[2023-06-13 10:49:25,609] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:49:25,611] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:49:25,611] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d3c3cb7-4074-422f-a8e0-02878829640d/dqc_reference
[2023-06-13 10:49:26,793] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:49:26,794] [INFO] Task started: Prodigal
[2023-06-13 10:49:26,795] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d152d44-43fc-4c60-97e2-32dae6e7eed0/GCA_022646045.1_ASM2264604v1_genomic.fna.gz | prodigal -d GCA_022646045.1_ASM2264604v1_genomic.fna/cds.fna -a GCA_022646045.1_ASM2264604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:49:33,885] [INFO] Task succeeded: Prodigal
[2023-06-13 10:49:33,886] [INFO] Task started: HMMsearch
[2023-06-13 10:49:33,886] [INFO] Running command: hmmsearch --tblout GCA_022646045.1_ASM2264604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d3c3cb7-4074-422f-a8e0-02878829640d/dqc_reference/reference_markers.hmm GCA_022646045.1_ASM2264604v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:49:34,121] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:49:34,123] [INFO] Found 6/6 markers.
[2023-06-13 10:49:34,148] [INFO] Query marker FASTA was written to GCA_022646045.1_ASM2264604v1_genomic.fna/markers.fasta
[2023-06-13 10:49:34,149] [INFO] Task started: Blastn
[2023-06-13 10:49:34,149] [INFO] Running command: blastn -query GCA_022646045.1_ASM2264604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d3c3cb7-4074-422f-a8e0-02878829640d/dqc_reference/reference_markers.fasta -out GCA_022646045.1_ASM2264604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:49:34,915] [INFO] Task succeeded: Blastn
[2023-06-13 10:49:34,919] [INFO] Selected 19 target genomes.
[2023-06-13 10:49:34,920] [INFO] Target genome list was writen to GCA_022646045.1_ASM2264604v1_genomic.fna/target_genomes.txt
[2023-06-13 10:49:34,925] [INFO] Task started: fastANI
[2023-06-13 10:49:34,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d152d44-43fc-4c60-97e2-32dae6e7eed0/GCA_022646045.1_ASM2264604v1_genomic.fna.gz --refList GCA_022646045.1_ASM2264604v1_genomic.fna/target_genomes.txt --output GCA_022646045.1_ASM2264604v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:49:46,246] [INFO] Task succeeded: fastANI
[2023-06-13 10:49:46,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d3c3cb7-4074-422f-a8e0-02878829640d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:49:46,247] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d3c3cb7-4074-422f-a8e0-02878829640d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:49:46,263] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2023-06-13 10:49:46,264] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 10:49:46,264] [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 indonesiensis	strain=NBRC 16471	GCA_007991075.1	104101	104101	type	True	96.9209	723	770	95	conclusive
Acetobacter indonesiensis	strain=5H-1	GCA_000963945.1	104101	104101	type	True	96.9059	727	770	95	conclusive
Acetobacter senegalensis	strain=LMG 23690	GCA_001580995.1	446692	446692	type	True	81.3197	508	770	95	below_threshold
Acetobacter tropicalis	strain=LMG 19825	GCA_001580915.1	104102	104102	type	True	81.2352	522	770	95	below_threshold
Acetobacter tropicalis	strain=NBRC 16470	GCA_000787635.2	104102	104102	type	True	81.2087	527	770	95	below_threshold
Acetobacter tropicalis	strain=NBRC 16470	GCA_007989245.1	104102	104102	type	True	81.1781	538	770	95	below_threshold
Acetobacter orleanensis	strain=JCM 7639T	GCA_000964205.1	104099	104099	type	True	79.6701	357	770	95	below_threshold
Acetobacter orleanensis	strain=LMG 1583	GCA_001581005.1	104099	104099	type	True	79.6034	372	770	95	below_threshold
Acetobacter cerevisiae	strain=LMG 1625	GCA_001580535.1	178900	178900	type	True	79.3963	391	770	95	below_threshold
Acetobacter malorum	strain=LMG 1746	GCA_001580615.1	178901	178901	suspected-type	True	79.3702	388	770	95	below_threshold
Acetobacter pomorum	strain=LHT 2458	GCA_002738225.1	65959	65959	suspected-type	True	78.314	263	770	95	below_threshold
Acetobacter peroxydans	strain=NBRC 13755	GCA_006539345.1	104098	104098	type	True	77.4547	188	770	95	below_threshold
Acetobacter peroxydans	strain=LMG 1635	GCA_011516745.1	104098	104098	type	True	77.4188	189	770	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 10:49:46,266] [INFO] DFAST Taxonomy check result was written to GCA_022646045.1_ASM2264604v1_genomic.fna/tc_result.tsv
[2023-06-13 10:49:46,267] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:49:46,267] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:49:46,267] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d3c3cb7-4074-422f-a8e0-02878829640d/dqc_reference/checkm_data
[2023-06-13 10:49:46,268] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:49:46,292] [INFO] Task started: CheckM
[2023-06-13 10:49:46,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022646045.1_ASM2264604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022646045.1_ASM2264604v1_genomic.fna/checkm_input GCA_022646045.1_ASM2264604v1_genomic.fna/checkm_result
[2023-06-13 10:50:12,727] [INFO] Task succeeded: CheckM
[2023-06-13 10:50:12,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 10:50:12,752] [INFO] ===== Completeness check finished =====
[2023-06-13 10:50:12,752] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:50:12,752] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022646045.1_ASM2264604v1_genomic.fna/markers.fasta)
[2023-06-13 10:50:12,753] [INFO] Task started: Blastn
[2023-06-13 10:50:12,753] [INFO] Running command: blastn -query GCA_022646045.1_ASM2264604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d3c3cb7-4074-422f-a8e0-02878829640d/dqc_reference/reference_markers_gtdb.fasta -out GCA_022646045.1_ASM2264604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:50:13,904] [INFO] Task succeeded: Blastn
[2023-06-13 10:50:13,910] [INFO] Selected 12 target genomes.
[2023-06-13 10:50:13,910] [INFO] Target genome list was writen to GCA_022646045.1_ASM2264604v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:50:13,937] [INFO] Task started: fastANI
[2023-06-13 10:50:13,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d152d44-43fc-4c60-97e2-32dae6e7eed0/GCA_022646045.1_ASM2264604v1_genomic.fna.gz --refList GCA_022646045.1_ASM2264604v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022646045.1_ASM2264604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:50:21,359] [INFO] Task succeeded: fastANI
[2023-06-13 10:50:21,368] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 10:50:21,369] [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_000963945.1	s__Acetobacter indonesiensis	96.9059	727	770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.28	96.85	0.92	0.88	4	conclusive
GCF_001580995.1	s__Acetobacter senegalensis	81.3197	508	770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.25	96.97	0.85	0.80	6	-
GCF_001580915.1	s__Acetobacter tropicalis	81.2431	522	770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.32	97.71	0.90	0.87	9	-
GCF_001581005.1	s__Acetobacter orleanensis	79.6308	370	770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	99.99	99.99	0.99	0.99	4	-
GCF_002153605.1	s__Acetobacter malorum_A	79.5938	369	770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.53	96.53	0.89	0.89	2	-
GCF_001580535.1	s__Acetobacter cerevisiae	79.3963	391	770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.52	96.47	0.88	0.86	4	-
GCF_001580615.1	s__Acetobacter malorum	79.3769	387	770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	95.98	95.83	0.82	0.80	5	-
GCF_011516935.1	s__Acetobacter farinalis	79.3526	367	770	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	77.4547	188	770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2023-06-13 10:50:21,371] [INFO] GTDB search result was written to GCA_022646045.1_ASM2264604v1_genomic.fna/result_gtdb.tsv
[2023-06-13 10:50:21,372] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:50:21,376] [INFO] DFAST_QC result json was written to GCA_022646045.1_ASM2264604v1_genomic.fna/dqc_result.json
[2023-06-13 10:50:21,376] [INFO] DFAST_QC completed!
[2023-06-13 10:50:21,376] [INFO] Total running time: 0h0m56s