[2024-01-24 13:36:43,505] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:43,507] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:43,507] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c627ce7-96d4-4adf-b587-04655276d114/dqc_reference
[2024-01-24 13:36:44,740] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:44,741] [INFO] Task started: Prodigal
[2024-01-24 13:36:44,741] [INFO] Running command: gunzip -c /var/lib/cwl/stg2acdaeef-ffb1-432c-af5c-ccebf0ea3830/GCF_008728855.1_ASM872885v1_genomic.fna.gz | prodigal -d GCF_008728855.1_ASM872885v1_genomic.fna/cds.fna -a GCF_008728855.1_ASM872885v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:01,891] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:01,891] [INFO] Task started: HMMsearch
[2024-01-24 13:37:01,891] [INFO] Running command: hmmsearch --tblout GCF_008728855.1_ASM872885v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c627ce7-96d4-4adf-b587-04655276d114/dqc_reference/reference_markers.hmm GCF_008728855.1_ASM872885v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:02,277] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:02,278] [INFO] Found 6/6 markers.
[2024-01-24 13:37:02,364] [INFO] Query marker FASTA was written to GCF_008728855.1_ASM872885v1_genomic.fna/markers.fasta
[2024-01-24 13:37:02,365] [INFO] Task started: Blastn
[2024-01-24 13:37:02,365] [INFO] Running command: blastn -query GCF_008728855.1_ASM872885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c627ce7-96d4-4adf-b587-04655276d114/dqc_reference/reference_markers.fasta -out GCF_008728855.1_ASM872885v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:03,237] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:03,241] [INFO] Selected 24 target genomes.
[2024-01-24 13:37:03,241] [INFO] Target genome list was writen to GCF_008728855.1_ASM872885v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:03,263] [INFO] Task started: fastANI
[2024-01-24 13:37:03,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg2acdaeef-ffb1-432c-af5c-ccebf0ea3830/GCF_008728855.1_ASM872885v1_genomic.fna.gz --refList GCF_008728855.1_ASM872885v1_genomic.fna/target_genomes.txt --output GCF_008728855.1_ASM872885v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:32,293] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:32,294] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c627ce7-96d4-4adf-b587-04655276d114/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:32,294] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c627ce7-96d4-4adf-b587-04655276d114/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:32,313] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:32,313] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:32,313] [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
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	100.0	1964	1964	95	conclusive
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	85.9051	1463	1964	95	below_threshold
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	78.2107	448	1964	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	77.4903	322	1964	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	77.2619	549	1964	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	77.2521	546	1964	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	77.168	277	1964	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	77.1477	431	1964	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	77.1262	386	1964	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	77.0877	380	1964	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	77.0734	358	1964	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	77.0718	434	1964	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.8867	454	1964	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	76.8672	423	1964	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	76.8423	427	1964	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.7799	360	1964	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.7791	460	1964	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	76.7696	437	1964	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.669	364	1964	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	76.5094	321	1964	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	76.494	328	1964	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.4226	321	1964	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	76.3693	286	1964	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.1953	275	1964	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:32,315] [INFO] DFAST Taxonomy check result was written to GCF_008728855.1_ASM872885v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:32,315] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:32,316] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:32,316] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c627ce7-96d4-4adf-b587-04655276d114/dqc_reference/checkm_data
[2024-01-24 13:37:32,317] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:32,379] [INFO] Task started: CheckM
[2024-01-24 13:37:32,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008728855.1_ASM872885v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008728855.1_ASM872885v1_genomic.fna/checkm_input GCF_008728855.1_ASM872885v1_genomic.fna/checkm_result
[2024-01-24 13:38:25,867] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:25,869] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:25,893] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:25,894] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:25,894] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008728855.1_ASM872885v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:25,894] [INFO] Task started: Blastn
[2024-01-24 13:38:25,895] [INFO] Running command: blastn -query GCF_008728855.1_ASM872885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c627ce7-96d4-4adf-b587-04655276d114/dqc_reference/reference_markers_gtdb.fasta -out GCF_008728855.1_ASM872885v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:27,324] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:27,328] [INFO] Selected 17 target genomes.
[2024-01-24 13:38:27,328] [INFO] Target genome list was writen to GCF_008728855.1_ASM872885v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:27,345] [INFO] Task started: fastANI
[2024-01-24 13:38:27,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg2acdaeef-ffb1-432c-af5c-ccebf0ea3830/GCF_008728855.1_ASM872885v1_genomic.fna.gz --refList GCF_008728855.1_ASM872885v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008728855.1_ASM872885v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:45,946] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:45,973] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:45,973] [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_008728855.1	s__Hypericibacter terrae	100.0	1964	1964	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008728835.1	s__Hypericibacter adhaerens	85.9196	1459	1964	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826565.1	s__CADEFF01 sp902826565	79.8092	667	1964	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__CADEFF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363235.1	s__Dongia mobilis	78.2155	447	1964	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Dongia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	78.0675	459	1964	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885795.1	s__VFKA01 sp009885795	77.4794	422	1964	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__VFKA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	77.377	490	1964	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	77.3411	410	1964	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869645.1	s__SHVW01 sp016869645	77.1665	407	1964	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014925385.1	s__WHTV01 sp014925385	77.1074	379	1964	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002195995.1	s__Inquilinus limosus_C	77.0782	503	1964	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000009985.1	s__Phaeospirillum magneticum	76.9698	261	1964	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938675.2	s__Inquilinus sp005938675	76.9136	549	1964	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876155.1	s__Azospirillum rugosum	76.8235	430	1964	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016201015.1	s__JACQDQ01 sp016201015	76.7301	323	1964	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__JACQDQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377445.1	s__WHUA01 sp009377445	76.6479	278	1964	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__WHUA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197795.1	s__Rhodospira goensis	76.3573	286	1964	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:45,975] [INFO] GTDB search result was written to GCF_008728855.1_ASM872885v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:45,975] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:45,980] [INFO] DFAST_QC result json was written to GCF_008728855.1_ASM872885v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:45,980] [INFO] DFAST_QC completed!
[2024-01-24 13:38:45,980] [INFO] Total running time: 0h2m2s