[2024-01-24 14:46:55,037] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:55,041] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:55,042] [INFO] DQC Reference Directory: /var/lib/cwl/stgf86b5211-7962-407a-bd3e-ffec13ee0d5e/dqc_reference
[2024-01-24 14:46:58,013] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,014] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,015] [INFO] Running command: gunzip -c /var/lib/cwl/stge3685e11-33c5-4197-bf08-c10c8b2d6620/GCF_026162365.1_ASM2616236v1_genomic.fna.gz | prodigal -d GCF_026162365.1_ASM2616236v1_genomic.fna/cds.fna -a GCF_026162365.1_ASM2616236v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:13,732] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:13,732] [INFO] Task started: HMMsearch
[2024-01-24 14:47:13,733] [INFO] Running command: hmmsearch --tblout GCF_026162365.1_ASM2616236v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf86b5211-7962-407a-bd3e-ffec13ee0d5e/dqc_reference/reference_markers.hmm GCF_026162365.1_ASM2616236v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:14,047] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:14,049] [INFO] Found 6/6 markers.
[2024-01-24 14:47:14,096] [INFO] Query marker FASTA was written to GCF_026162365.1_ASM2616236v1_genomic.fna/markers.fasta
[2024-01-24 14:47:14,097] [INFO] Task started: Blastn
[2024-01-24 14:47:14,097] [INFO] Running command: blastn -query GCF_026162365.1_ASM2616236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf86b5211-7962-407a-bd3e-ffec13ee0d5e/dqc_reference/reference_markers.fasta -out GCF_026162365.1_ASM2616236v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:15,163] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:15,168] [INFO] Selected 21 target genomes.
[2024-01-24 14:47:15,169] [INFO] Target genome list was writen to GCF_026162365.1_ASM2616236v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:15,177] [INFO] Task started: fastANI
[2024-01-24 14:47:15,178] [INFO] Running command: fastANI --query /var/lib/cwl/stge3685e11-33c5-4197-bf08-c10c8b2d6620/GCF_026162365.1_ASM2616236v1_genomic.fna.gz --refList GCF_026162365.1_ASM2616236v1_genomic.fna/target_genomes.txt --output GCF_026162365.1_ASM2616236v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:37,845] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:37,845] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf86b5211-7962-407a-bd3e-ffec13ee0d5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:37,846] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf86b5211-7962-407a-bd3e-ffec13ee0d5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:37,865] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:47:37,865] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:47:37,866] [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
Chelativorans xinjiangense	strain=lm93	GCA_009812055.1	2681485	2681485	type	True	80.734	840	1621	95	below_threshold
Chelativorans alearense	strain=UJN715	GCA_010993735.1	2681495	2681495	type	True	80.6582	845	1621	95	below_threshold
Nitratireductor soli	strain=ZZ-1	GCA_001050155.1	1670619	1670619	type	True	79.9636	695	1621	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	79.8373	669	1621	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	79.7136	619	1621	95	below_threshold
Nitratireductor kimnyeongensis	strain=KACC 11904	GCA_019891395.1	430679	430679	type	True	78.5608	450	1621	95	below_threshold
Mesorhizobium camelthorni	strain=CCNWXJ 40-4	GCA_011045125.1	475069	475069	type	True	78.5408	573	1621	95	below_threshold
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	78.4435	406	1621	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	78.4278	463	1621	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	78.4191	523	1621	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	78.3961	508	1621	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	78.3338	520	1621	95	below_threshold
Aquamicrobium lusatiense	strain=DSM 11099	GCA_014201615.1	89772	89772	type	True	78.3003	367	1621	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	78.2581	533	1621	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	78.1866	497	1621	95	below_threshold
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	78.1639	485	1621	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	78.1521	498	1621	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	78.1175	507	1621	95	below_threshold
Mesorhizobium sangaii	strain=DSM 100039	GCA_014207355.1	505389	505389	type	True	78.1123	505	1621	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	77.5003	396	1621	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.4932	397	1621	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:37,867] [INFO] DFAST Taxonomy check result was written to GCF_026162365.1_ASM2616236v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:37,868] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:37,868] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:37,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf86b5211-7962-407a-bd3e-ffec13ee0d5e/dqc_reference/checkm_data
[2024-01-24 14:47:37,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:37,918] [INFO] Task started: CheckM
[2024-01-24 14:47:37,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026162365.1_ASM2616236v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026162365.1_ASM2616236v1_genomic.fna/checkm_input GCF_026162365.1_ASM2616236v1_genomic.fna/checkm_result
[2024-01-24 14:48:24,286] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:24,287] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:24,308] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:24,308] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:24,309] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026162365.1_ASM2616236v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:24,309] [INFO] Task started: Blastn
[2024-01-24 14:48:24,309] [INFO] Running command: blastn -query GCF_026162365.1_ASM2616236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf86b5211-7962-407a-bd3e-ffec13ee0d5e/dqc_reference/reference_markers_gtdb.fasta -out GCF_026162365.1_ASM2616236v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:26,171] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:26,177] [INFO] Selected 23 target genomes.
[2024-01-24 14:48:26,178] [INFO] Target genome list was writen to GCF_026162365.1_ASM2616236v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:26,198] [INFO] Task started: fastANI
[2024-01-24 14:48:26,199] [INFO] Running command: fastANI --query /var/lib/cwl/stge3685e11-33c5-4197-bf08-c10c8b2d6620/GCF_026162365.1_ASM2616236v1_genomic.fna.gz --refList GCF_026162365.1_ASM2616236v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026162365.1_ASM2616236v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:48,613] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:48,635] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:48:48,635] [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_009812055.1	s__Chelativorans xinjiangense	80.7424	838	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993735.1	s__Chelativorans alearense	80.6697	842	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009749525.1	s__Im94 sp009749525	80.2571	613	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Im94	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050155.1	s__Nitratireductor soli	79.9795	692	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300335.1	s__Nitratireductor pacificus	79.7349	616	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255295.1	s__Nitratireductor aquimarinus	79.0729	581	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	98.42	98.07	0.93	0.92	7	-
GCA_002697745.1	s__Nitratireductor sp002697745	78.8461	455	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577315.1	s__Aquamicrobium_A sp003577315	78.7395	456	1621	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	78.6942	523	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791025.1	s__Mesorhizobium sp004791025	78.6707	524	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.99	98.05	0.93	0.88	18	-
GCA_017794765.1	s__Nitratireductor sp017794765	78.6479	408	1621	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	78.5325	506	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952425.1	s__Mesorhizobium sp003952425	78.5109	524	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.51	95.02	0.90	0.84	19	-
GCA_004017535.1	s__Mesorhizobium sp004017535	78.4836	511	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.05	98.03	0.89	0.85	7	-
GCF_004801285.1	s__Mesorhizobium composti	78.4353	461	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.99	96.99	0.90	0.90	2	-
GCF_003590645.1	s__Pseudaminobacter sp900116595	78.4319	491	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	98.40	97.54	0.93	0.88	4	-
GCF_011045115.1	s__Pseudaminobacter zhangyensis	78.3959	508	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000824785.1	s__Mesorhizobium plurifarium	78.3528	541	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.23	96.62	0.87	0.84	6	-
GCF_004919685.1	s__Mesorhizobium norvegicum	78.3158	523	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_014201615.1	s__Mesorhizobium lusatiense	78.3003	367	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014189435.1	s__Mesorhizobium loti_G	78.2633	529	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002270415.1	s__Mesorhizobium sophorae	78.1121	509	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001603335.1	s__Alpha-05 sp001603335	76.6174	65	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Alpha-05	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:48,638] [INFO] GTDB search result was written to GCF_026162365.1_ASM2616236v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:48,638] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:48,643] [INFO] DFAST_QC result json was written to GCF_026162365.1_ASM2616236v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:48,644] [INFO] DFAST_QC completed!
[2024-01-24 14:48:48,644] [INFO] Total running time: 0h1m54s