[2023-06-05 18:40:43,760] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:40:43,761] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:40:43,761] [INFO] DQC Reference Directory: /var/lib/cwl/stgea101ea4-1317-4fb1-a4e9-708bde86eff6/dqc_reference
[2023-06-05 18:40:45,155] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:40:45,156] [INFO] Task started: Prodigal
[2023-06-05 18:40:45,156] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3273e23-352d-4a92-81fd-0c49e64e9962/GCA_004017145.1_ASM401714v1_genomic.fna.gz | prodigal -d GCA_004017145.1_ASM401714v1_genomic.fna/cds.fna -a GCA_004017145.1_ASM401714v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:41:02,865] [INFO] Task succeeded: Prodigal
[2023-06-05 18:41:02,865] [INFO] Task started: HMMsearch
[2023-06-05 18:41:02,865] [INFO] Running command: hmmsearch --tblout GCA_004017145.1_ASM401714v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea101ea4-1317-4fb1-a4e9-708bde86eff6/dqc_reference/reference_markers.hmm GCA_004017145.1_ASM401714v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:41:03,329] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:41:03,332] [INFO] Found 6/6 markers.
[2023-06-05 18:41:03,447] [INFO] Query marker FASTA was written to GCA_004017145.1_ASM401714v1_genomic.fna/markers.fasta
[2023-06-05 18:41:03,448] [INFO] Task started: Blastn
[2023-06-05 18:41:03,448] [INFO] Running command: blastn -query GCA_004017145.1_ASM401714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea101ea4-1317-4fb1-a4e9-708bde86eff6/dqc_reference/reference_markers.fasta -out GCA_004017145.1_ASM401714v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:41:04,644] [INFO] Task succeeded: Blastn
[2023-06-05 18:41:04,647] [INFO] Selected 18 target genomes.
[2023-06-05 18:41:04,647] [INFO] Target genome list was writen to GCA_004017145.1_ASM401714v1_genomic.fna/target_genomes.txt
[2023-06-05 18:41:04,648] [INFO] Task started: fastANI
[2023-06-05 18:41:04,648] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3273e23-352d-4a92-81fd-0c49e64e9962/GCA_004017145.1_ASM401714v1_genomic.fna.gz --refList GCA_004017145.1_ASM401714v1_genomic.fna/target_genomes.txt --output GCA_004017145.1_ASM401714v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:41:34,271] [INFO] Task succeeded: fastANI
[2023-06-05 18:41:34,271] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea101ea4-1317-4fb1-a4e9-708bde86eff6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:41:34,272] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea101ea4-1317-4fb1-a4e9-708bde86eff6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:41:34,283] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:41:34,283] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:41:34,283] [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 australicum	strain=WSM2073	GCA_000230995.3	536018	536018	type	True	91.2936	1598	2059	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	88.6375	1540	2059	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	88.5378	1646	2059	95	below_threshold
Mesorhizobium japonicum	strain=MAFF 303099	GCA_000009625.1	2066070	2066070	type	True	88.5098	1626	2059	95	below_threshold
Mesorhizobium jarvisii	strain=ATCC 33669	GCA_013170785.1	1777867	1777867	type	True	88.454	1600	2059	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	88.3135	1618	2059	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	88.1101	1623	2059	95	below_threshold
Mesorhizobium intechi	strain=BD68	GCA_002879535.2	537601	537601	type	True	87.9366	1458	2059	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	87.4067	1546	2059	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	87.3961	1599	2059	95	below_threshold
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	87.2344	1585	2059	95	below_threshold
Mesorhizobium qingshengii	strain=CGMCC 1.12097	GCA_900103325.1	1165689	1165689	type	True	87.148	1505	2059	95	below_threshold
Mesorhizobium sangaii	strain=DSM 100039	GCA_014207355.1	505389	505389	type	True	87.0061	1516	2059	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	86.7926	1531	2059	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	84.488	1305	2059	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.2102	680	2059	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.203	681	2059	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	78.8479	594	2059	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:41:34,285] [INFO] DFAST Taxonomy check result was written to GCA_004017145.1_ASM401714v1_genomic.fna/tc_result.tsv
[2023-06-05 18:41:34,285] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:41:34,286] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:41:34,286] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea101ea4-1317-4fb1-a4e9-708bde86eff6/dqc_reference/checkm_data
[2023-06-05 18:41:34,286] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:41:34,346] [INFO] Task started: CheckM
[2023-06-05 18:41:34,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004017145.1_ASM401714v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004017145.1_ASM401714v1_genomic.fna/checkm_input GCA_004017145.1_ASM401714v1_genomic.fna/checkm_result
[2023-06-05 18:42:24,851] [INFO] Task succeeded: CheckM
[2023-06-05 18:42:24,852] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:42:24,870] [INFO] ===== Completeness check finished =====
[2023-06-05 18:42:24,870] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:42:24,871] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004017145.1_ASM401714v1_genomic.fna/markers.fasta)
[2023-06-05 18:42:24,871] [INFO] Task started: Blastn
[2023-06-05 18:42:24,871] [INFO] Running command: blastn -query GCA_004017145.1_ASM401714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea101ea4-1317-4fb1-a4e9-708bde86eff6/dqc_reference/reference_markers_gtdb.fasta -out GCA_004017145.1_ASM401714v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:42:27,038] [INFO] Task succeeded: Blastn
[2023-06-05 18:42:27,043] [INFO] Selected 12 target genomes.
[2023-06-05 18:42:27,043] [INFO] Target genome list was writen to GCA_004017145.1_ASM401714v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:42:27,044] [INFO] Task started: fastANI
[2023-06-05 18:42:27,045] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3273e23-352d-4a92-81fd-0c49e64e9962/GCA_004017145.1_ASM401714v1_genomic.fna.gz --refList GCA_004017145.1_ASM401714v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004017145.1_ASM401714v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:42:48,506] [INFO] Task succeeded: fastANI
[2023-06-05 18:42:48,520] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:42:48,520] [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_004791165.1	s__Mesorhizobium sp004791165	98.6792	1929	2059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.22	95.93	0.90	0.87	21	conclusive
GCF_006439515.1	s__Mesorhizobium sp006439515	92.376	1566	2059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.05	98.05	0.91	0.91	2	-
GCF_000513935.1	s__Mesorhizobium sp000513935	92.321	1532	2059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.99	96.65	0.86	0.84	7	-
GCF_008520305.1	s__Mesorhizobium sp008520305	92.1096	1584	2059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006442205.1	s__Mesorhizobium sp006442205	91.7881	1612	2059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000230995.2	s__Mesorhizobium australicum	91.2996	1597	2059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.45	95.19	0.87	0.83	12	-
GCF_000688075.1	s__Mesorhizobium sp000688075	88.7328	1625	2059	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	88.5956	1670	2059	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	88.5434	1646	2059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014189455.1	s__Mesorhizobium huakuii_A	88.4899	1658	2059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013170705.1	s__Mesorhizobium loti_D	88.3523	1601	2059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.67	99.16	0.95	0.91	4	-
GCF_003996995.1	s__Mesorhizobium sp003996995	87.537	1280	2059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.83	97.35	0.87	0.74	32	-
--------------------------------------------------------------------------------
[2023-06-05 18:42:48,524] [INFO] GTDB search result was written to GCA_004017145.1_ASM401714v1_genomic.fna/result_gtdb.tsv
[2023-06-05 18:42:48,525] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:42:48,528] [INFO] DFAST_QC result json was written to GCA_004017145.1_ASM401714v1_genomic.fna/dqc_result.json
[2023-06-05 18:42:48,528] [INFO] DFAST_QC completed!
[2023-06-05 18:42:48,528] [INFO] Total running time: 0h2m5s