[2024-01-24 13:01:12,400] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:12,403] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:12,403] [INFO] DQC Reference Directory: /var/lib/cwl/stg46f70789-de8a-4476-b92d-943aca7da91a/dqc_reference
[2024-01-24 13:01:13,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:13,788] [INFO] Task started: Prodigal
[2024-01-24 13:01:13,788] [INFO] Running command: gunzip -c /var/lib/cwl/stg14c087a0-e015-4926-8fa7-2284843632cc/GCF_000820105.1_PRJEB7038_genomic.fna.gz | prodigal -d GCF_000820105.1_PRJEB7038_genomic.fna/cds.fna -a GCF_000820105.1_PRJEB7038_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:26,319] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:26,320] [INFO] Task started: HMMsearch
[2024-01-24 13:01:26,320] [INFO] Running command: hmmsearch --tblout GCF_000820105.1_PRJEB7038_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46f70789-de8a-4476-b92d-943aca7da91a/dqc_reference/reference_markers.hmm GCF_000820105.1_PRJEB7038_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:26,689] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:26,690] [INFO] Found 6/6 markers.
[2024-01-24 13:01:26,728] [INFO] Query marker FASTA was written to GCF_000820105.1_PRJEB7038_genomic.fna/markers.fasta
[2024-01-24 13:01:26,729] [INFO] Task started: Blastn
[2024-01-24 13:01:26,729] [INFO] Running command: blastn -query GCF_000820105.1_PRJEB7038_genomic.fna/markers.fasta -db /var/lib/cwl/stg46f70789-de8a-4476-b92d-943aca7da91a/dqc_reference/reference_markers.fasta -out GCF_000820105.1_PRJEB7038_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:27,705] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:27,709] [INFO] Selected 10 target genomes.
[2024-01-24 13:01:27,710] [INFO] Target genome list was writen to GCF_000820105.1_PRJEB7038_genomic.fna/target_genomes.txt
[2024-01-24 13:01:27,714] [INFO] Task started: fastANI
[2024-01-24 13:01:27,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg14c087a0-e015-4926-8fa7-2284843632cc/GCF_000820105.1_PRJEB7038_genomic.fna.gz --refList GCF_000820105.1_PRJEB7038_genomic.fna/target_genomes.txt --output GCF_000820105.1_PRJEB7038_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:37,015] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:37,015] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46f70789-de8a-4476-b92d-943aca7da91a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:37,015] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46f70789-de8a-4476-b92d-943aca7da91a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:37,025] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:01:37,026] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:37,026] [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 schubertii	strain=CECT 4240	GCA_000820105.2	652	652	type	True	100.0	1324	1330	95	conclusive
Aeromonas schubertii	strain=ATCC 43700	GCA_001481395.1	652	652	type	True	99.9936	1324	1330	95	conclusive
Aeromonas diversa	strain=2478-85	GCA_000367845.1	502790	502790	type	True	90.3902	1093	1330	95	below_threshold
Aeromonas diversa	strain=CECT 4254	GCA_000819805.1	502790	502790	type	True	90.3448	1133	1330	95	below_threshold
Aeromonas simiae	strain=CIP 107798	GCA_000820125.1	218936	218936	type	True	84.5722	875	1330	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.9839	131	1330	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.9173	181	1330	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.7694	164	1330	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	76.6138	126	1330	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.4859	132	1330	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:37,028] [INFO] DFAST Taxonomy check result was written to GCF_000820105.1_PRJEB7038_genomic.fna/tc_result.tsv
[2024-01-24 13:01:37,030] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:37,030] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:37,030] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46f70789-de8a-4476-b92d-943aca7da91a/dqc_reference/checkm_data
[2024-01-24 13:01:37,031] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:37,074] [INFO] Task started: CheckM
[2024-01-24 13:01:37,074] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000820105.1_PRJEB7038_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000820105.1_PRJEB7038_genomic.fna/checkm_input GCF_000820105.1_PRJEB7038_genomic.fna/checkm_result
[2024-01-24 13:02:15,922] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:15,924] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:15,946] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:15,946] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:15,947] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000820105.1_PRJEB7038_genomic.fna/markers.fasta)
[2024-01-24 13:02:15,947] [INFO] Task started: Blastn
[2024-01-24 13:02:15,947] [INFO] Running command: blastn -query GCF_000820105.1_PRJEB7038_genomic.fna/markers.fasta -db /var/lib/cwl/stg46f70789-de8a-4476-b92d-943aca7da91a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000820105.1_PRJEB7038_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:17,600] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:17,604] [INFO] Selected 11 target genomes.
[2024-01-24 13:02:17,604] [INFO] Target genome list was writen to GCF_000820105.1_PRJEB7038_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:17,611] [INFO] Task started: fastANI
[2024-01-24 13:02:17,611] [INFO] Running command: fastANI --query /var/lib/cwl/stg14c087a0-e015-4926-8fa7-2284843632cc/GCF_000820105.1_PRJEB7038_genomic.fna.gz --refList GCF_000820105.1_PRJEB7038_genomic.fna/target_genomes_gtdb.txt --output GCF_000820105.1_PRJEB7038_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:27,946] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:27,956] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:27,956] [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_000820105.1	s__Aeromonas schubertii	100.0	1324	1330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	99.15	98.66	0.97	0.94	4	conclusive
GCF_000819805.1	s__Aeromonas diversa	90.331	1134	1330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000820125.1	s__Aeromonas simiae	84.5724	875	1330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.54	96.54	0.89	0.89	2	-
GCF_000820165.1	s__Aeromonas taiwanensis	82.8032	846	1330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.19	97.81	0.94	0.93	7	-
GCF_000820085.1	s__Aeromonas sanarellii	82.7699	839	1330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.21	98.21	0.95	0.95	3	-
GCF_000820305.1	s__Aeromonas dhakensis	82.7352	922	1330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.35	96.54	0.93	0.90	55	-
GCF_000819785.1	s__Aeromonas caviae	82.5441	829	1330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.93	97.49	0.90	0.83	112	-
GCF_000819985.1	s__Aeromonas media	82.4355	815	1330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.95	97.16	0.92	0.87	16	-
GCF_000819765.1	s__Aeromonas bivalvium	82.3077	832	1330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.28	98.27	0.92	0.92	5	-
GCF_002812985.1	s__Aeromonas lusitana	81.9311	858	1330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156095.1	s__Aeromonas sp900156095	81.3931	707	1330	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 13:02:27,961] [INFO] GTDB search result was written to GCF_000820105.1_PRJEB7038_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:27,962] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:27,967] [INFO] DFAST_QC result json was written to GCF_000820105.1_PRJEB7038_genomic.fna/dqc_result.json
[2024-01-24 13:02:27,967] [INFO] DFAST_QC completed!
[2024-01-24 13:02:27,967] [INFO] Total running time: 0h1m16s