[2024-01-24 11:05:25,221] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:25,237] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:25,238] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9135dd3-beea-4ceb-97ca-2e59f8ba49ad/dqc_reference
[2024-01-24 11:05:26,690] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:26,690] [INFO] Task started: Prodigal
[2024-01-24 11:05:26,691] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0e9c606-db41-43f9-a574-04b58b24b5ea/GCF_018360025.1_ASM1836002v1_genomic.fna.gz | prodigal -d GCF_018360025.1_ASM1836002v1_genomic.fna/cds.fna -a GCF_018360025.1_ASM1836002v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:41,222] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:41,222] [INFO] Task started: HMMsearch
[2024-01-24 11:05:41,223] [INFO] Running command: hmmsearch --tblout GCF_018360025.1_ASM1836002v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9135dd3-beea-4ceb-97ca-2e59f8ba49ad/dqc_reference/reference_markers.hmm GCF_018360025.1_ASM1836002v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:41,522] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:41,523] [INFO] Found 6/6 markers.
[2024-01-24 11:05:41,563] [INFO] Query marker FASTA was written to GCF_018360025.1_ASM1836002v1_genomic.fna/markers.fasta
[2024-01-24 11:05:41,564] [INFO] Task started: Blastn
[2024-01-24 11:05:41,564] [INFO] Running command: blastn -query GCF_018360025.1_ASM1836002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9135dd3-beea-4ceb-97ca-2e59f8ba49ad/dqc_reference/reference_markers.fasta -out GCF_018360025.1_ASM1836002v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:42,558] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:42,561] [INFO] Selected 11 target genomes.
[2024-01-24 11:05:42,561] [INFO] Target genome list was writen to GCF_018360025.1_ASM1836002v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:42,566] [INFO] Task started: fastANI
[2024-01-24 11:05:42,567] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0e9c606-db41-43f9-a574-04b58b24b5ea/GCF_018360025.1_ASM1836002v1_genomic.fna.gz --refList GCF_018360025.1_ASM1836002v1_genomic.fna/target_genomes.txt --output GCF_018360025.1_ASM1836002v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:53,263] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:53,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9135dd3-beea-4ceb-97ca-2e59f8ba49ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:53,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9135dd3-beea-4ceb-97ca-2e59f8ba49ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:53,277] [INFO] Found 11 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 11:05:53,277] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:53,277] [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 hydrophila	strain=ATCC 7966	GCA_018360025.1	644	644	type	True	100.0	1547	1549	95	conclusive
Aeromonas hydrophila	strain=NCTC8049	GCA_900445175.1	644	644	type	True	99.9985	1549	1549	95	conclusive
Aeromonas hydrophila subsp. hydrophila	strain=ATCC 7966	GCA_000014805.1	196023	644	type	True	99.9984	1549	1549	95	conclusive
Aeromonas hydrophila	strain=ATCC 7966	GCA_001999685.1	644	644	type	True	99.9626	1506	1549	95	conclusive
Aeromonas hydrophila subsp. ranae	strain=CIP 107985	GCA_000820325.1	208958	644	type	True	96.8391	1379	1549	95	conclusive
Aeromonas caviae	strain=CECT 838	GCA_018360005.1	648	648	type	True	88.97	1216	1549	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	77.2005	289	1549	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.8686	213	1549	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	76.7873	141	1549	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.7764	169	1549	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.5108	208	1549	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:53,279] [INFO] DFAST Taxonomy check result was written to GCF_018360025.1_ASM1836002v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:53,280] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:53,280] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:53,280] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9135dd3-beea-4ceb-97ca-2e59f8ba49ad/dqc_reference/checkm_data
[2024-01-24 11:05:53,281] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:53,326] [INFO] Task started: CheckM
[2024-01-24 11:05:53,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018360025.1_ASM1836002v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018360025.1_ASM1836002v1_genomic.fna/checkm_input GCF_018360025.1_ASM1836002v1_genomic.fna/checkm_result
[2024-01-24 11:06:37,273] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:37,274] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:37,295] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:37,295] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:37,296] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018360025.1_ASM1836002v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:37,296] [INFO] Task started: Blastn
[2024-01-24 11:06:37,296] [INFO] Running command: blastn -query GCF_018360025.1_ASM1836002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9135dd3-beea-4ceb-97ca-2e59f8ba49ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_018360025.1_ASM1836002v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:38,909] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:38,914] [INFO] Selected 14 target genomes.
[2024-01-24 11:06:38,914] [INFO] Target genome list was writen to GCF_018360025.1_ASM1836002v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:38,927] [INFO] Task started: fastANI
[2024-01-24 11:06:38,927] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0e9c606-db41-43f9-a574-04b58b24b5ea/GCF_018360025.1_ASM1836002v1_genomic.fna.gz --refList GCF_018360025.1_ASM1836002v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018360025.1_ASM1836002v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:53,782] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:53,803] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:53,804] [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_000014805.1	s__Aeromonas hydrophila	99.9984	1549	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.01	96.24	0.92	0.87	120	conclusive
GCF_000820305.1	s__Aeromonas dhakensis	93.8598	1369	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.35	96.54	0.93	0.90	55	-
GCF_000819745.1	s__Aeromonas bestiarum	90.4321	1383	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.5033	97.44	97.31	0.93	0.91	4	-
GCF_000819785.1	s__Aeromonas caviae	88.9763	1193	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.93	97.49	0.90	0.83	112	-
GCF_000820085.1	s__Aeromonas sanarellii	88.9488	1170	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.21	98.21	0.95	0.95	3	-
GCF_000820165.1	s__Aeromonas taiwanensis	88.7939	1158	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.19	97.81	0.94	0.93	7	-
GCF_000764665.1	s__Aeromonas lacus	87.7946	1163	1549	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	87.7607	1204	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.8323	96.79	96.38	0.92	0.87	26	-
GCF_019048265.1	s__Aeromonas veronii_A	87.7434	1209	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.07	95.82	0.91	0.90	4	-
GCF_000764645.1	s__Aeromonas finlandensis	87.6733	1081	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819845.1	s__Aeromonas enteropelogenes	87.6621	1162	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.20	96.87	0.93	0.91	7	-
GCF_014204135.1	s__Aeromonas fluvialis_A	87.4277	1077	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819885.1	s__Aeromonas fluvialis	87.3275	1023	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819725.1	s__Aeromonas australiensis	87.0993	1073	1549	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 11:06:53,805] [INFO] GTDB search result was written to GCF_018360025.1_ASM1836002v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:53,806] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:53,810] [INFO] DFAST_QC result json was written to GCF_018360025.1_ASM1836002v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:53,810] [INFO] DFAST_QC completed!
[2024-01-24 11:06:53,811] [INFO] Total running time: 0h1m29s