[2024-01-25 19:47:05,552] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:05,553] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:05,553] [INFO] DQC Reference Directory: /var/lib/cwl/stg44aa99d8-3302-479b-9607-33506af61da7/dqc_reference
[2024-01-25 19:47:06,724] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:06,732] [INFO] Task started: Prodigal
[2024-01-25 19:47:06,732] [INFO] Running command: gunzip -c /var/lib/cwl/stgb46d4e36-2725-421d-95ca-0871bcee0b2e/GCF_014197205.1_ASM1419720v1_genomic.fna.gz | prodigal -d GCF_014197205.1_ASM1419720v1_genomic.fna/cds.fna -a GCF_014197205.1_ASM1419720v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:10,954] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:10,955] [INFO] Task started: HMMsearch
[2024-01-25 19:47:10,955] [INFO] Running command: hmmsearch --tblout GCF_014197205.1_ASM1419720v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44aa99d8-3302-479b-9607-33506af61da7/dqc_reference/reference_markers.hmm GCF_014197205.1_ASM1419720v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:11,164] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:11,165] [INFO] Found 6/6 markers.
[2024-01-25 19:47:11,188] [INFO] Query marker FASTA was written to GCF_014197205.1_ASM1419720v1_genomic.fna/markers.fasta
[2024-01-25 19:47:11,188] [INFO] Task started: Blastn
[2024-01-25 19:47:11,188] [INFO] Running command: blastn -query GCF_014197205.1_ASM1419720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44aa99d8-3302-479b-9607-33506af61da7/dqc_reference/reference_markers.fasta -out GCF_014197205.1_ASM1419720v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:11,745] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:11,747] [INFO] Selected 27 target genomes.
[2024-01-25 19:47:11,747] [INFO] Target genome list was writen to GCF_014197205.1_ASM1419720v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:11,789] [INFO] Task started: fastANI
[2024-01-25 19:47:11,790] [INFO] Running command: fastANI --query /var/lib/cwl/stgb46d4e36-2725-421d-95ca-0871bcee0b2e/GCF_014197205.1_ASM1419720v1_genomic.fna.gz --refList GCF_014197205.1_ASM1419720v1_genomic.fna/target_genomes.txt --output GCF_014197205.1_ASM1419720v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:25,973] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:25,973] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44aa99d8-3302-479b-9607-33506af61da7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:25,973] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44aa99d8-3302-479b-9607-33506af61da7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:25,977] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:47:25,978] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:47:25,978] [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
Canibacter oris	strain=DSM 27064	GCA_014197205.1	1365628	1365628	type	True	100.0	535	540	95	conclusive
Leucobacter muris	strain=DSM 101948	GCA_004028235.1	1935379	1935379	type	True	77.2087	60	540	95	below_threshold
Leucobacter chironomi	strain=DSM 19883	GCA_000421845.1	491918	491918	type	True	76.8086	61	540	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:25,982] [INFO] DFAST Taxonomy check result was written to GCF_014197205.1_ASM1419720v1_genomic.fna/tc_result.tsv
[2024-01-25 19:47:25,982] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:25,982] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:25,982] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44aa99d8-3302-479b-9607-33506af61da7/dqc_reference/checkm_data
[2024-01-25 19:47:25,983] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:26,007] [INFO] Task started: CheckM
[2024-01-25 19:47:26,007] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014197205.1_ASM1419720v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014197205.1_ASM1419720v1_genomic.fna/checkm_input GCF_014197205.1_ASM1419720v1_genomic.fna/checkm_result
[2024-01-25 19:47:43,475] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:43,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:43,493] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:43,493] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:43,493] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014197205.1_ASM1419720v1_genomic.fna/markers.fasta)
[2024-01-25 19:47:43,493] [INFO] Task started: Blastn
[2024-01-25 19:47:43,494] [INFO] Running command: blastn -query GCF_014197205.1_ASM1419720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44aa99d8-3302-479b-9607-33506af61da7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014197205.1_ASM1419720v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:44,280] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:44,282] [INFO] Selected 26 target genomes.
[2024-01-25 19:47:44,282] [INFO] Target genome list was writen to GCF_014197205.1_ASM1419720v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:44,306] [INFO] Task started: fastANI
[2024-01-25 19:47:44,306] [INFO] Running command: fastANI --query /var/lib/cwl/stgb46d4e36-2725-421d-95ca-0871bcee0b2e/GCF_014197205.1_ASM1419720v1_genomic.fna.gz --refList GCF_014197205.1_ASM1419720v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014197205.1_ASM1419720v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:47:56,057] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:56,062] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:47:56,063] [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_014197205.1	s__Canibacter oris	100.0	534	540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Canibacter	95.0	98.44	98.44	0.92	0.92	2	conclusive
GCF_011752015.1	s__Canibacter sp011752015	78.1648	81	540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Canibacter	95.0	98.76	98.76	0.97	0.97	2	-
GCF_003859945.1	s__Canibacter sp003859945	77.9474	102	540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Canibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004028235.1	s__Leucobacter muris	77.6003	62	540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.77	98.77	0.90	0.90	2	-
GCF_000421845.1	s__Leucobacter chironomi	77.3386	62	540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531145.1	s__Canibacter sp018531145	76.9328	57	540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Canibacter	95.0	99.13	99.13	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:47:56,064] [INFO] GTDB search result was written to GCF_014197205.1_ASM1419720v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:47:56,064] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:47:56,066] [INFO] DFAST_QC result json was written to GCF_014197205.1_ASM1419720v1_genomic.fna/dqc_result.json
[2024-01-25 19:47:56,066] [INFO] DFAST_QC completed!
[2024-01-25 19:47:56,066] [INFO] Total running time: 0h0m51s