[2024-01-25 17:51:35,737] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:51:35,739] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:51:35,739] [INFO] DQC Reference Directory: /var/lib/cwl/stga7bc15e8-2ac2-49bf-a047-4abdd39d0a71/dqc_reference
[2024-01-25 17:51:36,824] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:51:36,825] [INFO] Task started: Prodigal
[2024-01-25 17:51:36,825] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e1d496f-f6bf-4297-b9b8-5d13af74b387/GCF_002812985.1_MDC2473_genomic.fna.gz | prodigal -d GCF_002812985.1_MDC2473_genomic.fna/cds.fna -a GCF_002812985.1_MDC2473_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:51:48,976] [INFO] Task succeeded: Prodigal
[2024-01-25 17:51:48,976] [INFO] Task started: HMMsearch
[2024-01-25 17:51:48,976] [INFO] Running command: hmmsearch --tblout GCF_002812985.1_MDC2473_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7bc15e8-2ac2-49bf-a047-4abdd39d0a71/dqc_reference/reference_markers.hmm GCF_002812985.1_MDC2473_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:51:49,265] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:51:49,266] [INFO] Found 6/6 markers.
[2024-01-25 17:51:49,304] [INFO] Query marker FASTA was written to GCF_002812985.1_MDC2473_genomic.fna/markers.fasta
[2024-01-25 17:51:49,305] [INFO] Task started: Blastn
[2024-01-25 17:51:49,305] [INFO] Running command: blastn -query GCF_002812985.1_MDC2473_genomic.fna/markers.fasta -db /var/lib/cwl/stga7bc15e8-2ac2-49bf-a047-4abdd39d0a71/dqc_reference/reference_markers.fasta -out GCF_002812985.1_MDC2473_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:50,305] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:50,309] [INFO] Selected 16 target genomes.
[2024-01-25 17:51:50,309] [INFO] Target genome list was writen to GCF_002812985.1_MDC2473_genomic.fna/target_genomes.txt
[2024-01-25 17:51:50,325] [INFO] Task started: fastANI
[2024-01-25 17:51:50,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e1d496f-f6bf-4297-b9b8-5d13af74b387/GCF_002812985.1_MDC2473_genomic.fna.gz --refList GCF_002812985.1_MDC2473_genomic.fna/target_genomes.txt --output GCF_002812985.1_MDC2473_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:52:06,471] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:06,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7bc15e8-2ac2-49bf-a047-4abdd39d0a71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:52:06,472] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7bc15e8-2ac2-49bf-a047-4abdd39d0a71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:52:06,483] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:52:06,483] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:52:06,483] [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 lusitana	strain=MDC 2473	GCA_002812985.1	931529	931529	type	True	100.0	1475	1482	95	conclusive
Aeromonas tecta	strain=CECT 7082	GCA_000820185.2	324617	324617	type	True	91.0395	1380	1482	95	below_threshold
Aeromonas eucrenophila	strain=CECT 4224	GCA_000819865.1	649	649	type	True	90.6945	1299	1482	95	below_threshold
Aeromonas aquatica	strain=AE235	GCA_000764655.1	558964	558964	type	True	90.0396	1235	1482	95	below_threshold
Aeromonas encheleia	strain=CECT 4342	GCA_000819825.1	73010	73010	type	True	89.2717	1274	1482	95	below_threshold
Aeromonas media	strain=CECT 4232	GCA_000819985.1	651	651	type	True	88.7277	1137	1482	95	below_threshold
Aeromonas hydrophila	strain=NCTC8049	GCA_900445175.1	644	644	type	True	87.4546	1208	1482	95	below_threshold
Aeromonas hydrophila subsp. hydrophila	strain=ATCC 7966	GCA_000014805.1	196023	644	type	True	87.4486	1199	1482	95	below_threshold
Aeromonas hydrophila	strain=ATCC 7966	GCA_018360025.1	644	644	type	True	87.4208	1217	1482	95	below_threshold
Aeromonas hydrophila	strain=ATCC 7966	GCA_001999685.1	644	644	type	True	87.411	1179	1482	95	below_threshold
Aeromonas hydrophila subsp. ranae	strain=CIP 107985	GCA_000820325.1	208958	644	type	True	87.3815	1184	1482	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.6155	173	1482	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.5336	183	1482	95	below_threshold
Shewanella salipaludis	strain=SHSM-M6	GCA_012911865.1	2723052	2723052	type	True	76.3392	150	1482	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.22	176	1482	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.1933	177	1482	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:52:06,485] [INFO] DFAST Taxonomy check result was written to GCF_002812985.1_MDC2473_genomic.fna/tc_result.tsv
[2024-01-25 17:52:06,485] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:52:06,485] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:52:06,485] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7bc15e8-2ac2-49bf-a047-4abdd39d0a71/dqc_reference/checkm_data
[2024-01-25 17:52:06,486] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:52:06,532] [INFO] Task started: CheckM
[2024-01-25 17:52:06,532] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002812985.1_MDC2473_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002812985.1_MDC2473_genomic.fna/checkm_input GCF_002812985.1_MDC2473_genomic.fna/checkm_result
[2024-01-25 17:52:43,445] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:43,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:43,464] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:43,464] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:43,464] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002812985.1_MDC2473_genomic.fna/markers.fasta)
[2024-01-25 17:52:43,465] [INFO] Task started: Blastn
[2024-01-25 17:52:43,465] [INFO] Running command: blastn -query GCF_002812985.1_MDC2473_genomic.fna/markers.fasta -db /var/lib/cwl/stga7bc15e8-2ac2-49bf-a047-4abdd39d0a71/dqc_reference/reference_markers_gtdb.fasta -out GCF_002812985.1_MDC2473_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:45,042] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:45,045] [INFO] Selected 12 target genomes.
[2024-01-25 17:52:45,045] [INFO] Target genome list was writen to GCF_002812985.1_MDC2473_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:52:45,057] [INFO] Task started: fastANI
[2024-01-25 17:52:45,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e1d496f-f6bf-4297-b9b8-5d13af74b387/GCF_002812985.1_MDC2473_genomic.fna.gz --refList GCF_002812985.1_MDC2473_genomic.fna/target_genomes_gtdb.txt --output GCF_002812985.1_MDC2473_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:52:58,216] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:58,225] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:52:58,226] [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_002812985.1	s__Aeromonas lusitana	100.0	1475	1482	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_000820185.1	s__Aeromonas tecta	91.0395	1380	1482	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	90.6945	1299	1482	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	90.0396	1235	1482	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	89.2396	1289	1482	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	88.7277	1137	1482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.95	97.16	0.92	0.87	16	-
GCF_000820085.1	s__Aeromonas sanarellii	88.6042	1168	1482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.21	98.21	0.95	0.95	3	-
GCF_000014805.1	s__Aeromonas hydrophila	87.4486	1199	1482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.01	96.24	0.92	0.87	120	-
GCF_000820305.1	s__Aeromonas dhakensis	87.2935	1208	1482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.35	96.54	0.93	0.90	55	-
GCF_000820005.1	s__Aeromonas piscicola	87.1028	1211	1482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.5033	97.81	97.81	0.93	0.93	2	-
GCF_000764645.1	s__Aeromonas finlandensis	85.235	1004	1482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819955.1	s__Aeromonas jandaei	84.8066	1101	1482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.8323	96.79	96.38	0.92	0.87	26	-
--------------------------------------------------------------------------------
[2024-01-25 17:52:58,227] [INFO] GTDB search result was written to GCF_002812985.1_MDC2473_genomic.fna/result_gtdb.tsv
[2024-01-25 17:52:58,227] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:52:58,230] [INFO] DFAST_QC result json was written to GCF_002812985.1_MDC2473_genomic.fna/dqc_result.json
[2024-01-25 17:52:58,230] [INFO] DFAST_QC completed!
[2024-01-25 17:52:58,230] [INFO] Total running time: 0h1m22s