[2023-06-30 00:38:45,058] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:38:45,060] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:38:45,060] [INFO] DQC Reference Directory: /var/lib/cwl/stg11583752-7471-45b4-a1d0-56f65996edbf/dqc_reference
[2023-06-30 00:38:46,266] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:38:46,267] [INFO] Task started: Prodigal
[2023-06-30 00:38:46,267] [INFO] Running command: gunzip -c /var/lib/cwl/stg10198e69-eb08-45e1-9ad7-985d33ee592e/GCA_024227135.1_ASM2422713v1_genomic.fna.gz | prodigal -d GCA_024227135.1_ASM2422713v1_genomic.fna/cds.fna -a GCA_024227135.1_ASM2422713v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:39:00,881] [INFO] Task succeeded: Prodigal
[2023-06-30 00:39:00,881] [INFO] Task started: HMMsearch
[2023-06-30 00:39:00,881] [INFO] Running command: hmmsearch --tblout GCA_024227135.1_ASM2422713v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11583752-7471-45b4-a1d0-56f65996edbf/dqc_reference/reference_markers.hmm GCA_024227135.1_ASM2422713v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:39:01,118] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:39:01,120] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg10198e69-eb08-45e1-9ad7-985d33ee592e/GCA_024227135.1_ASM2422713v1_genomic.fna.gz]
[2023-06-30 00:39:01,162] [INFO] Query marker FASTA was written to GCA_024227135.1_ASM2422713v1_genomic.fna/markers.fasta
[2023-06-30 00:39:01,163] [INFO] Task started: Blastn
[2023-06-30 00:39:01,163] [INFO] Running command: blastn -query GCA_024227135.1_ASM2422713v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11583752-7471-45b4-a1d0-56f65996edbf/dqc_reference/reference_markers.fasta -out GCA_024227135.1_ASM2422713v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:39:01,776] [INFO] Task succeeded: Blastn
[2023-06-30 00:39:01,780] [INFO] Selected 27 target genomes.
[2023-06-30 00:39:01,780] [INFO] Target genome list was writen to GCA_024227135.1_ASM2422713v1_genomic.fna/target_genomes.txt
[2023-06-30 00:39:01,784] [INFO] Task started: fastANI
[2023-06-30 00:39:01,784] [INFO] Running command: fastANI --query /var/lib/cwl/stg10198e69-eb08-45e1-9ad7-985d33ee592e/GCA_024227135.1_ASM2422713v1_genomic.fna.gz --refList GCA_024227135.1_ASM2422713v1_genomic.fna/target_genomes.txt --output GCA_024227135.1_ASM2422713v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:39:17,642] [INFO] Task succeeded: fastANI
[2023-06-30 00:39:17,642] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11583752-7471-45b4-a1d0-56f65996edbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:39:17,643] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11583752-7471-45b4-a1d0-56f65996edbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:39:17,647] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:39:17,647] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 00:39:17,647] [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
Sedimenticola thiotaurini	strain=SIP-G1	GCA_001007875.1	1543721	1543721	type	True	75.8448	92	1643	95	below_threshold
Sedimenticola selenatireducens	strain=DSM 17993	GCA_000428045.1	191960	191960	type	True	75.706	85	1643	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 00:39:17,649] [INFO] DFAST Taxonomy check result was written to GCA_024227135.1_ASM2422713v1_genomic.fna/tc_result.tsv
[2023-06-30 00:39:17,650] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:39:17,650] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:39:17,650] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11583752-7471-45b4-a1d0-56f65996edbf/dqc_reference/checkm_data
[2023-06-30 00:39:17,652] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:39:17,710] [INFO] Task started: CheckM
[2023-06-30 00:39:17,711] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024227135.1_ASM2422713v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024227135.1_ASM2422713v1_genomic.fna/checkm_input GCA_024227135.1_ASM2422713v1_genomic.fna/checkm_result
[2023-06-30 00:40:02,889] [INFO] Task succeeded: CheckM
[2023-06-30 00:40:02,890] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 00:40:02,911] [INFO] ===== Completeness check finished =====
[2023-06-30 00:40:02,911] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:40:02,912] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024227135.1_ASM2422713v1_genomic.fna/markers.fasta)
[2023-06-30 00:40:02,912] [INFO] Task started: Blastn
[2023-06-30 00:40:02,912] [INFO] Running command: blastn -query GCA_024227135.1_ASM2422713v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11583752-7471-45b4-a1d0-56f65996edbf/dqc_reference/reference_markers_gtdb.fasta -out GCA_024227135.1_ASM2422713v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:40:03,738] [INFO] Task succeeded: Blastn
[2023-06-30 00:40:03,741] [INFO] Selected 24 target genomes.
[2023-06-30 00:40:03,741] [INFO] Target genome list was writen to GCA_024227135.1_ASM2422713v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:40:03,748] [INFO] Task started: fastANI
[2023-06-30 00:40:03,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg10198e69-eb08-45e1-9ad7-985d33ee592e/GCA_024227135.1_ASM2422713v1_genomic.fna.gz --refList GCA_024227135.1_ASM2422713v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024227135.1_ASM2422713v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:40:15,973] [INFO] Task succeeded: fastANI
[2023-06-30 00:40:15,981] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 00:40:15,981] [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_002020805.1	s__GCF-002020805 sp002020805	75.9403	61	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__GCF-002020805	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003062205.1	s__Sedimenticola_A endophacoides	75.9328	59	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola_A	95.0	99.88	99.76	0.97	0.95	6	-
GCA_011051715.1	s__HyVt-443 sp011051715	75.8859	93	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__HyVt-443	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001007875.1	s__Sedimenticola thiotaurini	75.8448	92	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007713595.1	s__Sedimenticola thiotaurini_A	75.732	50	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428045.1	s__Sedimenticola selenatireducens	75.7059	87	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola	95.0	98.15	98.15	0.90	0.90	2	-
GCA_002869585.1	s__BM503 sp002869585	75.704	54	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__BM503	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 00:40:15,983] [INFO] GTDB search result was written to GCA_024227135.1_ASM2422713v1_genomic.fna/result_gtdb.tsv
[2023-06-30 00:40:15,984] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:40:15,986] [INFO] DFAST_QC result json was written to GCA_024227135.1_ASM2422713v1_genomic.fna/dqc_result.json
[2023-06-30 00:40:15,986] [INFO] DFAST_QC completed!
[2023-06-30 00:40:15,987] [INFO] Total running time: 0h1m31s