[2024-01-25 17:40:05,495] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:05,497] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:05,497] [INFO] DQC Reference Directory: /var/lib/cwl/stg59d05d85-0e46-4650-afc8-f6123872feac/dqc_reference
[2024-01-25 17:40:06,600] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:06,600] [INFO] Task started: Prodigal
[2024-01-25 17:40:06,600] [INFO] Running command: gunzip -c /var/lib/cwl/stgde3e064b-836f-47b5-9c81-2b639b835318/GCF_016583875.1_ASM1658387v1_genomic.fna.gz | prodigal -d GCF_016583875.1_ASM1658387v1_genomic.fna/cds.fna -a GCF_016583875.1_ASM1658387v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:15,815] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:15,815] [INFO] Task started: HMMsearch
[2024-01-25 17:40:15,816] [INFO] Running command: hmmsearch --tblout GCF_016583875.1_ASM1658387v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59d05d85-0e46-4650-afc8-f6123872feac/dqc_reference/reference_markers.hmm GCF_016583875.1_ASM1658387v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:16,019] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:16,020] [INFO] Found 6/6 markers.
[2024-01-25 17:40:16,048] [INFO] Query marker FASTA was written to GCF_016583875.1_ASM1658387v1_genomic.fna/markers.fasta
[2024-01-25 17:40:16,048] [INFO] Task started: Blastn
[2024-01-25 17:40:16,048] [INFO] Running command: blastn -query GCF_016583875.1_ASM1658387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59d05d85-0e46-4650-afc8-f6123872feac/dqc_reference/reference_markers.fasta -out GCF_016583875.1_ASM1658387v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:17,004] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:17,006] [INFO] Selected 19 target genomes.
[2024-01-25 17:40:17,007] [INFO] Target genome list was writen to GCF_016583875.1_ASM1658387v1_genomic.fna/target_genomes.txt
[2024-01-25 17:40:17,034] [INFO] Task started: fastANI
[2024-01-25 17:40:17,034] [INFO] Running command: fastANI --query /var/lib/cwl/stgde3e064b-836f-47b5-9c81-2b639b835318/GCF_016583875.1_ASM1658387v1_genomic.fna.gz --refList GCF_016583875.1_ASM1658387v1_genomic.fna/target_genomes.txt --output GCF_016583875.1_ASM1658387v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:35,649] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:35,650] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59d05d85-0e46-4650-afc8-f6123872feac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:35,650] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59d05d85-0e46-4650-afc8-f6123872feac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:35,661] [INFO] Found 19 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 17:40:35,661] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:40:35,661] [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
Rhodothalassium salexigens	strain=DSM 2132	GCA_016583875.1	1086	1086	type	True	100.0	1043	1051	95	conclusive
Rhodothalassium salexigens	strain=DSM 2132	GCA_014197775.1	1086	1086	type	True	99.9853	1038	1051	95	conclusive
Rhodothalassium salexigens	strain=DSM 2132	GCA_004341375.1	1086	1086	type	True	99.9834	1040	1051	95	conclusive
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.7579	187	1051	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	76.7419	225	1051	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.6902	260	1051	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	76.6708	146	1051	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_014196255.1	413712	413712	type	True	76.5833	160	1051	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	76.4508	266	1051	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.4182	128	1051	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	76.4094	204	1051	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	76.3795	220	1051	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.3498	199	1051	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	76.3493	217	1051	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	76.3472	190	1051	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	76.3152	183	1051	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	76.1735	264	1051	95	below_threshold
Azospirillum griseum	strain=L-25-5 w-1	GCA_003966125.1	2496639	2496639	type	True	76.1289	196	1051	95	below_threshold
Paracoccus isoporae	strain=DSM 22220	GCA_900101865.1	591205	591205	type	True	76.0277	128	1051	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:35,663] [INFO] DFAST Taxonomy check result was written to GCF_016583875.1_ASM1658387v1_genomic.fna/tc_result.tsv
[2024-01-25 17:40:35,663] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:35,663] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:35,664] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59d05d85-0e46-4650-afc8-f6123872feac/dqc_reference/checkm_data
[2024-01-25 17:40:35,664] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:35,701] [INFO] Task started: CheckM
[2024-01-25 17:40:35,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016583875.1_ASM1658387v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016583875.1_ASM1658387v1_genomic.fna/checkm_input GCF_016583875.1_ASM1658387v1_genomic.fna/checkm_result
[2024-01-25 17:41:07,119] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:07,120] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:07,135] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:07,135] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:07,135] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016583875.1_ASM1658387v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:07,135] [INFO] Task started: Blastn
[2024-01-25 17:41:07,136] [INFO] Running command: blastn -query GCF_016583875.1_ASM1658387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59d05d85-0e46-4650-afc8-f6123872feac/dqc_reference/reference_markers_gtdb.fasta -out GCF_016583875.1_ASM1658387v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:09,134] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:09,136] [INFO] Selected 26 target genomes.
[2024-01-25 17:41:09,137] [INFO] Target genome list was writen to GCF_016583875.1_ASM1658387v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:09,158] [INFO] Task started: fastANI
[2024-01-25 17:41:09,159] [INFO] Running command: fastANI --query /var/lib/cwl/stgde3e064b-836f-47b5-9c81-2b639b835318/GCF_016583875.1_ASM1658387v1_genomic.fna.gz --refList GCF_016583875.1_ASM1658387v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016583875.1_ASM1658387v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:41:30,644] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:30,658] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:41:30,659] [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_004341375.1	s__Rhodothalassium salexigens	99.9834	1040	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Rhodothalassiaceae;g__Rhodothalassium	95.0	97.98	95.92	0.96	0.92	5	conclusive
GCF_001618175.1	s__Oceanibaculum pacificum	76.7691	185	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650635.1	s__Magnetospirillum moscoviense	76.7675	214	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	96.81	95.25	0.84	0.84	3	-
GCF_003233655.1	s__Azospirillum ramasamyi	76.7325	224	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102465.1	s__Thalassobaculum litoreum	76.7211	219	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCF_015482775.1	s__Kaustia mangrovi	76.7174	186	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Im1;g__Kaustia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	76.6843	262	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004923295.1	s__Azospirillum sp003115975	76.6618	230	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	99.99	99.99	0.99	0.99	2	-
GCA_003694205.1	s__J134 sp003694205	76.6258	109	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Rhodothalassiaceae;g__J134	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003568845.1	s__Indioceanicola profundi	76.4938	165	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Indioceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340565.1	s__HLUCCA09 sp003340565	76.471	208	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339215.1	s__DUSC01 sp008933895	76.4225	156	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	99.82	99.82	0.93	0.93	2	-
GCF_001477495.1	s__Sphingomonas yabuuchiae_A	76.387	148	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014194975.1	s__Sphingomonas sp014194975	76.3588	205	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106695.1	s__Albimonas donghaensis	76.3575	216	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	97.11	97.08	0.90	0.88	3	-
GCF_017876165.1	s__Azospirillum soli	76.3559	197	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428585.1	s__Sedimentitalea sp016428585	76.3285	100	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345855.1	s__Sphingomonas sp004345855	76.3104	225	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903643065.1	s__Sphingomonas sp903643065	76.3101	109	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307375.1	s__JAFKFH01 sp017307375	76.2475	253	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192915.1	s__Azospirillum sp014192915	76.2414	239	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903878085.1	s__Pseudolabrys sp903878085	76.2326	153	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.95	99.95	0.96	0.96	2	-
GCF_003349955.1	s__Azospirillum brasilense_B	76.2253	234	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCA_002298965.1	s__Pinisolibacter sp002298965	76.203	183	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Pinisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966125.1	s__Azospirillum griseum	76.1284	196	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014699075.1	s__Microvirga sp014699075	76.1133	122	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:41:30,660] [INFO] GTDB search result was written to GCF_016583875.1_ASM1658387v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:41:30,661] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:41:30,664] [INFO] DFAST_QC result json was written to GCF_016583875.1_ASM1658387v1_genomic.fna/dqc_result.json
[2024-01-25 17:41:30,665] [INFO] DFAST_QC completed!
[2024-01-25 17:41:30,665] [INFO] Total running time: 0h1m25s