[2024-01-24 12:31:18,879] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:18,880] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:18,881] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ba525dc-a7d1-4b00-aeae-29480934e7b4/dqc_reference
[2024-01-24 12:31:20,151] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:20,152] [INFO] Task started: Prodigal
[2024-01-24 12:31:20,152] [INFO] Running command: gunzip -c /var/lib/cwl/stgab94fd25-cd19-43d2-b05d-b7eb5aa181d9/GCF_000820005.1_PRJEB7033_genomic.fna.gz | prodigal -d GCF_000820005.1_PRJEB7033_genomic.fna/cds.fna -a GCF_000820005.1_PRJEB7033_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:35,939] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:35,939] [INFO] Task started: HMMsearch
[2024-01-24 12:31:35,939] [INFO] Running command: hmmsearch --tblout GCF_000820005.1_PRJEB7033_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ba525dc-a7d1-4b00-aeae-29480934e7b4/dqc_reference/reference_markers.hmm GCF_000820005.1_PRJEB7033_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:36,292] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:36,294] [INFO] Found 6/6 markers.
[2024-01-24 12:31:36,350] [INFO] Query marker FASTA was written to GCF_000820005.1_PRJEB7033_genomic.fna/markers.fasta
[2024-01-24 12:31:36,350] [INFO] Task started: Blastn
[2024-01-24 12:31:36,351] [INFO] Running command: blastn -query GCF_000820005.1_PRJEB7033_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ba525dc-a7d1-4b00-aeae-29480934e7b4/dqc_reference/reference_markers.fasta -out GCF_000820005.1_PRJEB7033_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:37,330] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:37,333] [INFO] Selected 14 target genomes.
[2024-01-24 12:31:37,334] [INFO] Target genome list was writen to GCF_000820005.1_PRJEB7033_genomic.fna/target_genomes.txt
[2024-01-24 12:31:37,339] [INFO] Task started: fastANI
[2024-01-24 12:31:37,340] [INFO] Running command: fastANI --query /var/lib/cwl/stgab94fd25-cd19-43d2-b05d-b7eb5aa181d9/GCF_000820005.1_PRJEB7033_genomic.fna.gz --refList GCF_000820005.1_PRJEB7033_genomic.fna/target_genomes.txt --output GCF_000820005.1_PRJEB7033_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:51,635] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:51,636] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ba525dc-a7d1-4b00-aeae-29480934e7b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:51,636] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ba525dc-a7d1-4b00-aeae-29480934e7b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:51,652] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:31:51,652] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:31:51,652] [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
Aeromonas piscicola	strain=LMG 24783	GCA_000820005.1	600645	600645	type	True	100.0	1677	1690	95	inconclusive
Aeromonas bestiarum	strain=CECT 4227	GCA_000819745.1	105751	105751	type	True	95.426	1383	1690	95	inconclusive
Aeromonas popoffii	strain=CIP 105493	GCA_000820025.1	70856	70856	type	True	92.5351	1273	1690	95	below_threshold
Aeromonas salmonicida subsp. masoucida	strain=NBRC 13784	GCA_000647955.1	197700	645	type	True	92.0992	1227	1690	95	below_threshold
Aeromonas salmonicida subsp. salmonicida	strain=CIP 103209	GCA_000820065.1	29491	645	type	True	91.9313	1314	1690	95	below_threshold
Aeromonas salmonicida	strain=NCTC12959	GCA_900445115.1	645	645	type	True	91.88	1350	1690	95	below_threshold
Aeromonas salmonicida subsp. salmonicida	strain=ATCC 33658	GCA_001643305.1	29491	645	type	True	91.875	1313	1690	95	below_threshold
Aeromonas salmonicida subsp. pectinolytica	strain=34mel	GCA_000447435.2	96473	645	type	True	91.7187	1258	1690	95	below_threshold
Aeromonas salmonicida subsp. pectinolytica	strain=34mel	GCA_002735225.1	96473	645	type	True	91.6598	1324	1690	95	below_threshold
Leminorella grimontii	strain=JCM 5902	GCA_024343555.1	82981	82981	type	True	76.9902	90	1690	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.3357	151	1690	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.3152	154	1690	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.2887	150	1690	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.2677	163	1690	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:51,655] [INFO] DFAST Taxonomy check result was written to GCF_000820005.1_PRJEB7033_genomic.fna/tc_result.tsv
[2024-01-24 12:31:51,660] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:51,660] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:51,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ba525dc-a7d1-4b00-aeae-29480934e7b4/dqc_reference/checkm_data
[2024-01-24 12:31:51,662] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:51,717] [INFO] Task started: CheckM
[2024-01-24 12:31:51,717] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000820005.1_PRJEB7033_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000820005.1_PRJEB7033_genomic.fna/checkm_input GCF_000820005.1_PRJEB7033_genomic.fna/checkm_result
[2024-01-24 12:32:37,281] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:37,282] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:37,300] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:37,300] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:37,301] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000820005.1_PRJEB7033_genomic.fna/markers.fasta)
[2024-01-24 12:32:37,301] [INFO] Task started: Blastn
[2024-01-24 12:32:37,301] [INFO] Running command: blastn -query GCF_000820005.1_PRJEB7033_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ba525dc-a7d1-4b00-aeae-29480934e7b4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000820005.1_PRJEB7033_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:38,854] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:38,857] [INFO] Selected 8 target genomes.
[2024-01-24 12:32:38,858] [INFO] Target genome list was writen to GCF_000820005.1_PRJEB7033_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:38,864] [INFO] Task started: fastANI
[2024-01-24 12:32:38,864] [INFO] Running command: fastANI --query /var/lib/cwl/stgab94fd25-cd19-43d2-b05d-b7eb5aa181d9/GCF_000820005.1_PRJEB7033_genomic.fna.gz --refList GCF_000820005.1_PRJEB7033_genomic.fna/target_genomes_gtdb.txt --output GCF_000820005.1_PRJEB7033_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:48,051] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:48,062] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:48,062] [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_000820005.1	s__Aeromonas piscicola	100.0	1677	1690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.5033	97.81	97.81	0.93	0.93	2	conclusive
GCF_000819745.1	s__Aeromonas bestiarum	95.426	1383	1690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.5033	97.44	97.31	0.93	0.91	4	-
GCF_000820025.1	s__Aeromonas popoffii	92.5351	1273	1690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.17	98.00	0.92	0.89	4	-
GCF_001643305.1	s__Aeromonas salmonicida	91.895	1312	1690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	99.08	96.89	0.95	0.86	74	-
GCF_000014805.1	s__Aeromonas hydrophila	89.7122	1352	1690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.01	96.24	0.92	0.87	120	-
GCF_900637545.1	s__Aeromonas encheleia	88.2615	1246	1690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.38	97.80	0.95	0.91	5	-
GCF_000820045.1	s__Aeromonas rivuli	84.5103	1049	1690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000388115.1	s__Aeromonas molluscorum	84.3262	949	1690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:48,064] [INFO] GTDB search result was written to GCF_000820005.1_PRJEB7033_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:48,066] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:48,069] [INFO] DFAST_QC result json was written to GCF_000820005.1_PRJEB7033_genomic.fna/dqc_result.json
[2024-01-24 12:32:48,069] [INFO] DFAST_QC completed!
[2024-01-24 12:32:48,070] [INFO] Total running time: 0h1m29s