[2024-01-24 12:28:34,797] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:28:34,800] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:28:34,800] [INFO] DQC Reference Directory: /var/lib/cwl/stgbaf58141-3299-42d8-a050-63828d0fced5/dqc_reference
[2024-01-24 12:28:35,991] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:28:35,992] [INFO] Task started: Prodigal
[2024-01-24 12:28:35,992] [INFO] Running command: gunzip -c /var/lib/cwl/stg7cda49c9-3e55-44cc-9fa6-ff3cb8411a9e/GCF_008727875.1_ASM872787v1_genomic.fna.gz | prodigal -d GCF_008727875.1_ASM872787v1_genomic.fna/cds.fna -a GCF_008727875.1_ASM872787v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:17,756] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:17,756] [INFO] Task started: HMMsearch
[2024-01-24 12:29:17,756] [INFO] Running command: hmmsearch --tblout GCF_008727875.1_ASM872787v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbaf58141-3299-42d8-a050-63828d0fced5/dqc_reference/reference_markers.hmm GCF_008727875.1_ASM872787v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:18,122] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:18,124] [INFO] Found 6/6 markers.
[2024-01-24 12:29:18,189] [INFO] Query marker FASTA was written to GCF_008727875.1_ASM872787v1_genomic.fna/markers.fasta
[2024-01-24 12:29:18,189] [INFO] Task started: Blastn
[2024-01-24 12:29:18,190] [INFO] Running command: blastn -query GCF_008727875.1_ASM872787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaf58141-3299-42d8-a050-63828d0fced5/dqc_reference/reference_markers.fasta -out GCF_008727875.1_ASM872787v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:18,811] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:18,817] [INFO] Selected 8 target genomes.
[2024-01-24 12:29:18,817] [INFO] Target genome list was writen to GCF_008727875.1_ASM872787v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:18,831] [INFO] Task started: fastANI
[2024-01-24 12:29:18,831] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cda49c9-3e55-44cc-9fa6-ff3cb8411a9e/GCF_008727875.1_ASM872787v1_genomic.fna.gz --refList GCF_008727875.1_ASM872787v1_genomic.fna/target_genomes.txt --output GCF_008727875.1_ASM872787v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:32,846] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:32,847] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbaf58141-3299-42d8-a050-63828d0fced5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:32,848] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbaf58141-3299-42d8-a050-63828d0fced5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:32,860] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:29:32,860] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:32,860] [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
Larkinella humicola	strain=MA1	GCA_008727875.1	2607654	2607654	type	True	100.0	2608	2608	95	conclusive
Larkinella punicea	strain=ZZJ9	GCA_003334855.1	2315727	2315727	type	True	92.5456	2230	2608	95	below_threshold
Larkinella knui	strain=KCTC42998	GCA_003858645.1	2025310	2025310	type	True	83.3368	1810	2608	95	below_threshold
Larkinella rosea	strain=KCTC52004	GCA_003858635.1	2025312	2025312	type	True	81.7582	1703	2608	95	below_threshold
Larkinella terrae	strain=KCTC 52001	GCA_009668025.1	2025311	2025311	type	True	81.7543	1666	2608	95	below_threshold
Larkinella arboricola	strain=DSM 21851	GCA_003259745.1	643671	643671	type	True	80.0194	1259	2608	95	below_threshold
Spirosoma panaciterrae	strain=DSM 21099	GCA_000374025.1	496058	496058	type	True	76.2363	249	2608	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	75.0833	56	2608	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:32,863] [INFO] DFAST Taxonomy check result was written to GCF_008727875.1_ASM872787v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:32,864] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:32,864] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:32,864] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbaf58141-3299-42d8-a050-63828d0fced5/dqc_reference/checkm_data
[2024-01-24 12:29:32,865] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:32,959] [INFO] Task started: CheckM
[2024-01-24 12:29:32,959] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008727875.1_ASM872787v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008727875.1_ASM872787v1_genomic.fna/checkm_input GCF_008727875.1_ASM872787v1_genomic.fna/checkm_result
[2024-01-24 12:31:23,037] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:23,038] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:23,061] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:23,061] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:23,062] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008727875.1_ASM872787v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:23,062] [INFO] Task started: Blastn
[2024-01-24 12:31:23,062] [INFO] Running command: blastn -query GCF_008727875.1_ASM872787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaf58141-3299-42d8-a050-63828d0fced5/dqc_reference/reference_markers_gtdb.fasta -out GCF_008727875.1_ASM872787v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:23,837] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:23,841] [INFO] Selected 11 target genomes.
[2024-01-24 12:31:23,842] [INFO] Target genome list was writen to GCF_008727875.1_ASM872787v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:23,863] [INFO] Task started: fastANI
[2024-01-24 12:31:23,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cda49c9-3e55-44cc-9fa6-ff3cb8411a9e/GCF_008727875.1_ASM872787v1_genomic.fna.gz --refList GCF_008727875.1_ASM872787v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008727875.1_ASM872787v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:41,744] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:41,757] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:41,757] [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_008727875.1	s__Larkinella sp008727875	100.0	2608	2608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006149005.1	s__Larkinella sp006149005	92.8932	2242	2608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003334855.1	s__Larkinella punicea	92.5456	2230	2608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003858645.1	s__Larkinella knui	83.3453	1808	2608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003858635.1	s__Larkinella rosea	81.7599	1702	2608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009668025.1	s__Larkinella terrae	81.748	1668	2608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366505.1	s__Larkinella sp004366505	80.4297	1372	2608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:41,759] [INFO] GTDB search result was written to GCF_008727875.1_ASM872787v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:41,760] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:41,763] [INFO] DFAST_QC result json was written to GCF_008727875.1_ASM872787v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:41,763] [INFO] DFAST_QC completed!
[2024-01-24 12:31:41,763] [INFO] Total running time: 0h3m7s