[2024-01-25 18:40:05,512] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:40:05,513] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:40:05,513] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a6b6353-4d6f-41dd-b1f2-c7deaa470c30/dqc_reference
[2024-01-25 18:40:06,688] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:40:06,689] [INFO] Task started: Prodigal
[2024-01-25 18:40:06,690] [INFO] Running command: gunzip -c /var/lib/cwl/stg74ae6bdd-6736-479c-82f9-ed67b49a3320/GCF_024707545.1_ASM2470754v1_genomic.fna.gz | prodigal -d GCF_024707545.1_ASM2470754v1_genomic.fna/cds.fna -a GCF_024707545.1_ASM2470754v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:29,704] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:29,705] [INFO] Task started: HMMsearch
[2024-01-25 18:40:29,705] [INFO] Running command: hmmsearch --tblout GCF_024707545.1_ASM2470754v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a6b6353-4d6f-41dd-b1f2-c7deaa470c30/dqc_reference/reference_markers.hmm GCF_024707545.1_ASM2470754v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:29,978] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:29,980] [INFO] Found 6/6 markers.
[2024-01-25 18:40:30,038] [INFO] Query marker FASTA was written to GCF_024707545.1_ASM2470754v1_genomic.fna/markers.fasta
[2024-01-25 18:40:30,039] [INFO] Task started: Blastn
[2024-01-25 18:40:30,039] [INFO] Running command: blastn -query GCF_024707545.1_ASM2470754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a6b6353-4d6f-41dd-b1f2-c7deaa470c30/dqc_reference/reference_markers.fasta -out GCF_024707545.1_ASM2470754v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:31,007] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:31,010] [INFO] Selected 14 target genomes.
[2024-01-25 18:40:31,010] [INFO] Target genome list was writen to GCF_024707545.1_ASM2470754v1_genomic.fna/target_genomes.txt
[2024-01-25 18:40:31,014] [INFO] Task started: fastANI
[2024-01-25 18:40:31,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg74ae6bdd-6736-479c-82f9-ed67b49a3320/GCF_024707545.1_ASM2470754v1_genomic.fna.gz --refList GCF_024707545.1_ASM2470754v1_genomic.fna/target_genomes.txt --output GCF_024707545.1_ASM2470754v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:56,362] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:56,363] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a6b6353-4d6f-41dd-b1f2-c7deaa470c30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:56,363] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a6b6353-4d6f-41dd-b1f2-c7deaa470c30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:56,372] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:40:56,372] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:40:56,372] [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
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	100.0	2513	2515	95	conclusive
Mesorhizobium temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	94.7974	1889	2515	95	below_threshold
Mesorhizobium wenxiniae	strain=WYCCWR 10195	GCA_002284535.1	2014805	2014805	type	True	92.9341	1758	2515	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	92.3671	1775	2515	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	87.9688	1428	2515	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	87.2443	1335	2515	95	below_threshold
Mesorhizobium qingshengii	strain=CGMCC 1.12097	GCA_900103325.1	1165689	1165689	type	True	85.2878	1347	2515	95	below_threshold
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	85.235	1391	2515	95	below_threshold
Mesorhizobium sangaii	strain=DSM 100039	GCA_014207355.1	505389	505389	type	True	85.1151	1455	2515	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	84.9959	1457	2515	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	84.0717	1239	2515	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.1618	624	2515	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.0118	690	2515	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	78.9132	610	2515	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:40:56,374] [INFO] DFAST Taxonomy check result was written to GCF_024707545.1_ASM2470754v1_genomic.fna/tc_result.tsv
[2024-01-25 18:40:56,374] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:56,374] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:56,375] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a6b6353-4d6f-41dd-b1f2-c7deaa470c30/dqc_reference/checkm_data
[2024-01-25 18:40:56,375] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:56,444] [INFO] Task started: CheckM
[2024-01-25 18:40:56,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024707545.1_ASM2470754v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024707545.1_ASM2470754v1_genomic.fna/checkm_input GCF_024707545.1_ASM2470754v1_genomic.fna/checkm_result
[2024-01-25 18:42:00,097] [INFO] Task succeeded: CheckM
[2024-01-25 18:42:00,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:42:00,123] [INFO] ===== Completeness check finished =====
[2024-01-25 18:42:00,124] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:42:00,126] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024707545.1_ASM2470754v1_genomic.fna/markers.fasta)
[2024-01-25 18:42:00,126] [INFO] Task started: Blastn
[2024-01-25 18:42:00,126] [INFO] Running command: blastn -query GCF_024707545.1_ASM2470754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a6b6353-4d6f-41dd-b1f2-c7deaa470c30/dqc_reference/reference_markers_gtdb.fasta -out GCF_024707545.1_ASM2470754v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:02,154] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:02,157] [INFO] Selected 14 target genomes.
[2024-01-25 18:42:02,157] [INFO] Target genome list was writen to GCF_024707545.1_ASM2470754v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:42:02,180] [INFO] Task started: fastANI
[2024-01-25 18:42:02,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg74ae6bdd-6736-479c-82f9-ed67b49a3320/GCF_024707545.1_ASM2470754v1_genomic.fna.gz --refList GCF_024707545.1_ASM2470754v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024707545.1_ASM2470754v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:33,561] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:33,570] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:42:33,571] [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_002284575.1	s__Mesorhizobium temperatum	94.808	1888	2515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	95.74	95.09	0.81	0.81	3	-
GCA_004020645.1	s__Mesorhizobium sp004020645	94.3714	1878	2515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.46	97.82	0.90	0.85	20	-
GCF_900156895.1	s__Mesorhizobium prunaredense	93.1361	1818	2515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002284535.1	s__Mesorhizobium wenxiniae	92.9193	1760	2515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.50	95.53	0.83	0.79	62	-
GCA_004020315.1	s__Mesorhizobium sp004020315	92.4936	1737	2515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.08	99.08	0.89	0.89	2	-
GCF_900099905.1	s__Mesorhizobium muleiense	92.3671	1775	2515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.77	96.33	0.85	0.80	57	-
GCF_016756595.1	s__Mesorhizobium sp004020105	92.0407	1763	2515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.38	95.83	0.84	0.81	7	-
GCF_002284565.1	s__Mesorhizobium mediterraneum_A	91.9481	1743	2515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.16	97.72	0.92	0.89	20	-
GCA_004962925.1	s__Mesorhizobium sp004962925	91.9348	1521	2515	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	85.8164	1472	2515	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	85.4207	1488	2515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519305.1	s__Mesorhizobium ciceri_B	85.1414	1374	2515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207355.1	s__Mesorhizobium sangaii	85.1111	1456	2515	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	85.0003	1455	2515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:33,572] [INFO] GTDB search result was written to GCF_024707545.1_ASM2470754v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:33,572] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:33,582] [INFO] DFAST_QC result json was written to GCF_024707545.1_ASM2470754v1_genomic.fna/dqc_result.json
[2024-01-25 18:42:33,582] [INFO] DFAST_QC completed!
[2024-01-25 18:42:33,582] [INFO] Total running time: 0h2m28s