[2024-01-25 18:13:20,506] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:13:20,507] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:13:20,507] [INFO] DQC Reference Directory: /var/lib/cwl/stg00892ba1-a61e-4adb-932c-8a448a330870/dqc_reference
[2024-01-25 18:13:21,822] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:13:21,823] [INFO] Task started: Prodigal
[2024-01-25 18:13:21,823] [INFO] Running command: gunzip -c /var/lib/cwl/stg823eca1c-127d-4675-9e13-a181ca5f4735/GCF_024054035.1_ASM2405403v1_genomic.fna.gz | prodigal -d GCF_024054035.1_ASM2405403v1_genomic.fna/cds.fna -a GCF_024054035.1_ASM2405403v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:13:30,321] [INFO] Task succeeded: Prodigal
[2024-01-25 18:13:30,321] [INFO] Task started: HMMsearch
[2024-01-25 18:13:30,321] [INFO] Running command: hmmsearch --tblout GCF_024054035.1_ASM2405403v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00892ba1-a61e-4adb-932c-8a448a330870/dqc_reference/reference_markers.hmm GCF_024054035.1_ASM2405403v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:13:30,525] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:13:30,526] [INFO] Found 6/6 markers.
[2024-01-25 18:13:30,551] [INFO] Query marker FASTA was written to GCF_024054035.1_ASM2405403v1_genomic.fna/markers.fasta
[2024-01-25 18:13:30,552] [INFO] Task started: Blastn
[2024-01-25 18:13:30,552] [INFO] Running command: blastn -query GCF_024054035.1_ASM2405403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00892ba1-a61e-4adb-932c-8a448a330870/dqc_reference/reference_markers.fasta -out GCF_024054035.1_ASM2405403v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:31,206] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:31,209] [INFO] Selected 10 target genomes.
[2024-01-25 18:13:31,209] [INFO] Target genome list was writen to GCF_024054035.1_ASM2405403v1_genomic.fna/target_genomes.txt
[2024-01-25 18:13:31,218] [INFO] Task started: fastANI
[2024-01-25 18:13:31,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg823eca1c-127d-4675-9e13-a181ca5f4735/GCF_024054035.1_ASM2405403v1_genomic.fna.gz --refList GCF_024054035.1_ASM2405403v1_genomic.fna/target_genomes.txt --output GCF_024054035.1_ASM2405403v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:13:38,692] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:38,692] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00892ba1-a61e-4adb-932c-8a448a330870/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:13:38,692] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00892ba1-a61e-4adb-932c-8a448a330870/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:13:38,699] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:13:38,699] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:13:38,700] [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
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	100.0	1062	1064	95	conclusive
Asaia bogorensis	strain=NBRC 16594	GCA_001547995.1	91915	91915	suspected-type	True	83.0388	715	1064	95	below_threshold
Asaia bogorensis	strain=NBRC 16594	GCA_007989265.1	91915	91915	suspected-type	True	82.9077	734	1064	95	below_threshold
Asaia siamensis	strain=CCM 7132	GCA_014635085.1	110479	110479	type	True	81.799	633	1064	95	below_threshold
Asaia platycodi	strain=JCM 25414	GCA_000614545.1	610243	610243	type	True	81.5955	631	1064	95	below_threshold
Asaia astilbis	strain=JCM 15831	GCA_000613845.1	610244	610244	type	True	80.3673	522	1064	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	78.1069	181	1064	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.4506	60	1064	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	76.0499	64	1064	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:13:38,702] [INFO] DFAST Taxonomy check result was written to GCF_024054035.1_ASM2405403v1_genomic.fna/tc_result.tsv
[2024-01-25 18:13:38,702] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:13:38,702] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:13:38,703] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00892ba1-a61e-4adb-932c-8a448a330870/dqc_reference/checkm_data
[2024-01-25 18:13:38,703] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:13:38,737] [INFO] Task started: CheckM
[2024-01-25 18:13:38,737] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024054035.1_ASM2405403v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024054035.1_ASM2405403v1_genomic.fna/checkm_input GCF_024054035.1_ASM2405403v1_genomic.fna/checkm_result
[2024-01-25 18:14:07,667] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:07,668] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:07,705] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:07,705] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:07,706] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024054035.1_ASM2405403v1_genomic.fna/markers.fasta)
[2024-01-25 18:14:07,706] [INFO] Task started: Blastn
[2024-01-25 18:14:07,706] [INFO] Running command: blastn -query GCF_024054035.1_ASM2405403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00892ba1-a61e-4adb-932c-8a448a330870/dqc_reference/reference_markers_gtdb.fasta -out GCF_024054035.1_ASM2405403v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:08,793] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:08,795] [INFO] Selected 13 target genomes.
[2024-01-25 18:14:08,795] [INFO] Target genome list was writen to GCF_024054035.1_ASM2405403v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:08,808] [INFO] Task started: fastANI
[2024-01-25 18:14:08,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg823eca1c-127d-4675-9e13-a181ca5f4735/GCF_024054035.1_ASM2405403v1_genomic.fna.gz --refList GCF_024054035.1_ASM2405403v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024054035.1_ASM2405403v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:14:16,705] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:16,711] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:14:16,711] [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_001547995.1	s__Asaia bogorensis	83.0388	715	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	96.55	95.04	0.93	0.88	6	-
GCF_900465345.1	s__Asaia bogorensis_A	82.8018	676	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003994335.1	s__Asaia sp003994335	82.144	640	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635085.1	s__Asaia siamensis	81.8142	631	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000614545.1	s__Asaia platycodi	81.5961	631	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007988945.1	s__Swaminathania salitolerans	80.6408	493	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Swaminathania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613885.1	s__Asaia prunellae	80.5456	535	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613845.1	s__Asaia astilbis	80.3783	521	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:14:16,712] [INFO] GTDB search result was written to GCF_024054035.1_ASM2405403v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:14:16,713] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:14:16,715] [INFO] DFAST_QC result json was written to GCF_024054035.1_ASM2405403v1_genomic.fna/dqc_result.json
[2024-01-25 18:14:16,715] [INFO] DFAST_QC completed!
[2024-01-25 18:14:16,715] [INFO] Total running time: 0h0m56s