[2024-01-25 19:42:20,614] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:42:20,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:42:20,616] [INFO] DQC Reference Directory: /var/lib/cwl/stg83bca793-0c24-4a3e-ba7d-6bd8dfdb87ee/dqc_reference
[2024-01-25 19:42:21,830] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:42:21,836] [INFO] Task started: Prodigal
[2024-01-25 19:42:21,837] [INFO] Running command: gunzip -c /var/lib/cwl/stge92e54a6-987b-46b6-8365-bb3bf26c9eda/GCF_016908775.1_ASM1690877v1_genomic.fna.gz | prodigal -d GCF_016908775.1_ASM1690877v1_genomic.fna/cds.fna -a GCF_016908775.1_ASM1690877v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:42:27,466] [INFO] Task succeeded: Prodigal
[2024-01-25 19:42:27,466] [INFO] Task started: HMMsearch
[2024-01-25 19:42:27,466] [INFO] Running command: hmmsearch --tblout GCF_016908775.1_ASM1690877v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83bca793-0c24-4a3e-ba7d-6bd8dfdb87ee/dqc_reference/reference_markers.hmm GCF_016908775.1_ASM1690877v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:42:27,752] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:42:27,753] [INFO] Found 6/6 markers.
[2024-01-25 19:42:27,783] [INFO] Query marker FASTA was written to GCF_016908775.1_ASM1690877v1_genomic.fna/markers.fasta
[2024-01-25 19:42:27,784] [INFO] Task started: Blastn
[2024-01-25 19:42:27,784] [INFO] Running command: blastn -query GCF_016908775.1_ASM1690877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83bca793-0c24-4a3e-ba7d-6bd8dfdb87ee/dqc_reference/reference_markers.fasta -out GCF_016908775.1_ASM1690877v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:28,360] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:28,364] [INFO] Selected 18 target genomes.
[2024-01-25 19:42:28,364] [INFO] Target genome list was writen to GCF_016908775.1_ASM1690877v1_genomic.fna/target_genomes.txt
[2024-01-25 19:42:28,390] [INFO] Task started: fastANI
[2024-01-25 19:42:28,391] [INFO] Running command: fastANI --query /var/lib/cwl/stge92e54a6-987b-46b6-8365-bb3bf26c9eda/GCF_016908775.1_ASM1690877v1_genomic.fna.gz --refList GCF_016908775.1_ASM1690877v1_genomic.fna/target_genomes.txt --output GCF_016908775.1_ASM1690877v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:42:38,468] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:38,468] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83bca793-0c24-4a3e-ba7d-6bd8dfdb87ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:42:38,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83bca793-0c24-4a3e-ba7d-6bd8dfdb87ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:42:38,472] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:42:38,472] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:42:38,472] [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
Defluviitalea raffinosedens	strain=DSM 28090	GCA_016908775.1	1450156	1450156	type	True	100.0	1037	1039	95	conclusive
Defluviitalea phaphyphila	strain=Alg1	GCA_001466305.1	1473580	1473580	type	True	77.8849	251	1039	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:42:38,474] [INFO] DFAST Taxonomy check result was written to GCF_016908775.1_ASM1690877v1_genomic.fna/tc_result.tsv
[2024-01-25 19:42:38,475] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:42:38,475] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:42:38,475] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83bca793-0c24-4a3e-ba7d-6bd8dfdb87ee/dqc_reference/checkm_data
[2024-01-25 19:42:38,476] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:42:38,509] [INFO] Task started: CheckM
[2024-01-25 19:42:38,509] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016908775.1_ASM1690877v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016908775.1_ASM1690877v1_genomic.fna/checkm_input GCF_016908775.1_ASM1690877v1_genomic.fna/checkm_result
[2024-01-25 19:43:00,510] [INFO] Task succeeded: CheckM
[2024-01-25 19:43:00,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:43:00,535] [INFO] ===== Completeness check finished =====
[2024-01-25 19:43:00,536] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:43:00,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016908775.1_ASM1690877v1_genomic.fna/markers.fasta)
[2024-01-25 19:43:00,536] [INFO] Task started: Blastn
[2024-01-25 19:43:00,536] [INFO] Running command: blastn -query GCF_016908775.1_ASM1690877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83bca793-0c24-4a3e-ba7d-6bd8dfdb87ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_016908775.1_ASM1690877v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:01,299] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:01,302] [INFO] Selected 13 target genomes.
[2024-01-25 19:43:01,302] [INFO] Target genome list was writen to GCF_016908775.1_ASM1690877v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:43:01,313] [INFO] Task started: fastANI
[2024-01-25 19:43:01,313] [INFO] Running command: fastANI --query /var/lib/cwl/stge92e54a6-987b-46b6-8365-bb3bf26c9eda/GCF_016908775.1_ASM1690877v1_genomic.fna.gz --refList GCF_016908775.1_ASM1690877v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016908775.1_ASM1690877v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:43:08,604] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:08,609] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:43:08,610] [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_016908775.1	s__Defluviitalea_A raffinosedens	100.0	1037	1039	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Defluviitaleaceae;g__Defluviitalea_A	95.0	99.48	99.46	0.95	0.94	3	conclusive
GCA_012519955.1	s__Defluviitalea_A sp012519955	84.2659	603	1039	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Defluviitaleaceae;g__Defluviitalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012521175.1	s__Defluviitalea_A sp012521175	83.0483	499	1039	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Defluviitaleaceae;g__Defluviitalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001466305.1	s__Defluviitalea phaphyphila	77.9036	249	1039	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Defluviitaleaceae;g__Defluviitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012519205.1	s__JAAYQR01 sp012519205	77.4029	170	1039	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Defluviitaleaceae;g__JAAYQR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012521395.1	s__JAAYML01 sp012521395	77.3089	159	1039	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Defluviitaleaceae;g__JAAYML01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012518815.1	s__JAAYML01 sp012518815	77.0814	171	1039	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Defluviitaleaceae;g__JAAYML01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:43:08,611] [INFO] GTDB search result was written to GCF_016908775.1_ASM1690877v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:43:08,611] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:43:08,613] [INFO] DFAST_QC result json was written to GCF_016908775.1_ASM1690877v1_genomic.fna/dqc_result.json
[2024-01-25 19:43:08,614] [INFO] DFAST_QC completed!
[2024-01-25 19:43:08,614] [INFO] Total running time: 0h0m48s