[2024-01-24 13:31:57,691] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:57,697] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:57,697] [INFO] DQC Reference Directory: /var/lib/cwl/stgc20740f9-4b0f-45f9-9a25-cde2e2cd9386/dqc_reference
[2024-01-24 13:31:59,015] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:59,015] [INFO] Task started: Prodigal
[2024-01-24 13:31:59,016] [INFO] Running command: gunzip -c /var/lib/cwl/stg1630fc92-30f3-4e6e-a009-2a3871971b01/GCF_008728835.1_ASM872883v1_genomic.fna.gz | prodigal -d GCF_008728835.1_ASM872883v1_genomic.fna/cds.fna -a GCF_008728835.1_ASM872883v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:16,430] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:16,430] [INFO] Task started: HMMsearch
[2024-01-24 13:32:16,430] [INFO] Running command: hmmsearch --tblout GCF_008728835.1_ASM872883v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc20740f9-4b0f-45f9-9a25-cde2e2cd9386/dqc_reference/reference_markers.hmm GCF_008728835.1_ASM872883v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:16,682] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:16,684] [INFO] Found 6/6 markers.
[2024-01-24 13:32:16,736] [INFO] Query marker FASTA was written to GCF_008728835.1_ASM872883v1_genomic.fna/markers.fasta
[2024-01-24 13:32:16,736] [INFO] Task started: Blastn
[2024-01-24 13:32:16,737] [INFO] Running command: blastn -query GCF_008728835.1_ASM872883v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc20740f9-4b0f-45f9-9a25-cde2e2cd9386/dqc_reference/reference_markers.fasta -out GCF_008728835.1_ASM872883v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:17,595] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:17,598] [INFO] Selected 19 target genomes.
[2024-01-24 13:32:17,598] [INFO] Target genome list was writen to GCF_008728835.1_ASM872883v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:17,609] [INFO] Task started: fastANI
[2024-01-24 13:32:17,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg1630fc92-30f3-4e6e-a009-2a3871971b01/GCF_008728835.1_ASM872883v1_genomic.fna.gz --refList GCF_008728835.1_ASM872883v1_genomic.fna/target_genomes.txt --output GCF_008728835.1_ASM872883v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:39,884] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:39,885] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc20740f9-4b0f-45f9-9a25-cde2e2cd9386/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:39,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc20740f9-4b0f-45f9-9a25-cde2e2cd9386/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:39,902] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:39,902] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:39,903] [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 adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	100.0	1955	1955	95	conclusive
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	85.9721	1459	1955	95	below_threshold
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	78.3341	468	1955	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	77.5187	406	1955	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	77.4224	626	1955	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	77.367	648	1955	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	77.1951	290	1955	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	77.1851	583	1955	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	77.0933	446	1955	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	77.0298	440	1955	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	77.0262	484	1955	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.9726	503	1955	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.9587	422	1955	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.9137	537	1955	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.6802	430	1955	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.4837	396	1955	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	76.4577	360	1955	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	76.3411	330	1955	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.1559	177	1955	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:39,909] [INFO] DFAST Taxonomy check result was written to GCF_008728835.1_ASM872883v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:39,909] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:39,910] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:39,910] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc20740f9-4b0f-45f9-9a25-cde2e2cd9386/dqc_reference/checkm_data
[2024-01-24 13:32:39,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:39,969] [INFO] Task started: CheckM
[2024-01-24 13:32:39,969] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008728835.1_ASM872883v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008728835.1_ASM872883v1_genomic.fna/checkm_input GCF_008728835.1_ASM872883v1_genomic.fna/checkm_result
[2024-01-24 13:33:37,988] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:37,989] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:38,008] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:38,009] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:38,009] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008728835.1_ASM872883v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:38,009] [INFO] Task started: Blastn
[2024-01-24 13:33:38,010] [INFO] Running command: blastn -query GCF_008728835.1_ASM872883v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc20740f9-4b0f-45f9-9a25-cde2e2cd9386/dqc_reference/reference_markers_gtdb.fasta -out GCF_008728835.1_ASM872883v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:39,530] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:39,533] [INFO] Selected 15 target genomes.
[2024-01-24 13:33:39,533] [INFO] Target genome list was writen to GCF_008728835.1_ASM872883v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:39,558] [INFO] Task started: fastANI
[2024-01-24 13:33:39,559] [INFO] Running command: fastANI --query /var/lib/cwl/stg1630fc92-30f3-4e6e-a009-2a3871971b01/GCF_008728835.1_ASM872883v1_genomic.fna.gz --refList GCF_008728835.1_ASM872883v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008728835.1_ASM872883v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:55,008] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:55,033] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:55,033] [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_008728835.1	s__Hypericibacter adhaerens	100.0	1955	1955	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_008728855.1	s__Hypericibacter terrae	85.9772	1458	1955	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	80.0802	698	1955	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	78.3115	467	1955	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	77.9963	509	1955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014925385.1	s__WHTV01 sp014925385	77.4787	410	1955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377445.1	s__WHUA01 sp009377445	76.9794	300	1955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__WHUA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699855.1	s__GCA-016699855 sp016699855	76.9743	424	1955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__GCA-016699855	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009909005.1	s__JAAAOG01 sp009909005	76.9514	257	1955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__JAAAOG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355985.1	s__Desertibacter sp017355985	76.9342	426	1955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Desertibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793045.1	s__JAEUKZ01 sp016793045	76.866	426	1955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__JAEUKZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016202695.1	s__JACQOE01 sp016202695	76.7699	289	1955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JACQOE01;f__JACQOE01;g__JACQOE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793965.1	s__JAEULF01 sp016793965	76.4603	326	1955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JAEULF01;f__JAEULF01;g__JAEULF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002770725.1	s__Pleomorphomonas carboxyditropha	76.4563	359	1955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	98.10	98.10	0.89	0.89	2	-
GCF_008124525.1	s__Oceanicella actignis	76.3375	327	1955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:55,038] [INFO] GTDB search result was written to GCF_008728835.1_ASM872883v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:55,038] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:55,042] [INFO] DFAST_QC result json was written to GCF_008728835.1_ASM872883v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:55,042] [INFO] DFAST_QC completed!
[2024-01-24 13:33:55,042] [INFO] Total running time: 0h1m57s