[2024-01-24 14:28:02,811] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:02,813] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:02,813] [INFO] DQC Reference Directory: /var/lib/cwl/stga283c04a-a2a7-4f2a-b25b-688c10a10911/dqc_reference
[2024-01-24 14:28:04,090] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:04,091] [INFO] Task started: Prodigal
[2024-01-24 14:28:04,091] [INFO] Running command: gunzip -c /var/lib/cwl/stg589bbed5-7865-4cae-ac6f-4511172b854d/GCF_020097315.1_ASM2009731v1_genomic.fna.gz | prodigal -d GCF_020097315.1_ASM2009731v1_genomic.fna/cds.fna -a GCF_020097315.1_ASM2009731v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:19,766] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:19,767] [INFO] Task started: HMMsearch
[2024-01-24 14:28:19,767] [INFO] Running command: hmmsearch --tblout GCF_020097315.1_ASM2009731v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga283c04a-a2a7-4f2a-b25b-688c10a10911/dqc_reference/reference_markers.hmm GCF_020097315.1_ASM2009731v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:20,156] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:20,158] [INFO] Found 6/6 markers.
[2024-01-24 14:28:20,210] [INFO] Query marker FASTA was written to GCF_020097315.1_ASM2009731v1_genomic.fna/markers.fasta
[2024-01-24 14:28:20,211] [INFO] Task started: Blastn
[2024-01-24 14:28:20,211] [INFO] Running command: blastn -query GCF_020097315.1_ASM2009731v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga283c04a-a2a7-4f2a-b25b-688c10a10911/dqc_reference/reference_markers.fasta -out GCF_020097315.1_ASM2009731v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:21,232] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:21,236] [INFO] Selected 20 target genomes.
[2024-01-24 14:28:21,236] [INFO] Target genome list was writen to GCF_020097315.1_ASM2009731v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:21,263] [INFO] Task started: fastANI
[2024-01-24 14:28:21,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg589bbed5-7865-4cae-ac6f-4511172b854d/GCF_020097315.1_ASM2009731v1_genomic.fna.gz --refList GCF_020097315.1_ASM2009731v1_genomic.fna/target_genomes.txt --output GCF_020097315.1_ASM2009731v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:43,776] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:43,777] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga283c04a-a2a7-4f2a-b25b-688c10a10911/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:43,777] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga283c04a-a2a7-4f2a-b25b-688c10a10911/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:43,792] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:28:43,792] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:43,792] [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 enteropelogenes	strain=FDAARGOS_1509	GCA_020097315.1	29489	29489	type	True	100.0	1513	1513	95	conclusive
Aeromonas enteropelogenes	strain=CECT 4487	GCA_000819845.1	29489	29489	type	True	99.9697	1466	1513	95	conclusive
Aeromonas dhakensis	strain=CIP 107500	GCA_000820305.1	196024	196024	type	True	88.1535	1188	1513	95	below_threshold
Aeromonas hydrophila subsp. hydrophila	strain=ATCC 7966	GCA_000014805.1	196023	644	type	True	87.9247	1177	1513	95	below_threshold
Aeromonas hydrophila	strain=NCTC8049	GCA_900445175.1	644	644	type	True	87.9167	1181	1513	95	below_threshold
Aeromonas veronii	strain=CECT 4257	GCA_000820225.1	654	654	type	True	87.6577	1174	1513	95	below_threshold
Aeromonas veronii	strain=ATCC 35624	GCA_018359905.1	654	654	type	True	87.6305	1186	1513	95	below_threshold
Aeromonas jandaei	strain=FDAARGOS_986	GCA_016127195.1	650	650	type	True	87.4853	1213	1513	95	below_threshold
Aeromonas jandaei	strain=FDAARGOS_1523	GCA_020341535.1	650	650	type	True	87.4553	1223	1513	95	below_threshold
Aeromonas finlandensis	strain=4287D	GCA_000764645.1	1543375	1543375	type	True	87.4017	1083	1513	95	below_threshold
Aeromonas jandaei	strain=CECT 4228	GCA_000819955.1	650	650	type	True	87.3516	1175	1513	95	below_threshold
Aeromonas taiwanensis	strain=LMG 24683	GCA_000820165.1	633417	633417	type	True	87.3187	1048	1513	95	below_threshold
Aeromonas taiwanensis	strain=LMG 24683	GCA_000699185.1	633417	633417	type	True	87.1977	1074	1513	95	below_threshold
Aeromonas sanarellii	strain=LMG 24682	GCA_000820085.1	633415	633415	type	True	86.8839	1044	1513	95	below_threshold
Aeromonas caviae	strain=CECT 838	GCA_018360005.1	648	648	type	True	86.7024	1072	1513	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	77.0725	166	1513	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.7778	161	1513	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.6689	151	1513	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.6635	158	1513	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	76.5827	125	1513	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:43,794] [INFO] DFAST Taxonomy check result was written to GCF_020097315.1_ASM2009731v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:43,794] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:43,795] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:43,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga283c04a-a2a7-4f2a-b25b-688c10a10911/dqc_reference/checkm_data
[2024-01-24 14:28:43,796] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:43,842] [INFO] Task started: CheckM
[2024-01-24 14:28:43,842] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020097315.1_ASM2009731v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020097315.1_ASM2009731v1_genomic.fna/checkm_input GCF_020097315.1_ASM2009731v1_genomic.fna/checkm_result
[2024-01-24 14:29:32,074] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:32,076] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:32,103] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:32,104] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:32,104] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020097315.1_ASM2009731v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:32,104] [INFO] Task started: Blastn
[2024-01-24 14:29:32,105] [INFO] Running command: blastn -query GCF_020097315.1_ASM2009731v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga283c04a-a2a7-4f2a-b25b-688c10a10911/dqc_reference/reference_markers_gtdb.fasta -out GCF_020097315.1_ASM2009731v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:33,685] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:33,689] [INFO] Selected 12 target genomes.
[2024-01-24 14:29:33,689] [INFO] Target genome list was writen to GCF_020097315.1_ASM2009731v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:33,713] [INFO] Task started: fastANI
[2024-01-24 14:29:33,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg589bbed5-7865-4cae-ac6f-4511172b854d/GCF_020097315.1_ASM2009731v1_genomic.fna.gz --refList GCF_020097315.1_ASM2009731v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020097315.1_ASM2009731v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:46,832] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:46,851] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:46,852] [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_000819845.1	s__Aeromonas enteropelogenes	99.9697	1466	1513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.20	96.87	0.93	0.91	7	conclusive
GCF_000820305.1	s__Aeromonas dhakensis	88.1723	1186	1513	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	87.9167	1178	1513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.01	96.24	0.92	0.87	120	-
GCF_000820225.1	s__Aeromonas veronii	87.6464	1175	1513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.54	96.01	0.90	0.86	159	-
GCF_019048265.1	s__Aeromonas veronii_A	87.5764	1205	1513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.07	95.82	0.91	0.90	4	-
GCF_014204135.1	s__Aeromonas fluvialis_A	87.4165	1078	1513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764645.1	s__Aeromonas finlandensis	87.3998	1082	1513	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	87.3606	1174	1513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.8323	96.79	96.38	0.92	0.87	26	-
GCF_000764665.1	s__Aeromonas lacus	87.3493	1159	1513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.8323	96.97	96.97	0.94	0.94	2	-
GCF_000820165.1	s__Aeromonas taiwanensis	87.3121	1049	1513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.19	97.81	0.94	0.93	7	-
GCF_000820085.1	s__Aeromonas sanarellii	86.8911	1044	1513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.21	98.21	0.95	0.95	3	-
GCF_000819785.1	s__Aeromonas caviae	86.6301	1065	1513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.93	97.49	0.90	0.83	112	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:46,853] [INFO] GTDB search result was written to GCF_020097315.1_ASM2009731v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:46,854] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:46,858] [INFO] DFAST_QC result json was written to GCF_020097315.1_ASM2009731v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:46,859] [INFO] DFAST_QC completed!
[2024-01-24 14:29:46,859] [INFO] Total running time: 0h1m44s