[2024-01-24 13:17:33,392] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:33,396] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:33,396] [INFO] DQC Reference Directory: /var/lib/cwl/stg6275abba-d431-4f0c-a3d8-8c6b883059e2/dqc_reference
[2024-01-24 13:17:34,806] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:34,807] [INFO] Task started: Prodigal
[2024-01-24 13:17:34,807] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf947723-b7fb-4358-b695-3d8eb8716f0e/GCF_003726015.1_ASM372601v1_genomic.fna.gz | prodigal -d GCF_003726015.1_ASM372601v1_genomic.fna/cds.fna -a GCF_003726015.1_ASM372601v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:45,705] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:45,706] [INFO] Task started: HMMsearch
[2024-01-24 13:17:45,706] [INFO] Running command: hmmsearch --tblout GCF_003726015.1_ASM372601v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6275abba-d431-4f0c-a3d8-8c6b883059e2/dqc_reference/reference_markers.hmm GCF_003726015.1_ASM372601v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:45,964] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:45,966] [INFO] Found 6/6 markers.
[2024-01-24 13:17:45,990] [INFO] Query marker FASTA was written to GCF_003726015.1_ASM372601v1_genomic.fna/markers.fasta
[2024-01-24 13:17:45,990] [INFO] Task started: Blastn
[2024-01-24 13:17:45,990] [INFO] Running command: blastn -query GCF_003726015.1_ASM372601v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6275abba-d431-4f0c-a3d8-8c6b883059e2/dqc_reference/reference_markers.fasta -out GCF_003726015.1_ASM372601v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:46,730] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:46,733] [INFO] Selected 5 target genomes.
[2024-01-24 13:17:46,733] [INFO] Target genome list was writen to GCF_003726015.1_ASM372601v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:46,736] [INFO] Task started: fastANI
[2024-01-24 13:17:46,736] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf947723-b7fb-4358-b695-3d8eb8716f0e/GCF_003726015.1_ASM372601v1_genomic.fna.gz --refList GCF_003726015.1_ASM372601v1_genomic.fna/target_genomes.txt --output GCF_003726015.1_ASM372601v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:50,822] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:50,822] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6275abba-d431-4f0c-a3d8-8c6b883059e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:50,823] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6275abba-d431-4f0c-a3d8-8c6b883059e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:50,828] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:17:50,829] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:50,829] [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
Adlercreutzia equolifaciens subsp. celatus	strain=DSM 18785	GCA_003726015.1	394340	446660	type	True	100.0	936	938	95	conclusive
Adlercreutzia equolifaciens subsp. celatus	strain=DSM 18785	GCA_024171685.1	394340	446660	type	True	99.9965	926	938	95	conclusive
Adlercreutzia equolifaciens subsp. celatus	strain=JCM 14811	GCA_016865385.1	394340	446660	type	True	99.9911	936	938	95	conclusive
Adlercreutzia equolifaciens subsp. celatus	strain=JCM 14811	GCA_003428485.1	394340	446660	type	True	99.9592	893	938	95	conclusive
Adlercreutzia equolifaciens subsp. equolifaciens	strain=DSM 19450	GCA_000478885.1	2864143	446660	type	True	96.651	745	938	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:17:50,830] [INFO] DFAST Taxonomy check result was written to GCF_003726015.1_ASM372601v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:50,831] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:50,831] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:50,831] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6275abba-d431-4f0c-a3d8-8c6b883059e2/dqc_reference/checkm_data
[2024-01-24 13:17:50,832] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:50,867] [INFO] Task started: CheckM
[2024-01-24 13:17:50,868] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003726015.1_ASM372601v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003726015.1_ASM372601v1_genomic.fna/checkm_input GCF_003726015.1_ASM372601v1_genomic.fna/checkm_result
[2024-01-24 13:18:26,419] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:26,420] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:26,437] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:26,437] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:26,438] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003726015.1_ASM372601v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:26,438] [INFO] Task started: Blastn
[2024-01-24 13:18:26,438] [INFO] Running command: blastn -query GCF_003726015.1_ASM372601v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6275abba-d431-4f0c-a3d8-8c6b883059e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_003726015.1_ASM372601v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:27,687] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:27,690] [INFO] Selected 8 target genomes.
[2024-01-24 13:18:27,690] [INFO] Target genome list was writen to GCF_003726015.1_ASM372601v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:27,702] [INFO] Task started: fastANI
[2024-01-24 13:18:27,703] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf947723-b7fb-4358-b695-3d8eb8716f0e/GCF_003726015.1_ASM372601v1_genomic.fna.gz --refList GCF_003726015.1_ASM372601v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003726015.1_ASM372601v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:32,916] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:32,923] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:32,924] [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_000478885.1	s__Adlercreutzia equolifaciens	96.6215	746	938	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.05	95.56	0.84	0.79	7	conclusive
GCF_011405655.1	s__Adlercreutzia celatus_A	93.5901	716	938	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	96.32	95.52	0.87	0.80	16	-
GCA_910589165.1	s__Adlercreutzia sp910589165	84.4403	530	938	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008831045.1	s__Adlercreutzia muris	84.3604	554	938	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.80	97.69	0.87	0.84	7	-
GCF_000403355.2	s__Adlercreutzia caecimuris	84.1951	608	938	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.41	97.35	0.86	0.85	5	-
GCF_000422625.1	s__Adlercreutzia mucosicola	83.7794	550	938	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.91	97.91	0.87	0.87	2	-
GCF_013185065.1	s__CAAEEV01 sp013185065	81.1606	312	938	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01	95.0	97.04	97.04	0.76	0.76	2	-
GCF_000210055.1	s__Gordonibacter pamelaeae	80.1104	313	938	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.65	97.59	0.89	0.82	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:32,925] [INFO] GTDB search result was written to GCF_003726015.1_ASM372601v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:32,926] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:32,932] [INFO] DFAST_QC result json was written to GCF_003726015.1_ASM372601v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:32,932] [INFO] DFAST_QC completed!
[2024-01-24 13:18:32,932] [INFO] Total running time: 0h0m60s