[2024-01-24 11:34:54,513] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:54,517] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:54,517] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b269bd9-1c5d-48c7-afba-7ebb7b811d2f/dqc_reference
[2024-01-24 11:34:56,282] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:56,283] [INFO] Task started: Prodigal
[2024-01-24 11:34:56,283] [INFO] Running command: gunzip -c /var/lib/cwl/stg2795edea-8567-4ae7-a791-06581ffa9894/GCF_024105665.1_ASM2410566v1_genomic.fna.gz | prodigal -d GCF_024105665.1_ASM2410566v1_genomic.fna/cds.fna -a GCF_024105665.1_ASM2410566v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:08,611] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:08,611] [INFO] Task started: HMMsearch
[2024-01-24 11:35:08,611] [INFO] Running command: hmmsearch --tblout GCF_024105665.1_ASM2410566v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b269bd9-1c5d-48c7-afba-7ebb7b811d2f/dqc_reference/reference_markers.hmm GCF_024105665.1_ASM2410566v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:08,909] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:08,911] [INFO] Found 6/6 markers.
[2024-01-24 11:35:08,963] [INFO] Query marker FASTA was written to GCF_024105665.1_ASM2410566v1_genomic.fna/markers.fasta
[2024-01-24 11:35:08,963] [INFO] Task started: Blastn
[2024-01-24 11:35:08,963] [INFO] Running command: blastn -query GCF_024105665.1_ASM2410566v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b269bd9-1c5d-48c7-afba-7ebb7b811d2f/dqc_reference/reference_markers.fasta -out GCF_024105665.1_ASM2410566v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:09,979] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:09,984] [INFO] Selected 29 target genomes.
[2024-01-24 11:35:09,984] [INFO] Target genome list was writen to GCF_024105665.1_ASM2410566v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:09,997] [INFO] Task started: fastANI
[2024-01-24 11:35:09,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg2795edea-8567-4ae7-a791-06581ffa9894/GCF_024105665.1_ASM2410566v1_genomic.fna.gz --refList GCF_024105665.1_ASM2410566v1_genomic.fna/target_genomes.txt --output GCF_024105665.1_ASM2410566v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:43,248] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:43,248] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b269bd9-1c5d-48c7-afba-7ebb7b811d2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:43,249] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b269bd9-1c5d-48c7-afba-7ebb7b811d2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:43,274] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:43,274] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:43,274] [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
Aquibium carbonis	strain=B2.3	GCA_003970795.1	2495581	2495581	type	True	79.2566	518	1363	95	below_threshold
Nitratireductor soli	strain=ZZ-1	GCA_001050155.1	1670619	1670619	type	True	79.1169	492	1363	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	79.043	541	1363	95	below_threshold
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	79.0334	507	1363	95	below_threshold
Aquibium oceanicum	strain=B7	GCA_001889605.1	1670800	1670800	type	True	78.992	525	1363	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	78.9716	553	1363	95	below_threshold
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	78.9699	544	1363	95	below_threshold
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	78.9343	477	1363	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	78.9332	515	1363	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	78.9159	463	1363	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	78.9144	494	1363	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	78.8942	520	1363	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	78.8872	486	1363	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	78.8673	520	1363	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	78.8655	486	1363	95	below_threshold
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	78.8243	502	1363	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	78.8107	488	1363	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	78.8085	455	1363	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	78.7692	484	1363	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	78.7522	508	1363	95	below_threshold
Mesorhizobium qingshengii	strain=CGMCC 1.12097	GCA_900103325.1	1165689	1165689	type	True	78.752	497	1363	95	below_threshold
Aminobacter aminovorans	strain=NCTC10684	GCA_900445235.1	83263	83263	type	True	78.6905	501	1363	95	below_threshold
Aminobacter aminovorans	strain=DSM 7048	GCA_004341645.1	83263	83263	type	True	78.6899	491	1363	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	78.6838	496	1363	95	below_threshold
Mesorhizobium alhagi	strain=CCNWXJ12-2	GCA_000236565.2	475067	475067	type	True	78.602	511	1363	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	78.5877	530	1363	95	below_threshold
Nitratireductor indicus	strain=C115	GCA_000300515.1	721133	721133	type	True	78.5249	348	1363	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	78.1105	385	1363	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.1003	386	1363	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:43,276] [INFO] DFAST Taxonomy check result was written to GCF_024105665.1_ASM2410566v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:43,277] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:43,277] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:43,277] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b269bd9-1c5d-48c7-afba-7ebb7b811d2f/dqc_reference/checkm_data
[2024-01-24 11:35:43,279] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:43,320] [INFO] Task started: CheckM
[2024-01-24 11:35:43,320] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024105665.1_ASM2410566v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024105665.1_ASM2410566v1_genomic.fna/checkm_input GCF_024105665.1_ASM2410566v1_genomic.fna/checkm_result
[2024-01-24 11:36:21,693] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:21,694] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:21,717] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:21,717] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:21,717] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024105665.1_ASM2410566v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:21,718] [INFO] Task started: Blastn
[2024-01-24 11:36:21,718] [INFO] Running command: blastn -query GCF_024105665.1_ASM2410566v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b269bd9-1c5d-48c7-afba-7ebb7b811d2f/dqc_reference/reference_markers_gtdb.fasta -out GCF_024105665.1_ASM2410566v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:23,725] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:23,729] [INFO] Selected 22 target genomes.
[2024-01-24 11:36:23,730] [INFO] Target genome list was writen to GCF_024105665.1_ASM2410566v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:23,873] [INFO] Task started: fastANI
[2024-01-24 11:36:23,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg2795edea-8567-4ae7-a791-06581ffa9894/GCF_024105665.1_ASM2410566v1_genomic.fna.gz --refList GCF_024105665.1_ASM2410566v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024105665.1_ASM2410566v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:46,317] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:46,339] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:36:46,339] [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
GCA_016742175.1	s__Aliihoeflea sp016742175	82.9551	840	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aliihoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000497755.1	s__Aliihoeflea sp000497755	82.8422	821	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aliihoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008180155.1	s__Aquamicrobium_A microcysteis	80.5787	615	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014615.2	s__Aquamicrobium_A sp001014615	79.7595	625	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577315.1	s__Aquamicrobium_A sp003577315	79.7004	474	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860725.1	s__Aquamicrobium_A sp014860725	79.4499	316	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305835.1	s__RCIO01 sp017305835	79.3602	553	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970795.1	s__Mesorhizobium_E carbonis	79.2482	519	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590645.1	s__Pseudaminobacter sp900116595	79.2387	551	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	98.40	97.54	0.93	0.88	4	-
GCF_017874015.1	s__Pseudaminobacter sp017874015	79.1129	496	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050155.1	s__Nitratireductor soli	79.0953	495	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756535.1	s__Mesorhizobium sp016756535	79.0526	516	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045115.1	s__Pseudaminobacter zhangyensis	79.0386	541	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014495845.1	s__Mesorhizobium_E sp014495845	78.9862	552	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019091085.1	s__Mesorhizobium sp019091085	78.9603	522	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830515.1	s__Mesorhizobium tianshanense	78.9161	490	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756495.1	s__Mesorhizobium sp016756495	78.8972	503	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199455.1	s__Mesorhizobium carmichaelinearum	78.8821	522	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253745.1	s__Mesorhizobium kowhaii	78.7839	521	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688075.1	s__Mesorhizobium sp000688075	78.7627	500	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005063415.1	s__Mesorhizobium sp005063415	78.7529	407	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000502955.1	s__Mesorhizobium sp000502955	78.5061	499	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:46,341] [INFO] GTDB search result was written to GCF_024105665.1_ASM2410566v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:46,341] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:46,346] [INFO] DFAST_QC result json was written to GCF_024105665.1_ASM2410566v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:46,346] [INFO] DFAST_QC completed!
[2024-01-24 11:36:46,346] [INFO] Total running time: 0h1m52s