[2024-01-24 11:05:28,234] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:28,236] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:28,236] [INFO] DQC Reference Directory: /var/lib/cwl/stg820b3c39-63f3-46f0-b1e2-8747bbac8a8e/dqc_reference
[2024-01-24 11:05:29,570] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:29,574] [INFO] Task started: Prodigal
[2024-01-24 11:05:29,574] [INFO] Running command: gunzip -c /var/lib/cwl/stge65ab942-a21b-48b9-a584-2e818effbc6f/GCF_018360005.1_ASM1836000v1_genomic.fna.gz | prodigal -d GCF_018360005.1_ASM1836000v1_genomic.fna/cds.fna -a GCF_018360005.1_ASM1836000v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:43,445] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:43,446] [INFO] Task started: HMMsearch
[2024-01-24 11:05:43,446] [INFO] Running command: hmmsearch --tblout GCF_018360005.1_ASM1836000v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg820b3c39-63f3-46f0-b1e2-8747bbac8a8e/dqc_reference/reference_markers.hmm GCF_018360005.1_ASM1836000v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:43,777] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:43,778] [INFO] Found 6/6 markers.
[2024-01-24 11:05:43,831] [INFO] Query marker FASTA was written to GCF_018360005.1_ASM1836000v1_genomic.fna/markers.fasta
[2024-01-24 11:05:43,832] [INFO] Task started: Blastn
[2024-01-24 11:05:43,832] [INFO] Running command: blastn -query GCF_018360005.1_ASM1836000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg820b3c39-63f3-46f0-b1e2-8747bbac8a8e/dqc_reference/reference_markers.fasta -out GCF_018360005.1_ASM1836000v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:44,922] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:44,927] [INFO] Selected 14 target genomes.
[2024-01-24 11:05:44,928] [INFO] Target genome list was writen to GCF_018360005.1_ASM1836000v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:44,933] [INFO] Task started: fastANI
[2024-01-24 11:05:44,934] [INFO] Running command: fastANI --query /var/lib/cwl/stge65ab942-a21b-48b9-a584-2e818effbc6f/GCF_018360005.1_ASM1836000v1_genomic.fna.gz --refList GCF_018360005.1_ASM1836000v1_genomic.fna/target_genomes.txt --output GCF_018360005.1_ASM1836000v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:58,923] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:58,923] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg820b3c39-63f3-46f0-b1e2-8747bbac8a8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:58,924] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg820b3c39-63f3-46f0-b1e2-8747bbac8a8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:58,936] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:05:58,936] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:58,936] [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 caviae	strain=CECT 838	GCA_018360005.1	648	648	type	True	100.0	1469	1471	95	conclusive
Aeromonas caviae	strain=NCTC12244	GCA_900476005.1	648	648	type	True	99.9999	1470	1471	95	conclusive
Aeromonas caviae	strain=CECT 838	GCA_000819785.1	648	648	type	True	99.9642	1435	1471	95	conclusive
Aeromonas taiwanensis	strain=LMG 24683	GCA_000820165.1	633417	633417	type	True	91.0256	1197	1471	95	below_threshold
Aeromonas taiwanensis	strain=LMG 24683	GCA_000699185.1	633417	633417	type	True	90.8858	1199	1471	95	below_threshold
Aeromonas dhakensis	strain=CIP 107500	GCA_000820305.1	196024	196024	type	True	89.1397	1178	1471	95	below_threshold
Aeromonas hydrophila subsp. hydrophila	strain=ATCC 7966	GCA_000014805.1	196023	644	type	True	88.9924	1221	1471	95	below_threshold
Aeromonas hydrophila	strain=NCTC8049	GCA_900445175.1	644	644	type	True	88.9852	1216	1471	95	below_threshold
Aeromonas hydrophila subsp. ranae	strain=CIP 107985	GCA_000820325.1	208958	644	type	True	88.8938	1179	1471	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	77.201	259	1471	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.8628	135	1471	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	76.7595	134	1471	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.5586	172	1471	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	75.9576	108	1471	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:58,938] [INFO] DFAST Taxonomy check result was written to GCF_018360005.1_ASM1836000v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:58,939] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:58,939] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:58,939] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg820b3c39-63f3-46f0-b1e2-8747bbac8a8e/dqc_reference/checkm_data
[2024-01-24 11:05:58,940] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:58,990] [INFO] Task started: CheckM
[2024-01-24 11:05:58,991] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018360005.1_ASM1836000v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018360005.1_ASM1836000v1_genomic.fna/checkm_input GCF_018360005.1_ASM1836000v1_genomic.fna/checkm_result
[2024-01-24 11:06:43,095] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:43,097] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:43,123] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:43,124] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:43,124] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018360005.1_ASM1836000v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:43,125] [INFO] Task started: Blastn
[2024-01-24 11:06:43,125] [INFO] Running command: blastn -query GCF_018360005.1_ASM1836000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg820b3c39-63f3-46f0-b1e2-8747bbac8a8e/dqc_reference/reference_markers_gtdb.fasta -out GCF_018360005.1_ASM1836000v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:44,791] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:44,795] [INFO] Selected 10 target genomes.
[2024-01-24 11:06:44,795] [INFO] Target genome list was writen to GCF_018360005.1_ASM1836000v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:44,802] [INFO] Task started: fastANI
[2024-01-24 11:06:44,802] [INFO] Running command: fastANI --query /var/lib/cwl/stge65ab942-a21b-48b9-a584-2e818effbc6f/GCF_018360005.1_ASM1836000v1_genomic.fna.gz --refList GCF_018360005.1_ASM1836000v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018360005.1_ASM1836000v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:55,569] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:55,582] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:55,582] [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_000819785.1	s__Aeromonas caviae	99.9642	1435	1471	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.93	97.49	0.90	0.83	112	conclusive
GCF_000820085.1	s__Aeromonas sanarellii	91.6775	1199	1471	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	91.0138	1198	1471	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.19	97.81	0.94	0.93	7	-
GCF_000819985.1	s__Aeromonas media	90.0421	1170	1471	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	89.152	1177	1471	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	88.9924	1221	1471	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.01	96.24	0.92	0.87	120	-
GCF_000819845.1	s__Aeromonas enteropelogenes	86.6615	1089	1471	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	86.0893	984	1471	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764665.1	s__Aeromonas lacus	86.0455	1038	1471	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	86.0354	1064	1471	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 11:06:55,584] [INFO] GTDB search result was written to GCF_018360005.1_ASM1836000v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:55,584] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:55,588] [INFO] DFAST_QC result json was written to GCF_018360005.1_ASM1836000v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:55,588] [INFO] DFAST_QC completed!
[2024-01-24 11:06:55,588] [INFO] Total running time: 0h1m27s