[2024-01-24 13:28:44,380] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:44,382] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:44,382] [INFO] DQC Reference Directory: /var/lib/cwl/stg0840c132-c720-4177-95dd-da6751d2174d/dqc_reference
[2024-01-24 13:28:45,638] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:45,639] [INFO] Task started: Prodigal
[2024-01-24 13:28:45,640] [INFO] Running command: gunzip -c /var/lib/cwl/stgdcfb0a9b-beee-4a8b-ada8-4168da775d92/GCF_000427965.1_ASM42796v1_genomic.fna.gz | prodigal -d GCF_000427965.1_ASM42796v1_genomic.fna/cds.fna -a GCF_000427965.1_ASM42796v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:29:12,677] [INFO] Task succeeded: Prodigal
[2024-01-24 13:29:12,677] [INFO] Task started: HMMsearch
[2024-01-24 13:29:12,677] [INFO] Running command: hmmsearch --tblout GCF_000427965.1_ASM42796v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0840c132-c720-4177-95dd-da6751d2174d/dqc_reference/reference_markers.hmm GCF_000427965.1_ASM42796v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:29:13,020] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:29:13,022] [INFO] Found 6/6 markers.
[2024-01-24 13:29:13,076] [INFO] Query marker FASTA was written to GCF_000427965.1_ASM42796v1_genomic.fna/markers.fasta
[2024-01-24 13:29:13,076] [INFO] Task started: Blastn
[2024-01-24 13:29:13,076] [INFO] Running command: blastn -query GCF_000427965.1_ASM42796v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0840c132-c720-4177-95dd-da6751d2174d/dqc_reference/reference_markers.fasta -out GCF_000427965.1_ASM42796v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:13,684] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:13,691] [INFO] Selected 21 target genomes.
[2024-01-24 13:29:13,691] [INFO] Target genome list was writen to GCF_000427965.1_ASM42796v1_genomic.fna/target_genomes.txt
[2024-01-24 13:29:13,705] [INFO] Task started: fastANI
[2024-01-24 13:29:13,706] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcfb0a9b-beee-4a8b-ada8-4168da775d92/GCF_000427965.1_ASM42796v1_genomic.fna.gz --refList GCF_000427965.1_ASM42796v1_genomic.fna/target_genomes.txt --output GCF_000427965.1_ASM42796v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:30,161] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:30,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0840c132-c720-4177-95dd-da6751d2174d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:30,163] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0840c132-c720-4177-95dd-da6751d2174d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:30,174] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:29:30,174] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:30,175] [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
Olivibacter sitiensis	strain=DSM 17696	GCA_000427965.1	376470	376470	type	True	100.0	1621	1629	95	conclusive
Sphingobacterium lactis	strain=DSM 22361	GCA_011046555.1	797291	797291	type	True	78.3487	50	1629	95	below_threshold
Sphingobacterium lactis	strain=DSM 22361	GCA_900107985.1	797291	797291	type	True	78.1786	53	1629	95	below_threshold
Olivibacter domesticus	strain=DSM 18733	GCA_900109575.1	407022	407022	type	True	76.9253	85	1629	95	below_threshold
Parapedobacter luteus	strain=DSM 22899	GCA_900168055.1	623280	623280	type	True	76.7082	60	1629	95	below_threshold
Parapedobacter koreensis	strain=Jip14	GCA_900109365.1	332977	332977	type	True	76.5368	83	1629	95	below_threshold
Parapedobacter indicus	strain=RK1	GCA_002934635.1	1477437	1477437	type	True	76.2441	58	1629	95	below_threshold
Parapedobacter indicus	strain=RK1	GCA_900113765.1	1477437	1477437	type	True	76.1825	60	1629	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:30,179] [INFO] DFAST Taxonomy check result was written to GCF_000427965.1_ASM42796v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:30,180] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:30,180] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:30,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0840c132-c720-4177-95dd-da6751d2174d/dqc_reference/checkm_data
[2024-01-24 13:29:30,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:30,239] [INFO] Task started: CheckM
[2024-01-24 13:29:30,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000427965.1_ASM42796v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000427965.1_ASM42796v1_genomic.fna/checkm_input GCF_000427965.1_ASM42796v1_genomic.fna/checkm_result
[2024-01-24 13:30:45,734] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:45,735] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:45,758] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:45,758] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:45,759] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000427965.1_ASM42796v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:45,759] [INFO] Task started: Blastn
[2024-01-24 13:30:45,759] [INFO] Running command: blastn -query GCF_000427965.1_ASM42796v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0840c132-c720-4177-95dd-da6751d2174d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000427965.1_ASM42796v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:46,543] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:46,547] [INFO] Selected 26 target genomes.
[2024-01-24 13:30:46,548] [INFO] Target genome list was writen to GCF_000427965.1_ASM42796v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:46,594] [INFO] Task started: fastANI
[2024-01-24 13:30:46,595] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcfb0a9b-beee-4a8b-ada8-4168da775d92/GCF_000427965.1_ASM42796v1_genomic.fna.gz --refList GCF_000427965.1_ASM42796v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000427965.1_ASM42796v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:10,251] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:10,262] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:31:10,262] [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_000427965.1	s__Olivibacter sitiensis	100.0	1621	1629	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Olivibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004368405.1	s__Pseudosphingobacterium sp004368405	78.8625	109	1629	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pseudosphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011046555.1	s__Sphingobacterium lactis	78.2414	51	1629	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014334135.1	s__Pseudosphingobacterium sp014334135	77.3622	102	1629	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pseudosphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000192845.1	s__Pseudosphingobacterium jilunii	77.3327	96	1629	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pseudosphingobacterium	95.0	98.40	98.36	0.86	0.86	3	-
GCF_011030405.1	s__Sphingobacterium sp011030405	77.1963	57	1629	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109575.1	s__Pseudosphingobacterium domesticum	76.8972	84	1629	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pseudosphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168055.1	s__Parapedobacter luteus	76.7046	59	1629	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Parapedobacter	95.0	99.02	99.02	0.90	0.90	2	-
GCF_900113765.1	s__Parapedobacter indicus	76.1723	59	1629	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Parapedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004364125.1	s__Sphingobacterium paludis	76.0254	50	1629	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:31:10,264] [INFO] GTDB search result was written to GCF_000427965.1_ASM42796v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:10,266] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:10,269] [INFO] DFAST_QC result json was written to GCF_000427965.1_ASM42796v1_genomic.fna/dqc_result.json
[2024-01-24 13:31:10,270] [INFO] DFAST_QC completed!
[2024-01-24 13:31:10,270] [INFO] Total running time: 0h2m26s