[2024-01-24 11:51:36,751] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:36,753] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:36,753] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d516df9-bd95-4cc7-a739-ab4a685eeef1/dqc_reference
[2024-01-24 11:51:38,014] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:38,015] [INFO] Task started: Prodigal
[2024-01-24 11:51:38,016] [INFO] Running command: gunzip -c /var/lib/cwl/stg741f8401-9d0b-4d32-a872-b5e23f364c65/GCF_022655595.1_ASM2265559v1_genomic.fna.gz | prodigal -d GCF_022655595.1_ASM2265559v1_genomic.fna/cds.fna -a GCF_022655595.1_ASM2265559v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:44,056] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:44,056] [INFO] Task started: HMMsearch
[2024-01-24 11:51:44,056] [INFO] Running command: hmmsearch --tblout GCF_022655595.1_ASM2265559v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d516df9-bd95-4cc7-a739-ab4a685eeef1/dqc_reference/reference_markers.hmm GCF_022655595.1_ASM2265559v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:44,316] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:44,317] [INFO] Found 6/6 markers.
[2024-01-24 11:51:44,348] [INFO] Query marker FASTA was written to GCF_022655595.1_ASM2265559v1_genomic.fna/markers.fasta
[2024-01-24 11:51:44,349] [INFO] Task started: Blastn
[2024-01-24 11:51:44,349] [INFO] Running command: blastn -query GCF_022655595.1_ASM2265559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d516df9-bd95-4cc7-a739-ab4a685eeef1/dqc_reference/reference_markers.fasta -out GCF_022655595.1_ASM2265559v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:44,987] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:44,991] [INFO] Selected 20 target genomes.
[2024-01-24 11:51:44,992] [INFO] Target genome list was writen to GCF_022655595.1_ASM2265559v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:45,022] [INFO] Task started: fastANI
[2024-01-24 11:51:45,023] [INFO] Running command: fastANI --query /var/lib/cwl/stg741f8401-9d0b-4d32-a872-b5e23f364c65/GCF_022655595.1_ASM2265559v1_genomic.fna.gz --refList GCF_022655595.1_ASM2265559v1_genomic.fna/target_genomes.txt --output GCF_022655595.1_ASM2265559v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:53,875] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:53,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d516df9-bd95-4cc7-a739-ab4a685eeef1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:53,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d516df9-bd95-4cc7-a739-ab4a685eeef1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:53,887] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:51:53,887] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:51:53,887] [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
Ignatzschineria indica	strain=KCTC 22643	GCA_003121925.1	472583	472583	type	True	78.9128	267	1024	95	below_threshold
Ignatzschineria cameli	strain=UAE-HKU57	GCA_003121895.1	2182793	2182793	type	True	78.7083	276	1024	95	below_threshold
Ignatzschineria indica	strain=KCTC 22643	GCA_014652015.1	472583	472583	type	True	78.708	258	1024	95	below_threshold
Ignatzschineria larvae	strain=DSM 13226	GCA_000510805.1	112009	112009	type	True	78.6411	233	1024	95	below_threshold
Ignatzschineria ureiclastica	strain=KCTC 22644	GCA_003121845.1	472582	472582	type	True	78.4169	259	1024	95	below_threshold
Ignatzschineria ureiclastica	strain=KCTC 22644	GCA_014652035.1	472582	472582	type	True	78.3422	255	1024	95	below_threshold
Wohlfahrtiimonas populi	strain=34C10-3-10	GCA_002006795.1	1940240	1940240	type	True	76.3313	58	1024	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:53,889] [INFO] DFAST Taxonomy check result was written to GCF_022655595.1_ASM2265559v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:53,891] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:53,891] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:53,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d516df9-bd95-4cc7-a739-ab4a685eeef1/dqc_reference/checkm_data
[2024-01-24 11:51:53,892] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:53,928] [INFO] Task started: CheckM
[2024-01-24 11:51:53,928] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022655595.1_ASM2265559v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022655595.1_ASM2265559v1_genomic.fna/checkm_input GCF_022655595.1_ASM2265559v1_genomic.fna/checkm_result
[2024-01-24 11:52:18,325] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:18,327] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:18,348] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:18,348] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:18,349] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022655595.1_ASM2265559v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:18,349] [INFO] Task started: Blastn
[2024-01-24 11:52:18,349] [INFO] Running command: blastn -query GCF_022655595.1_ASM2265559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d516df9-bd95-4cc7-a739-ab4a685eeef1/dqc_reference/reference_markers_gtdb.fasta -out GCF_022655595.1_ASM2265559v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:19,350] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:19,354] [INFO] Selected 21 target genomes.
[2024-01-24 11:52:19,354] [INFO] Target genome list was writen to GCF_022655595.1_ASM2265559v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:19,371] [INFO] Task started: fastANI
[2024-01-24 11:52:19,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg741f8401-9d0b-4d32-a872-b5e23f364c65/GCF_022655595.1_ASM2265559v1_genomic.fna.gz --refList GCF_022655595.1_ASM2265559v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022655595.1_ASM2265559v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:29,996] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:30,007] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:52:30,007] [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
GCA_019113305.1	s__Ignatzschineria merdigallinarum	81.4318	450	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Ignatzschineria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121925.1	s__Ignatzschineria indica	78.8969	268	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Ignatzschineria	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002252045.1	s__Ignatzschineria sp002252045	78.8547	269	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Ignatzschineria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121895.1	s__Ignatzschineria cameli	78.716	275	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Ignatzschineria	95.0	99.12	98.86	0.95	0.93	5	-
GCF_000510805.1	s__Ignatzschineria larvae	78.648	232	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Ignatzschineria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121845.1	s__Ignatzschineria ureiclastica	78.431	257	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Ignatzschineria	95.0	100.00	100.00	1.00	1.00	2	-
GCA_012513365.1	s__JAAZCI01 sp012513365	77.2359	76	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__JAAZCI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002006795.1	s__Wohlfahrtiimonas populi	76.3173	57	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Wohlfahrtiimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:30,008] [INFO] GTDB search result was written to GCF_022655595.1_ASM2265559v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:30,009] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:30,011] [INFO] DFAST_QC result json was written to GCF_022655595.1_ASM2265559v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:30,011] [INFO] DFAST_QC completed!
[2024-01-24 11:52:30,011] [INFO] Total running time: 0h0m53s