[2024-01-25 18:02:05,366] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:02:05,367] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:02:05,368] [INFO] DQC Reference Directory: /var/lib/cwl/stg708604f7-942b-4e44-8572-7686dc341f88/dqc_reference
[2024-01-25 18:02:06,515] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:02:06,515] [INFO] Task started: Prodigal
[2024-01-25 18:02:06,515] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4ee5559-cc75-4c69-a066-8431fe6478db/GCF_003072645.1_ASM307264v1_genomic.fna.gz | prodigal -d GCF_003072645.1_ASM307264v1_genomic.fna/cds.fna -a GCF_003072645.1_ASM307264v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:02:18,033] [INFO] Task succeeded: Prodigal
[2024-01-25 18:02:18,034] [INFO] Task started: HMMsearch
[2024-01-25 18:02:18,034] [INFO] Running command: hmmsearch --tblout GCF_003072645.1_ASM307264v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg708604f7-942b-4e44-8572-7686dc341f88/dqc_reference/reference_markers.hmm GCF_003072645.1_ASM307264v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:02:18,348] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:02:18,349] [INFO] Found 6/6 markers.
[2024-01-25 18:02:18,393] [INFO] Query marker FASTA was written to GCF_003072645.1_ASM307264v1_genomic.fna/markers.fasta
[2024-01-25 18:02:18,393] [INFO] Task started: Blastn
[2024-01-25 18:02:18,393] [INFO] Running command: blastn -query GCF_003072645.1_ASM307264v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg708604f7-942b-4e44-8572-7686dc341f88/dqc_reference/reference_markers.fasta -out GCF_003072645.1_ASM307264v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:19,189] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:19,192] [INFO] Selected 29 target genomes.
[2024-01-25 18:02:19,192] [INFO] Target genome list was writen to GCF_003072645.1_ASM307264v1_genomic.fna/target_genomes.txt
[2024-01-25 18:02:19,213] [INFO] Task started: fastANI
[2024-01-25 18:02:19,213] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4ee5559-cc75-4c69-a066-8431fe6478db/GCF_003072645.1_ASM307264v1_genomic.fna.gz --refList GCF_003072645.1_ASM307264v1_genomic.fna/target_genomes.txt --output GCF_003072645.1_ASM307264v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:02:41,680] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:41,681] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg708604f7-942b-4e44-8572-7686dc341f88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:02:41,681] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg708604f7-942b-4e44-8572-7686dc341f88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:02:41,695] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:02:41,695] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:02:41,695] [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
Dongshaea marina	strain=DM2	GCA_003072645.1	2047966	2047966	type	True	100.0	1703	1703	95	conclusive
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.1402	59	1703	95	below_threshold
Aeromonas encheleia	strain=NCTC12917	GCA_900637545.1	73010	73010	type	True	78.7561	103	1703	95	below_threshold
Aeromonas salmonicida	strain=NCTC12959	GCA_900445115.1	645	645	type	True	78.4301	105	1703	95	below_threshold
Aeromonas jandaei	strain=FDAARGOS_986	GCA_016127195.1	650	650	type	True	78.3929	127	1703	95	below_threshold
Aeromonas salmonicida subsp. pectinolytica	strain=34mel	GCA_002735225.1	96473	645	type	True	78.3233	103	1703	95	below_threshold
Aeromonas jandaei	strain=FDAARGOS_1523	GCA_020341535.1	650	650	type	True	78.2324	125	1703	95	below_threshold
Aeromonas simiae	strain=CIP 107798	GCA_000820125.1	218936	218936	type	True	76.9427	99	1703	95	below_threshold
Shewanella indica	strain=KJW27	GCA_002836975.1	768528	768528	type	True	76.916	51	1703	95	below_threshold
Aeromonas encheleia	strain=CECT 4342	GCA_000819825.1	73010	73010	type	True	76.7756	90	1703	95	below_threshold
Aeromonas lusitana	strain=MDC 2473	GCA_002812985.1	931529	931529	type	True	76.7359	94	1703	95	below_threshold
Aeromonas piscicola	strain=LMG 24783	GCA_000820005.1	600645	600645	type	True	76.7131	94	1703	95	below_threshold
Aeromonas schubertii	strain=CECT 4240	GCA_000820105.2	652	652	type	True	76.6547	105	1703	95	below_threshold
Aeromonas rivuli	strain=DSM 22539	GCA_000820045.1	648794	648794	type	True	76.6253	99	1703	95	below_threshold
Zobellella taiwanensis	strain=JCM 13381	GCA_003012795.1	347535	347535	type	True	76.6142	75	1703	95	below_threshold
Aeromonas media	strain=CECT 4232	GCA_000819985.1	651	651	type	True	76.5882	93	1703	95	below_threshold
Zobellella endophytica	strain=59N8	GCA_003012775.1	2116700	2116700	type	True	76.5731	73	1703	95	below_threshold
Aeromonas jandaei	strain=CECT 4228	GCA_000819955.1	650	650	type	True	76.5359	111	1703	95	below_threshold
Zobellella denitrificans	strain=ZD1	GCA_002237365.1	347534	347534	type	True	76.535	76	1703	95	below_threshold
Aeromonas schubertii	strain=ATCC 43700	GCA_001481395.1	652	652	type	True	76.5021	105	1703	95	below_threshold
Ferrimonas sediminicola	strain=IMCC35001	GCA_005116715.1	2569538	2569538	type	True	76.4981	75	1703	95	below_threshold
Ferrimonas futtsuensis	strain=DSM 18154	GCA_000422645.1	364764	364764	type	True	76.4562	84	1703	95	below_threshold
Aeromonas media	strain=ATCC 33907	GCA_018359985.1	651	651	type	True	76.4222	94	1703	95	below_threshold
Ferrimonas marina	strain=DSM 16917	GCA_900129905.1	299255	299255	type	True	76.3015	79	1703	95	below_threshold
Aeromonas salmonicida subsp. pectinolytica	strain=34mel	GCA_000447435.2	96473	645	type	True	76.213	86	1703	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:02:41,697] [INFO] DFAST Taxonomy check result was written to GCF_003072645.1_ASM307264v1_genomic.fna/tc_result.tsv
[2024-01-25 18:02:41,697] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:02:41,697] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:02:41,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg708604f7-942b-4e44-8572-7686dc341f88/dqc_reference/checkm_data
[2024-01-25 18:02:41,698] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:02:41,748] [INFO] Task started: CheckM
[2024-01-25 18:02:41,748] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003072645.1_ASM307264v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003072645.1_ASM307264v1_genomic.fna/checkm_input GCF_003072645.1_ASM307264v1_genomic.fna/checkm_result
[2024-01-25 18:03:20,100] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:20,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:20,118] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:20,119] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:20,119] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003072645.1_ASM307264v1_genomic.fna/markers.fasta)
[2024-01-25 18:03:20,119] [INFO] Task started: Blastn
[2024-01-25 18:03:20,119] [INFO] Running command: blastn -query GCF_003072645.1_ASM307264v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg708604f7-942b-4e44-8572-7686dc341f88/dqc_reference/reference_markers_gtdb.fasta -out GCF_003072645.1_ASM307264v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:21,390] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:21,393] [INFO] Selected 25 target genomes.
[2024-01-25 18:03:21,393] [INFO] Target genome list was writen to GCF_003072645.1_ASM307264v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:21,405] [INFO] Task started: fastANI
[2024-01-25 18:03:21,405] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4ee5559-cc75-4c69-a066-8431fe6478db/GCF_003072645.1_ASM307264v1_genomic.fna.gz --refList GCF_003072645.1_ASM307264v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003072645.1_ASM307264v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:03:39,781] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:39,795] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:03:39,795] [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_003072645.1	s__Dongshaea marina	100.0	1702	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Dongshaea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900637545.1	s__Aeromonas encheleia	78.8106	103	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.38	97.80	0.95	0.91	5	-
GCF_019048265.1	s__Aeromonas veronii_A	78.5975	110	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.07	95.82	0.91	0.90	4	-
GCF_000819765.1	s__Aeromonas bivalvium	77.1445	90	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.28	98.27	0.92	0.92	5	-
GCF_000820125.1	s__Aeromonas simiae	76.8876	98	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.54	96.54	0.89	0.89	2	-
GCF_000819785.1	s__Aeromonas caviae	76.8797	90	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.93	97.49	0.90	0.83	112	-
GCF_001870485.1	s__Oceanisphaera psychrotolerans	76.7911	80	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764655.1	s__Aeromonas aquatica	76.7856	90	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010974825.1	s__Aeromonas rivipollensis	76.7749	90	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.26	95.18	0.91	0.86	15	-
GCF_003075035.1	s__Zobellella_A maritima	76.7368	77	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002812985.1	s__Aeromonas lusitana	76.701	93	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000820005.1	s__Aeromonas piscicola	76.678	93	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.5033	97.81	97.81	0.93	0.93	2	-
GCF_000820105.1	s__Aeromonas schubertii	76.6188	103	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	99.15	98.66	0.97	0.94	4	-
GCF_005116715.1	s__Ferrimonas sp005116715	76.6026	76	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000820045.1	s__Aeromonas rivuli	76.5726	99	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819985.1	s__Aeromonas media	76.5722	91	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.95	97.16	0.92	0.87	16	-
GCF_003012795.1	s__Zobellella_D taiwanensis	76.5672	74	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001643305.1	s__Aeromonas salmonicida	76.5275	90	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	99.08	96.89	0.95	0.86	74	-
GCF_003012775.1	s__Zobellella_C endophytica	76.5257	72	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819955.1	s__Aeromonas jandaei	76.5046	110	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.8323	96.79	96.38	0.92	0.87	26	-
GCF_002237365.1	s__Zobellella denitrificans	76.461	76	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella	95.0	98.78	98.78	0.93	0.93	2	-
GCA_001310455.1	s__JCM-19050 sp001310455	76.4547	61	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__JCM-19050	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422645.1	s__Ferrimonas futtsuensis	76.4302	83	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836945.1	s__Shewanella chilikensis	76.167	57	1703	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	99.40	98.79	0.97	0.93	5	-
--------------------------------------------------------------------------------
[2024-01-25 18:03:39,801] [INFO] GTDB search result was written to GCF_003072645.1_ASM307264v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:03:39,801] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:03:39,813] [INFO] DFAST_QC result json was written to GCF_003072645.1_ASM307264v1_genomic.fna/dqc_result.json
[2024-01-25 18:03:39,813] [INFO] DFAST_QC completed!
[2024-01-25 18:03:39,813] [INFO] Total running time: 0h1m34s