[2024-01-24 13:17:26,937] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:26,939] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:26,939] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c41ad64-5af0-4d90-9369-4e732d3b72fc/dqc_reference
[2024-01-24 13:17:28,135] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:28,136] [INFO] Task started: Prodigal
[2024-01-24 13:17:28,136] [INFO] Running command: gunzip -c /var/lib/cwl/stgef98d183-deeb-4b15-bad4-a55a9213bd04/GCF_008365315.1_ASM836531v1_genomic.fna.gz | prodigal -d GCF_008365315.1_ASM836531v1_genomic.fna/cds.fna -a GCF_008365315.1_ASM836531v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:38,324] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:38,324] [INFO] Task started: HMMsearch
[2024-01-24 13:17:38,324] [INFO] Running command: hmmsearch --tblout GCF_008365315.1_ASM836531v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c41ad64-5af0-4d90-9369-4e732d3b72fc/dqc_reference/reference_markers.hmm GCF_008365315.1_ASM836531v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:38,567] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:38,569] [INFO] Found 6/6 markers.
[2024-01-24 13:17:38,597] [INFO] Query marker FASTA was written to GCF_008365315.1_ASM836531v1_genomic.fna/markers.fasta
[2024-01-24 13:17:38,598] [INFO] Task started: Blastn
[2024-01-24 13:17:38,598] [INFO] Running command: blastn -query GCF_008365315.1_ASM836531v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c41ad64-5af0-4d90-9369-4e732d3b72fc/dqc_reference/reference_markers.fasta -out GCF_008365315.1_ASM836531v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:39,300] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:39,303] [INFO] Selected 17 target genomes.
[2024-01-24 13:17:39,303] [INFO] Target genome list was writen to GCF_008365315.1_ASM836531v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:39,318] [INFO] Task started: fastANI
[2024-01-24 13:17:39,319] [INFO] Running command: fastANI --query /var/lib/cwl/stgef98d183-deeb-4b15-bad4-a55a9213bd04/GCF_008365315.1_ASM836531v1_genomic.fna.gz --refList GCF_008365315.1_ASM836531v1_genomic.fna/target_genomes.txt --output GCF_008365315.1_ASM836531v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:48,057] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:48,058] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c41ad64-5af0-4d90-9369-4e732d3b72fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:48,058] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c41ad64-5af0-4d90-9369-4e732d3b72fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:48,071] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:17:48,072] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:17:48,072] [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
Acetobacter fabarum	strain=LMG 24244	GCA_011516925.1	483199	483199	type	True	80.1439	442	1027	95	below_threshold
Acetobacter okinawensis	strain=JCM 25146	GCA_000613865.1	1076594	1076594	type	True	79.9091	407	1027	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	79.8984	461	1027	95	below_threshold
Acetobacter ghanensis	strain=LMG 23848T	GCA_001499675.1	431306	431306	type	True	79.8728	401	1027	95	below_threshold
Acetobacter lovaniensis	strain=LMG 1617	GCA_011516875.1	104100	104100	type	True	79.8015	433	1027	95	below_threshold
Acetobacter ghanensis	strain=LMG 23848	GCA_011516865.1	431306	431306	type	True	79.7149	386	1027	95	below_threshold
Acetobacter peroxydans	strain=LMG 1635	GCA_011516745.1	104098	104098	type	True	79.6347	378	1027	95	below_threshold
Acetobacter peroxydans	strain=NBRC 13755	GCA_006539345.1	104098	104098	type	True	79.6006	393	1027	95	below_threshold
Acetobacter lambici	strain=LMG 27439	GCA_011516885.1	1332824	1332824	type	True	79.3978	403	1027	95	below_threshold
Acetobacter syzygii	strain=9H-2	GCA_000964225.1	146476	146476	type	True	79.0872	342	1027	95	below_threshold
Acetobacter syzygii	strain=NBRC 16604	GCA_007989285.1	146476	146476	type	True	79.0309	338	1027	95	below_threshold
Acetobacter malorum	strain=LMG 1746	GCA_001580615.1	178901	178901	suspected-type	True	78.5179	312	1027	95	below_threshold
Acetobacter cerevisiae	strain=LMG 1625	GCA_001580535.1	178900	178900	type	True	78.1975	328	1027	95	below_threshold
Asaia prunellae	strain=JCM 25354	GCA_000613885.1	610245	610245	type	True	76.8356	83	1027	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:48,074] [INFO] DFAST Taxonomy check result was written to GCF_008365315.1_ASM836531v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:48,074] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:48,074] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:48,074] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c41ad64-5af0-4d90-9369-4e732d3b72fc/dqc_reference/checkm_data
[2024-01-24 13:17:48,075] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:48,113] [INFO] Task started: CheckM
[2024-01-24 13:17:48,113] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008365315.1_ASM836531v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008365315.1_ASM836531v1_genomic.fna/checkm_input GCF_008365315.1_ASM836531v1_genomic.fna/checkm_result
[2024-01-24 13:18:22,014] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:22,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:22,034] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:22,034] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:22,035] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008365315.1_ASM836531v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:22,035] [INFO] Task started: Blastn
[2024-01-24 13:18:22,035] [INFO] Running command: blastn -query GCF_008365315.1_ASM836531v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c41ad64-5af0-4d90-9369-4e732d3b72fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_008365315.1_ASM836531v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:23,243] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:23,245] [INFO] Selected 16 target genomes.
[2024-01-24 13:18:23,246] [INFO] Target genome list was writen to GCF_008365315.1_ASM836531v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:23,278] [INFO] Task started: fastANI
[2024-01-24 13:18:23,278] [INFO] Running command: fastANI --query /var/lib/cwl/stgef98d183-deeb-4b15-bad4-a55a9213bd04/GCF_008365315.1_ASM836531v1_genomic.fna.gz --refList GCF_008365315.1_ASM836531v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008365315.1_ASM836531v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:33,575] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:33,587] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:33,587] [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_008365315.1	s__Acetobacter sp008365315	100.0	1026	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011516925.1	s__Acetobacter fabarum	80.1513	441	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.96	97.82	0.89	0.87	4	-
GCF_017377745.1	s__Acetobacter suratthaniensis	80.0016	435	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499675.1	s__Acetobacter ghanensis	79.9356	404	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017377735.1	s__Acetobacter sp017377735	79.9165	459	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613865.1	s__Acetobacter okinawensis	79.9091	407	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.60	97.58	0.84	0.82	3	-
GCF_014207635.1	s__Acetobacter lovaniensis	79.7686	436	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002153655.1	s__Acetobacter okinawensis_A	79.6142	395	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539345.1	s__Acetobacter peroxydans	79.6023	392	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_011516885.1	s__Acetobacter lambici	79.4041	402	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964225.1	s__Acetobacter syzygii	79.0872	342	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.87	98.22	0.97	0.90	7	-
GCF_002153605.1	s__Acetobacter malorum_A	78.7772	301	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.53	96.53	0.89	0.89	2	-
GCF_001580615.1	s__Acetobacter malorum	78.5182	311	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	95.98	95.83	0.82	0.80	5	-
GCF_001580535.1	s__Acetobacter cerevisiae	78.2132	329	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.52	96.47	0.88	0.86	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:33,596] [INFO] GTDB search result was written to GCF_008365315.1_ASM836531v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:33,597] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:33,602] [INFO] DFAST_QC result json was written to GCF_008365315.1_ASM836531v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:33,603] [INFO] DFAST_QC completed!
[2024-01-24 13:18:33,603] [INFO] Total running time: 0h1m7s