[2024-01-24 15:02:46,324] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:46,328] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:46,329] [INFO] DQC Reference Directory: /var/lib/cwl/stgd56fc01c-f467-40d0-8fb8-f6f2527405cf/dqc_reference
[2024-01-24 15:02:47,635] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:47,636] [INFO] Task started: Prodigal
[2024-01-24 15:02:47,636] [INFO] Running command: gunzip -c /var/lib/cwl/stg92521489-fb69-4522-9707-233e55994ab5/GCF_014644455.1_ASM1464445v1_genomic.fna.gz | prodigal -d GCF_014644455.1_ASM1464445v1_genomic.fna/cds.fna -a GCF_014644455.1_ASM1464445v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:00,691] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:00,692] [INFO] Task started: HMMsearch
[2024-01-24 15:03:00,692] [INFO] Running command: hmmsearch --tblout GCF_014644455.1_ASM1464445v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd56fc01c-f467-40d0-8fb8-f6f2527405cf/dqc_reference/reference_markers.hmm GCF_014644455.1_ASM1464445v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:01,074] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:01,075] [INFO] Found 6/6 markers.
[2024-01-24 15:03:01,125] [INFO] Query marker FASTA was written to GCF_014644455.1_ASM1464445v1_genomic.fna/markers.fasta
[2024-01-24 15:03:01,125] [INFO] Task started: Blastn
[2024-01-24 15:03:01,125] [INFO] Running command: blastn -query GCF_014644455.1_ASM1464445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd56fc01c-f467-40d0-8fb8-f6f2527405cf/dqc_reference/reference_markers.fasta -out GCF_014644455.1_ASM1464445v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:02,083] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:02,087] [INFO] Selected 19 target genomes.
[2024-01-24 15:03:02,087] [INFO] Target genome list was writen to GCF_014644455.1_ASM1464445v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:02,099] [INFO] Task started: fastANI
[2024-01-24 15:03:02,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg92521489-fb69-4522-9707-233e55994ab5/GCF_014644455.1_ASM1464445v1_genomic.fna.gz --refList GCF_014644455.1_ASM1464445v1_genomic.fna/target_genomes.txt --output GCF_014644455.1_ASM1464445v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:27,595] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:27,596] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd56fc01c-f467-40d0-8fb8-f6f2527405cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:27,596] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd56fc01c-f467-40d0-8fb8-f6f2527405cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:27,612] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:03:27,612] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:03:27,612] [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
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	81.0342	876	1580	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	79.8089	857	1580	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	79.6944	679	1580	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	79.5393	758	1580	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	79.3743	869	1580	95	below_threshold
Siccirubricoccus deserti	strain=CGMCC 1.15936	GCA_014644195.1	2013562	2013562	type	True	79.3664	877	1580	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	79.2768	693	1580	95	below_threshold
Belnapia arida	strain=T18	GCA_016773205.1	2804533	2804533	type	True	79.2664	805	1580	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	79.2359	840	1580	95	below_threshold
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	79.1077	819	1580	95	below_threshold
Roseomonas pecuniae	strain=DSM 25622	GCA_014199205.1	693023	693023	type	True	78.6768	686	1580	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.4764	604	1580	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.4399	647	1580	95	below_threshold
Roseomonas aerilata	strain=DSM 19363	GCA_000711725.1	452982	452982	type	True	78.4082	632	1580	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	78.3752	719	1580	95	below_threshold
Falsiroseomonas frigidaquae	strain=JCM 15073	GCA_012163145.1	487318	487318	type	True	78.3269	773	1580	95	below_threshold
Roseomonas rosea	strain=DSM 14916	GCA_900141905.1	198092	198092	type	True	78.14	657	1580	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	77.8388	509	1580	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.3558	598	1580	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:27,614] [INFO] DFAST Taxonomy check result was written to GCF_014644455.1_ASM1464445v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:27,614] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:27,614] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:27,615] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd56fc01c-f467-40d0-8fb8-f6f2527405cf/dqc_reference/checkm_data
[2024-01-24 15:03:27,616] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:27,667] [INFO] Task started: CheckM
[2024-01-24 15:03:27,667] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014644455.1_ASM1464445v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014644455.1_ASM1464445v1_genomic.fna/checkm_input GCF_014644455.1_ASM1464445v1_genomic.fna/checkm_result
[2024-01-24 15:04:25,522] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:25,523] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:25,544] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:25,544] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:25,544] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014644455.1_ASM1464445v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:25,545] [INFO] Task started: Blastn
[2024-01-24 15:04:25,545] [INFO] Running command: blastn -query GCF_014644455.1_ASM1464445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd56fc01c-f467-40d0-8fb8-f6f2527405cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_014644455.1_ASM1464445v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:27,485] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:27,489] [INFO] Selected 17 target genomes.
[2024-01-24 15:04:27,489] [INFO] Target genome list was writen to GCF_014644455.1_ASM1464445v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:27,501] [INFO] Task started: fastANI
[2024-01-24 15:04:27,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg92521489-fb69-4522-9707-233e55994ab5/GCF_014644455.1_ASM1464445v1_genomic.fna.gz --refList GCF_014644455.1_ASM1464445v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014644455.1_ASM1464445v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:54,228] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:54,244] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:54,245] [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_014644455.1	s__Caldovatus sediminis	100.0	1577	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Caldovatus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004761865.1	s__Crenalkalicoccus roseus	82.2566	931	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Crenalkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199195.1	s__Roseomonas_B alkaliterrae	80.9661	884	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.89	99.89	0.97	0.97	2	-
GCF_003258945.1	s__Paracraurococcus frigidaeris	80.2299	905	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129005.1	s__Roseomonas_B eburnea	80.1484	927	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129065.1	s__Roseomonas_B soli	80.1142	851	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013112485.1	s__Paracraurococcus sp013112485	79.9437	875	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343615.1	s__Paracraurococcus sp004343615	79.9363	894	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222755.1	s__Roseomonas_B sp005222755	79.893	894	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016106005.1	s__Roseomonas_B sp016106005	79.8336	736	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017813355.1	s__Roseomonas_B sp017813355	79.8282	860	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173615.1	s__Roseomonas_A sp003173615	79.6108	884	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019084075.1	s__G192 sp019084075	79.5983	875	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__G192	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002631185.1	s__Roseomonas rhizosphaerae	79.5726	750	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116135.1	s__Roseomonas aestuarii	79.3821	789	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000164635.1	s__Roseomonas cervicalis	79.2153	702	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101615.1	s__Belnapia rosea	79.1871	812	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	98.36	98.36	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:54,246] [INFO] GTDB search result was written to GCF_014644455.1_ASM1464445v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:54,247] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:54,252] [INFO] DFAST_QC result json was written to GCF_014644455.1_ASM1464445v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:54,252] [INFO] DFAST_QC completed!
[2024-01-24 15:04:54,252] [INFO] Total running time: 0h2m8s