[2024-01-24 11:35:34,506] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:34,507] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:34,508] [INFO] DQC Reference Directory: /var/lib/cwl/stg83f9d20b-a568-47ec-9dce-b61fd8c933b8/dqc_reference
[2024-01-24 11:35:35,730] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:35,730] [INFO] Task started: Prodigal
[2024-01-24 11:35:35,731] [INFO] Running command: gunzip -c /var/lib/cwl/stgb57d6f4e-f241-4008-bdd3-38bd939b5460/GCF_027587205.1_ASM2758720v1_genomic.fna.gz | prodigal -d GCF_027587205.1_ASM2758720v1_genomic.fna/cds.fna -a GCF_027587205.1_ASM2758720v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:36:01,025] [INFO] Task succeeded: Prodigal
[2024-01-24 11:36:01,025] [INFO] Task started: HMMsearch
[2024-01-24 11:36:01,025] [INFO] Running command: hmmsearch --tblout GCF_027587205.1_ASM2758720v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83f9d20b-a568-47ec-9dce-b61fd8c933b8/dqc_reference/reference_markers.hmm GCF_027587205.1_ASM2758720v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:36:01,425] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:36:01,427] [INFO] Found 6/6 markers.
[2024-01-24 11:36:01,499] [INFO] Query marker FASTA was written to GCF_027587205.1_ASM2758720v1_genomic.fna/markers.fasta
[2024-01-24 11:36:01,500] [INFO] Task started: Blastn
[2024-01-24 11:36:01,500] [INFO] Running command: blastn -query GCF_027587205.1_ASM2758720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83f9d20b-a568-47ec-9dce-b61fd8c933b8/dqc_reference/reference_markers.fasta -out GCF_027587205.1_ASM2758720v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:02,184] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:02,188] [INFO] Selected 8 target genomes.
[2024-01-24 11:36:02,188] [INFO] Target genome list was writen to GCF_027587205.1_ASM2758720v1_genomic.fna/target_genomes.txt
[2024-01-24 11:36:02,193] [INFO] Task started: fastANI
[2024-01-24 11:36:02,193] [INFO] Running command: fastANI --query /var/lib/cwl/stgb57d6f4e-f241-4008-bdd3-38bd939b5460/GCF_027587205.1_ASM2758720v1_genomic.fna.gz --refList GCF_027587205.1_ASM2758720v1_genomic.fna/target_genomes.txt --output GCF_027587205.1_ASM2758720v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:14,342] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:14,343] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83f9d20b-a568-47ec-9dce-b61fd8c933b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:14,343] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83f9d20b-a568-47ec-9dce-b61fd8c933b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:14,356] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:36:14,357] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:36:14,357] [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
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	81.2066	1482	3155	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	77.1522	907	3155	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	77.0936	853	3155	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	77.0595	825	3155	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	76.9115	979	3155	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	76.6242	775	3155	95	below_threshold
Patulibacter medicamentivorans	strain=I11	GCA_000240225.2	1097667	1097667	type	True	76.4371	700	3155	95	below_threshold
Patulibacter americanus	strain=DSM 16676	GCA_000420025.1	588672	588672	type	True	76.15	635	3155	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:14,359] [INFO] DFAST Taxonomy check result was written to GCF_027587205.1_ASM2758720v1_genomic.fna/tc_result.tsv
[2024-01-24 11:36:14,360] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:14,360] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:14,360] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83f9d20b-a568-47ec-9dce-b61fd8c933b8/dqc_reference/checkm_data
[2024-01-24 11:36:14,361] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:14,446] [INFO] Task started: CheckM
[2024-01-24 11:36:14,447] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027587205.1_ASM2758720v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027587205.1_ASM2758720v1_genomic.fna/checkm_input GCF_027587205.1_ASM2758720v1_genomic.fna/checkm_result
[2024-01-24 11:37:38,521] [INFO] Task succeeded: CheckM
[2024-01-24 11:37:38,523] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.48%
Strain heterogeneity: 83.33%
--------------------------------------------------------------------------------
[2024-01-24 11:37:38,545] [INFO] ===== Completeness check finished =====
[2024-01-24 11:37:38,546] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:37:38,546] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027587205.1_ASM2758720v1_genomic.fna/markers.fasta)
[2024-01-24 11:37:38,547] [INFO] Task started: Blastn
[2024-01-24 11:37:38,547] [INFO] Running command: blastn -query GCF_027587205.1_ASM2758720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83f9d20b-a568-47ec-9dce-b61fd8c933b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_027587205.1_ASM2758720v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:39,628] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:39,635] [INFO] Selected 10 target genomes.
[2024-01-24 11:37:39,635] [INFO] Target genome list was writen to GCF_027587205.1_ASM2758720v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:39,645] [INFO] Task started: fastANI
[2024-01-24 11:37:39,645] [INFO] Running command: fastANI --query /var/lib/cwl/stgb57d6f4e-f241-4008-bdd3-38bd939b5460/GCF_027587205.1_ASM2758720v1_genomic.fna.gz --refList GCF_027587205.1_ASM2758720v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027587205.1_ASM2758720v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:54,863] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:54,877] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:37:54,877] [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_000423665.1	s__Solirubrobacter soli	84.8998	2112	3155	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Solirubrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633755.1	s__Solirubrobacter pauli	81.1876	1486	3155	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Solirubrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344625.1	s__Solirubrobacter sp003344625	81.0296	1491	3155	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Solirubrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425945.1	s__Solirubrobacter sp000425945	80.5865	1334	3155	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Solirubrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016215085.1	s__Baekduia sp016215085	77.3504	601	3155	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268595.1	s__Conexibacter sp018268595	77.2641	651	3155	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016781085.1	s__LC5-1 sp016781085	77.2319	242	3155	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__LC5-1	95.0	99.49	99.49	0.89	0.89	2	-
GCA_017882425.1	s__F1-60-MAGs163 sp017882425	77.0568	473	3155	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__F1-60-MAGs163	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017084525.1	s__Baekduia sp017084525	76.9369	788	3155	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888335.1	s__VAWY01 sp005888335	76.9115	883	3155	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__VAWY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:54,879] [INFO] GTDB search result was written to GCF_027587205.1_ASM2758720v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:54,879] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:54,882] [INFO] DFAST_QC result json was written to GCF_027587205.1_ASM2758720v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:54,882] [INFO] DFAST_QC completed!
[2024-01-24 11:37:54,882] [INFO] Total running time: 0h2m20s