[2024-01-24 14:39:00,039] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:00,044] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:00,044] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f28f0be-f755-496f-beb3-9a5a546c73de/dqc_reference
[2024-01-24 14:39:01,389] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:01,389] [INFO] Task started: Prodigal
[2024-01-24 14:39:01,390] [INFO] Running command: gunzip -c /var/lib/cwl/stg422a5af1-0517-45aa-aa0f-eeb6070afdc5/GCF_003149475.2_ASM314947v2_genomic.fna.gz | prodigal -d GCF_003149475.2_ASM314947v2_genomic.fna/cds.fna -a GCF_003149475.2_ASM314947v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:13,698] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:13,698] [INFO] Task started: HMMsearch
[2024-01-24 14:39:13,698] [INFO] Running command: hmmsearch --tblout GCF_003149475.2_ASM314947v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f28f0be-f755-496f-beb3-9a5a546c73de/dqc_reference/reference_markers.hmm GCF_003149475.2_ASM314947v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:13,993] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:13,994] [INFO] Found 6/6 markers.
[2024-01-24 14:39:14,045] [INFO] Query marker FASTA was written to GCF_003149475.2_ASM314947v2_genomic.fna/markers.fasta
[2024-01-24 14:39:14,046] [INFO] Task started: Blastn
[2024-01-24 14:39:14,046] [INFO] Running command: blastn -query GCF_003149475.2_ASM314947v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f28f0be-f755-496f-beb3-9a5a546c73de/dqc_reference/reference_markers.fasta -out GCF_003149475.2_ASM314947v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:15,169] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:15,173] [INFO] Selected 25 target genomes.
[2024-01-24 14:39:15,173] [INFO] Target genome list was writen to GCF_003149475.2_ASM314947v2_genomic.fna/target_genomes.txt
[2024-01-24 14:39:15,225] [INFO] Task started: fastANI
[2024-01-24 14:39:15,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg422a5af1-0517-45aa-aa0f-eeb6070afdc5/GCF_003149475.2_ASM314947v2_genomic.fna.gz --refList GCF_003149475.2_ASM314947v2_genomic.fna/target_genomes.txt --output GCF_003149475.2_ASM314947v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:40,259] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:40,260] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f28f0be-f755-496f-beb3-9a5a546c73de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:40,260] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f28f0be-f755-496f-beb3-9a5a546c73de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:40,287] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:39:40,287] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:39:40,288] [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
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	78.6656	467	1187	95	below_threshold
Oricola thermophila	strain=MEBiC13590	GCA_013358405.1	2742145	2742145	type	True	78.4564	409	1187	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	78.1265	443	1187	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	78.1252	374	1187	95	below_threshold
Oricola cellulosilytica	strain=JCM 19534	GCA_019966575.1	1429082	1429082	type	True	78.0651	329	1187	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	78.0496	452	1187	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	78.045	410	1187	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.0401	391	1187	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	77.9856	411	1187	95	below_threshold
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	77.9802	393	1187	95	below_threshold
Hoeflea marina	strain=DSM 16791	GCA_003182275.1	274592	274592	type	True	77.9436	390	1187	95	below_threshold
Zhengella mangrovi	strain=X9-2-2	GCA_002727065.1	1982044	1982044	type	True	77.928	369	1187	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	77.9273	409	1187	95	below_threshold
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	77.7809	334	1187	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	77.7744	378	1187	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	77.6706	414	1187	95	below_threshold
Chelativorans xinjiangense	strain=lm93	GCA_009812055.1	2681485	2681485	type	True	77.643	381	1187	95	below_threshold
Rhizobium rhizolycopersici	strain=DBTS2	GCA_013378445.1	2746702	2746702	type	True	77.5275	311	1187	95	below_threshold
Shinella kummerowiae	strain=CCBAU 25048	GCA_009827055.1	417745	417745	type	True	77.4826	332	1187	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.4114	320	1187	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	77.4112	321	1187	95	below_threshold
Rhizobium changzhiense	strain=WYCCWR 11279	GCA_013087625.1	2692317	2692317	type	True	77.4061	285	1187	95	below_threshold
Nitratireductor indicus	strain=C115	GCA_000300515.1	721133	721133	type	True	77.3107	238	1187	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	77.3029	236	1187	95	below_threshold
Rhizobium pseudoryzae	strain=DSM 19479	GCA_011046245.1	379684	379684	type	True	77.179	286	1187	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:40,290] [INFO] DFAST Taxonomy check result was written to GCF_003149475.2_ASM314947v2_genomic.fna/tc_result.tsv
[2024-01-24 14:39:40,291] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:40,291] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:40,291] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f28f0be-f755-496f-beb3-9a5a546c73de/dqc_reference/checkm_data
[2024-01-24 14:39:40,294] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:40,332] [INFO] Task started: CheckM
[2024-01-24 14:39:40,332] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003149475.2_ASM314947v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003149475.2_ASM314947v2_genomic.fna/checkm_input GCF_003149475.2_ASM314947v2_genomic.fna/checkm_result
[2024-01-24 14:40:40,756] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:40,758] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.55%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:40,778] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:40,778] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:40,778] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003149475.2_ASM314947v2_genomic.fna/markers.fasta)
[2024-01-24 14:40:40,779] [INFO] Task started: Blastn
[2024-01-24 14:40:40,779] [INFO] Running command: blastn -query GCF_003149475.2_ASM314947v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f28f0be-f755-496f-beb3-9a5a546c73de/dqc_reference/reference_markers_gtdb.fasta -out GCF_003149475.2_ASM314947v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:42,897] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:42,902] [INFO] Selected 13 target genomes.
[2024-01-24 14:40:42,903] [INFO] Target genome list was writen to GCF_003149475.2_ASM314947v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:42,914] [INFO] Task started: fastANI
[2024-01-24 14:40:42,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg422a5af1-0517-45aa-aa0f-eeb6070afdc5/GCF_003149475.2_ASM314947v2_genomic.fna.gz --refList GCF_003149475.2_ASM314947v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003149475.2_ASM314947v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:57,488] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:57,504] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:57,504] [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_003149475.2	s__Roseitalea stylonematis	100.0	1187	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	98.99	98.97	0.96	0.95	13	conclusive
GCA_017642895.1	s__Roseitalea sp017642895	87.3133	948	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	99.99	99.99	1.00	1.00	3	-
GCF_004331955.1	s__Roseitalea porphyridii	83.3615	836	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904745.1	s__Oricola sp014904745	78.9819	534	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698425.1	s__Oricola sp002698425	78.7712	513	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706335.1	s__Oricola sp002706335	78.2086	453	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952485.1	s__Mesorhizobium sp003952485	78.0288	420	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.38	98.21	0.91	0.89	5	-
GCF_013520985.1	s__Mesorhizobium sp013520985	77.9691	395	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004020545.1	s__Mesorhizobium sp004020545	77.9629	395	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	97.54	0.89	0.86	9	-
GCF_012911015.1	s__Aliihoeflea sp012911015	77.7713	358	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aliihoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197615.1	s__Rhizobium esperanzae_A	77.4855	295	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014595955.1	s__Mesorhizobium_D sp014595955	77.3934	322	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_D	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003963455.1	s__Mesorhizobium sp003963455	77.0155	285	1187	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 14:40:57,506] [INFO] GTDB search result was written to GCF_003149475.2_ASM314947v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:57,506] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:57,510] [INFO] DFAST_QC result json was written to GCF_003149475.2_ASM314947v2_genomic.fna/dqc_result.json
[2024-01-24 14:40:57,510] [INFO] DFAST_QC completed!
[2024-01-24 14:40:57,510] [INFO] Total running time: 0h1m57s