[2024-01-24 12:21:53,977] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:53,979] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:53,980] [INFO] DQC Reference Directory: /var/lib/cwl/stgdad3a214-dc27-44b5-a5dd-d37e9ffd40fb/dqc_reference
[2024-01-24 12:21:55,168] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:55,169] [INFO] Task started: Prodigal
[2024-01-24 12:21:55,169] [INFO] Running command: gunzip -c /var/lib/cwl/stg199bdac1-e288-4e78-87fe-510ac0d65253/GCF_000820085.1_PRJEB7037_genomic.fna.gz | prodigal -d GCF_000820085.1_PRJEB7037_genomic.fna/cds.fna -a GCF_000820085.1_PRJEB7037_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:07,259] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:07,259] [INFO] Task started: HMMsearch
[2024-01-24 12:22:07,259] [INFO] Running command: hmmsearch --tblout GCF_000820085.1_PRJEB7037_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdad3a214-dc27-44b5-a5dd-d37e9ffd40fb/dqc_reference/reference_markers.hmm GCF_000820085.1_PRJEB7037_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:07,582] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:07,584] [INFO] Found 6/6 markers.
[2024-01-24 12:22:07,627] [INFO] Query marker FASTA was written to GCF_000820085.1_PRJEB7037_genomic.fna/markers.fasta
[2024-01-24 12:22:07,627] [INFO] Task started: Blastn
[2024-01-24 12:22:07,627] [INFO] Running command: blastn -query GCF_000820085.1_PRJEB7037_genomic.fna/markers.fasta -db /var/lib/cwl/stgdad3a214-dc27-44b5-a5dd-d37e9ffd40fb/dqc_reference/reference_markers.fasta -out GCF_000820085.1_PRJEB7037_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:08,695] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:08,698] [INFO] Selected 19 target genomes.
[2024-01-24 12:22:08,698] [INFO] Target genome list was writen to GCF_000820085.1_PRJEB7037_genomic.fna/target_genomes.txt
[2024-01-24 12:22:08,705] [INFO] Task started: fastANI
[2024-01-24 12:22:08,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg199bdac1-e288-4e78-87fe-510ac0d65253/GCF_000820085.1_PRJEB7037_genomic.fna.gz --refList GCF_000820085.1_PRJEB7037_genomic.fna/target_genomes.txt --output GCF_000820085.1_PRJEB7037_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:27,188] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:27,189] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdad3a214-dc27-44b5-a5dd-d37e9ffd40fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:27,189] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdad3a214-dc27-44b5-a5dd-d37e9ffd40fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:27,206] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:27,207] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:27,207] [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 sanarellii	strain=LMG 24682	GCA_000820085.1	633415	633415	type	True	100.0	1338	1348	95	conclusive
Aeromonas taiwanensis	strain=LMG 24683	GCA_000820165.1	633417	633417	type	True	92.1204	1148	1348	95	below_threshold
Aeromonas taiwanensis	strain=LMG 24683	GCA_000699185.1	633417	633417	type	True	91.9899	1156	1348	95	below_threshold
Aeromonas caviae	strain=CECT 838	GCA_018360005.1	648	648	type	True	91.7213	1202	1348	95	below_threshold
Aeromonas caviae	strain=CECT 838	GCA_000819785.1	648	648	type	True	91.7082	1184	1348	95	below_threshold
Aeromonas caviae	strain=NCTC12244	GCA_900476005.1	648	648	type	True	91.6692	1207	1348	95	below_threshold
Aeromonas dhakensis	strain=CIP 107500	GCA_000820305.1	196024	196024	type	True	89.1773	1132	1348	95	below_threshold
Aeromonas hydrophila subsp. ranae	strain=CIP 107985	GCA_000820325.1	208958	644	type	True	89.1138	1135	1348	95	below_threshold
Aeromonas hydrophila	strain=ATCC 7966	GCA_018360025.1	644	644	type	True	89.0322	1170	1348	95	below_threshold
Aeromonas hydrophila	strain=ATCC 7966	GCA_001999685.1	644	644	type	True	89.0167	1142	1348	95	below_threshold
Aeromonas hydrophila	strain=NCTC8049	GCA_900445175.1	644	644	type	True	88.9694	1178	1348	95	below_threshold
Aeromonas hydrophila subsp. hydrophila	strain=ATCC 7966	GCA_000014805.1	196023	644	type	True	88.9563	1189	1348	95	below_threshold
Aeromonas lusitana	strain=MDC 2473	GCA_002812985.1	931529	931529	type	True	88.6758	1164	1348	95	below_threshold
Aeromonas bivalvium	strain=CECT 7113	GCA_000819765.1	440079	440079	type	True	87.3132	1065	1348	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.684	121	1348	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.593	208	1348	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.5765	215	1348	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.5584	189	1348	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.5379	208	1348	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:27,213] [INFO] DFAST Taxonomy check result was written to GCF_000820085.1_PRJEB7037_genomic.fna/tc_result.tsv
[2024-01-24 12:22:27,216] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:27,217] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:27,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdad3a214-dc27-44b5-a5dd-d37e9ffd40fb/dqc_reference/checkm_data
[2024-01-24 12:22:27,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:27,269] [INFO] Task started: CheckM
[2024-01-24 12:22:27,269] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000820085.1_PRJEB7037_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000820085.1_PRJEB7037_genomic.fna/checkm_input GCF_000820085.1_PRJEB7037_genomic.fna/checkm_result
[2024-01-24 12:23:06,553] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:06,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:06,579] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:06,579] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:06,580] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000820085.1_PRJEB7037_genomic.fna/markers.fasta)
[2024-01-24 12:23:06,580] [INFO] Task started: Blastn
[2024-01-24 12:23:06,580] [INFO] Running command: blastn -query GCF_000820085.1_PRJEB7037_genomic.fna/markers.fasta -db /var/lib/cwl/stgdad3a214-dc27-44b5-a5dd-d37e9ffd40fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_000820085.1_PRJEB7037_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:08,256] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:08,260] [INFO] Selected 11 target genomes.
[2024-01-24 12:23:08,260] [INFO] Target genome list was writen to GCF_000820085.1_PRJEB7037_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:08,266] [INFO] Task started: fastANI
[2024-01-24 12:23:08,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg199bdac1-e288-4e78-87fe-510ac0d65253/GCF_000820085.1_PRJEB7037_genomic.fna.gz --refList GCF_000820085.1_PRJEB7037_genomic.fna/target_genomes_gtdb.txt --output GCF_000820085.1_PRJEB7037_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:20,706] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:20,717] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:20,717] [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_000820085.1	s__Aeromonas sanarellii	100.0	1338	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.21	98.21	0.95	0.95	3	conclusive
GCF_000820165.1	s__Aeromonas taiwanensis	92.1204	1148	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.19	97.81	0.94	0.93	7	-
GCF_000819785.1	s__Aeromonas caviae	91.7082	1184	1348	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	90.68	1160	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.95	97.16	0.92	0.87	16	-
GCF_000820305.1	s__Aeromonas dhakensis	89.1773	1132	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.35	96.54	0.93	0.90	55	-
GCF_000014805.1	s__Aeromonas hydrophila	88.9894	1186	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.01	96.24	0.92	0.87	120	-
GCF_002812985.1	s__Aeromonas lusitana	88.6758	1164	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819765.1	s__Aeromonas bivalvium	87.2988	1067	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.28	98.27	0.92	0.92	5	-
GCF_000819845.1	s__Aeromonas enteropelogenes	86.8592	1052	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.20	96.87	0.93	0.91	7	-
GCF_000764665.1	s__Aeromonas lacus	86.0539	1011	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.8323	96.97	96.97	0.94	0.94	2	-
GCF_000819955.1	s__Aeromonas jandaei	86.0445	1038	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.8323	96.79	96.38	0.92	0.87	26	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:20,719] [INFO] GTDB search result was written to GCF_000820085.1_PRJEB7037_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:20,719] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:20,723] [INFO] DFAST_QC result json was written to GCF_000820085.1_PRJEB7037_genomic.fna/dqc_result.json
[2024-01-24 12:23:20,724] [INFO] DFAST_QC completed!
[2024-01-24 12:23:20,724] [INFO] Total running time: 0h1m27s