txt
[2024-01-25 17:45:41,134] [INFO] Task started: fastANI
[2024-01-25 17:45:41,134] [INFO] Running command: fastANI --query /var/lib/cwl/stg9151cbbe-c7eb-4385-b205-31a2da66712d/GCF_014905095.1_ASM1490509v1_genomic.fna.gz --refList GCF_014905095.1_ASM1490509v1_genomic.fna/target_genomes.txt --output GCF_014905095.1_ASM1490509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:45:48,309] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:48,309] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf92b057-0079-4cab-ba8b-f4c65ba1af10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:45:48,310] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf92b057-0079-4cab-ba8b-f4c65ba1af10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:45:48,320] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:45:48,320] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:45:48,320] [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 paralvinellae	strain=GO25	GCA_014905135.1	317658	317658	type	True	79.1215	185	753	95	below_threshold
Sulfurimonas indica	strain=NW8N	GCA_009192995.1	2508707	2508707	type	True	78.9515	213	753	95	below_threshold
Sulfurimonas lithotrophica	strain=GYSZ_1	GCA_009258225.1	2590022	2590022	type	True	78.878	176	753	95	below_threshold
Sulfurimonas autotrophica	strain=DSM 16294	GCA_000147355.1	202747	202747	type	True	78.5056	201	753	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	78.4931	166	753	95	below_threshold
Sulfurimonas sediminis	strain=S2-6	GCA_014905115.1	2590020	2590020	type	True	78.4657	148	753	95	below_threshold
Candidatus Sulfurimonas marisnigri	strain=SoZ1	GCA_015265475.1	2740405	2740405	type	True	78.4054	157	753	95	below_threshold
Sulfurimonas hydrogeniphila	strain=NW10	GCA_009068765.1	2509341	2509341	type	True	78.001	147	753	95	below_threshold
Sulfurimonas xiamenensis	strain=1-1N	GCA_009258045.1	2590021	2590021	type	True	77.8765	123	753	95	below_threshold
Sulfurimonas crateris	strain=SN118	GCA_005217605.1	2574727	2574727	type	True	77.5106	108	753	95	below_threshold
Sulfurimonas hongkongensis	strain=AST-10	GCA_000445475.1	1172190	1172190	type	True	77.1694	120	753	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:45:48,324] [INFO] DFAST Taxonomy check result was written to GCF_014905095.1_ASM1490509v1_genomic.fna/tc_result.tsv
[2024-01-25 17:45:48,324] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:45:48,324] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:45:48,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf92b057-0079-4cab-ba8b-f4c65ba1af10/dqc_reference/checkm_data
[2024-01-25 17:45:48,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:45:48,358] [INFO] Task started: CheckM
[2024-01-25 17:45:48,358] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014905095.1_ASM1490509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014905095.1_ASM1490509v1_genomic.fna/checkm_input GCF_014905095.1_ASM1490509v1_genomic.fna/checkm_result
[2024-01-25 17:46:06,383] [INFO] Task succeeded: CheckM
[2024-01-25 17:46:06,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:46:06,401] [INFO] ===== Completeness check finished =====
[2024-01-25 17:46:06,402] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:46:06,402] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014905095.1_ASM1490509v1_genomic.fna/markers.fasta)
[2024-01-25 17:46:06,402] [INFO] Task started: Blastn
[2024-01-25 17:46:06,402] [INFO] Running command: blastn -query GCF_014905095.1_ASM1490509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf92b057-0079-4cab-ba8b-f4c65ba1af10/dqc_reference/reference_markers_gtdb.fasta -out GCF_014905095.1_ASM1490509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:07,172] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:07,177] [INFO] Selected 16 target genomes.
[2024-01-25 17:46:07,178] [INFO] Target genome list was writen to GCF_014905095.1_ASM1490509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:46:07,194] [INFO] Task started: fastANI
[2024-01-25 17:46:07,194] [INFO] Running command: fastANI --query /var/lib/cwl/stg9151cbbe-c7eb-4385-b205-31a2da66712d/GCF_014905095.1_ASM1490509v1_genomic.fna.gz --refList GCF_014905095.1_ASM1490509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014905095.1_ASM1490509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:46:14,191] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:14,201] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:46:14,201] [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_014905095.1	s__Sulfurimonas sp014905095	100.0	753	753	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_014905135.1	s__Sulfurimonas paralvinellae	78.9766	184	753	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	78.9515	213	753	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009258225.1	s__Sulfurimonas sp009258225	78.8412	178	753	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	78.5808	169	753	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	78.5056	201	753	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015265475.1	s__Sulfurimonas marisnigri	78.4115	157	753	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013607635.1	s__Sulfurimonas sp013607635	78.3687	165	753	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017357825.1	s__Sulfurimonas sp017357825	78.2555	185	753	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013791885.1	s__Sulfurimonas sp013791885	77.9043	139	753	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.38	98.60	0.95	0.92	8	-
GCA_016744025.1	s__Sulfurimonas sp016744025	77.7231	150	753	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002781365.1	s__Sulfurimonas sp002781365	77.5191	151	753	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.99	99.89	0.98	0.96	19	-
GCA_013153755.1	s__Sulfurimonas sp013153755	77.3338	130	753	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003978465.1	s__Sulfurimonas sp003978465	77.2236	107	753	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859695.1	s__Sulfurimonas sp014859695	77.0633	98	753	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001873135.1	s__Sulfurimonas sp001873135	76.8521	116	753	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:46:14,204] [INFO] GTDB search result was written to GCF_014905095.1_ASM1490509v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:46:14,205] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:46:14,208] [INFO] DFAST_QC result json was written to GCF_014905095.1_ASM1490509v1_genomic.fna/dqc_result.json
[2024-01-25 17:46:14,208] [INFO] DFAST_QC completed!
[2024-01-25 17:46:14,208] [INFO] Total running time: 0h0m39s