[2024-01-24 12:31:52,801] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:52,808] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:52,808] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc67dbdc-4a7e-481c-a562-7d8b611d1824/dqc_reference
[2024-01-24 12:31:54,105] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:54,106] [INFO] Task started: Prodigal
[2024-01-24 12:31:54,106] [INFO] Running command: gunzip -c /var/lib/cwl/stg37eb6cec-7e3f-43d0-b9de-8f1a97dbd533/GCF_000820185.1_PRJEB7042_genomic.fna.gz | prodigal -d GCF_000820185.1_PRJEB7042_genomic.fna/cds.fna -a GCF_000820185.1_PRJEB7042_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:08,857] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:08,857] [INFO] Task started: HMMsearch
[2024-01-24 12:32:08,857] [INFO] Running command: hmmsearch --tblout GCF_000820185.1_PRJEB7042_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc67dbdc-4a7e-481c-a562-7d8b611d1824/dqc_reference/reference_markers.hmm GCF_000820185.1_PRJEB7042_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:09,198] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:09,199] [INFO] Found 6/6 markers.
[2024-01-24 12:32:09,241] [INFO] Query marker FASTA was written to GCF_000820185.1_PRJEB7042_genomic.fna/markers.fasta
[2024-01-24 12:32:09,241] [INFO] Task started: Blastn
[2024-01-24 12:32:09,241] [INFO] Running command: blastn -query GCF_000820185.1_PRJEB7042_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc67dbdc-4a7e-481c-a562-7d8b611d1824/dqc_reference/reference_markers.fasta -out GCF_000820185.1_PRJEB7042_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:10,252] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:10,256] [INFO] Selected 13 target genomes.
[2024-01-24 12:32:10,256] [INFO] Target genome list was writen to GCF_000820185.1_PRJEB7042_genomic.fna/target_genomes.txt
[2024-01-24 12:32:10,261] [INFO] Task started: fastANI
[2024-01-24 12:32:10,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg37eb6cec-7e3f-43d0-b9de-8f1a97dbd533/GCF_000820185.1_PRJEB7042_genomic.fna.gz --refList GCF_000820185.1_PRJEB7042_genomic.fna/target_genomes.txt --output GCF_000820185.1_PRJEB7042_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:23,148] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:23,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc67dbdc-4a7e-481c-a562-7d8b611d1824/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:23,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc67dbdc-4a7e-481c-a562-7d8b611d1824/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:23,161] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:23,161] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:23,161] [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 tecta	strain=CECT 7082	GCA_000820185.2	324617	324617	type	True	100.0	1564	1565	95	conclusive
Aeromonas lusitana	strain=MDC 2473	GCA_002812985.1	931529	931529	type	True	91.0684	1359	1565	95	below_threshold
Aeromonas eucrenophila	strain=CECT 4224	GCA_000819865.1	649	649	type	True	90.3345	1358	1565	95	below_threshold
Aeromonas aquatica	strain=AE235	GCA_000764655.1	558964	558964	type	True	89.9095	1267	1565	95	below_threshold
Aeromonas encheleia	strain=CECT 4342	GCA_000819825.1	73010	73010	type	True	89.7559	1308	1565	95	below_threshold
Aeromonas encheleia	strain=NCTC12917	GCA_900637545.1	73010	73010	type	True	89.7424	1330	1565	95	below_threshold
Aeromonas bestiarum	strain=CECT 4227	GCA_000819745.1	105751	105751	type	True	87.5554	1210	1565	95	below_threshold
Aeromonas hydrophila subsp. ranae	strain=CIP 107985	GCA_000820325.1	208958	644	type	True	87.0702	1205	1565	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.537	156	1565	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	76.3481	132	1565	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.2456	172	1565	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	76.1566	126	1565	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	76.0352	129	1565	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:23,163] [INFO] DFAST Taxonomy check result was written to GCF_000820185.1_PRJEB7042_genomic.fna/tc_result.tsv
[2024-01-24 12:32:23,164] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:23,164] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:23,164] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc67dbdc-4a7e-481c-a562-7d8b611d1824/dqc_reference/checkm_data
[2024-01-24 12:32:23,166] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:23,224] [INFO] Task started: CheckM
[2024-01-24 12:32:23,225] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000820185.1_PRJEB7042_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000820185.1_PRJEB7042_genomic.fna/checkm_input GCF_000820185.1_PRJEB7042_genomic.fna/checkm_result
[2024-01-24 12:33:09,989] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:09,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:10,016] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:10,016] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:10,017] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000820185.1_PRJEB7042_genomic.fna/markers.fasta)
[2024-01-24 12:33:10,017] [INFO] Task started: Blastn
[2024-01-24 12:33:10,018] [INFO] Running command: blastn -query GCF_000820185.1_PRJEB7042_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc67dbdc-4a7e-481c-a562-7d8b611d1824/dqc_reference/reference_markers_gtdb.fasta -out GCF_000820185.1_PRJEB7042_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:11,616] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:11,619] [INFO] Selected 8 target genomes.
[2024-01-24 12:33:11,619] [INFO] Target genome list was writen to GCF_000820185.1_PRJEB7042_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:11,625] [INFO] Task started: fastANI
[2024-01-24 12:33:11,625] [INFO] Running command: fastANI --query /var/lib/cwl/stg37eb6cec-7e3f-43d0-b9de-8f1a97dbd533/GCF_000820185.1_PRJEB7042_genomic.fna.gz --refList GCF_000820185.1_PRJEB7042_genomic.fna/target_genomes_gtdb.txt --output GCF_000820185.1_PRJEB7042_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:20,672] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:20,684] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:20,684] [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_000820185.1	s__Aeromonas tecta	100.0	1564	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002812985.1	s__Aeromonas lusitana	91.0684	1359	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819865.1	s__Aeromonas eucrenophila	90.3345	1358	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764655.1	s__Aeromonas aquatica	89.9095	1267	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637545.1	s__Aeromonas encheleia	89.7424	1330	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.38	97.80	0.95	0.91	5	-
GCF_000819985.1	s__Aeromonas media	88.167	1154	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.95	97.16	0.92	0.87	16	-
GCF_000819745.1	s__Aeromonas bestiarum	87.5446	1211	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.5033	97.44	97.31	0.93	0.91	4	-
GCF_000820305.1	s__Aeromonas dhakensis	86.9852	1208	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.35	96.54	0.93	0.90	55	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:20,685] [INFO] GTDB search result was written to GCF_000820185.1_PRJEB7042_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:20,686] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:20,689] [INFO] DFAST_QC result json was written to GCF_000820185.1_PRJEB7042_genomic.fna/dqc_result.json
[2024-01-24 12:33:20,690] [INFO] DFAST_QC completed!
[2024-01-24 12:33:20,690] [INFO] Total running time: 0h1m28s