[2023-06-29 00:39:02,197] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:39:02,199] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:39:02,199] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5700da3-59f1-4677-97d7-ff842d382b6e/dqc_reference
[2023-06-29 00:39:03,438] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:39:03,439] [INFO] Task started: Prodigal
[2023-06-29 00:39:03,439] [INFO] Running command: gunzip -c /var/lib/cwl/stgf0e73afd-cf9f-4609-af32-96022833ae3c/GCA_020161665.1_ASM2016166v1_genomic.fna.gz | prodigal -d GCA_020161665.1_ASM2016166v1_genomic.fna/cds.fna -a GCA_020161665.1_ASM2016166v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:39:13,771] [INFO] Task succeeded: Prodigal
[2023-06-29 00:39:13,772] [INFO] Task started: HMMsearch
[2023-06-29 00:39:13,772] [INFO] Running command: hmmsearch --tblout GCA_020161665.1_ASM2016166v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5700da3-59f1-4677-97d7-ff842d382b6e/dqc_reference/reference_markers.hmm GCA_020161665.1_ASM2016166v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:39:14,028] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:39:14,029] [INFO] Found 6/6 markers.
[2023-06-29 00:39:14,062] [INFO] Query marker FASTA was written to GCA_020161665.1_ASM2016166v1_genomic.fna/markers.fasta
[2023-06-29 00:39:14,062] [INFO] Task started: Blastn
[2023-06-29 00:39:14,062] [INFO] Running command: blastn -query GCA_020161665.1_ASM2016166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5700da3-59f1-4677-97d7-ff842d382b6e/dqc_reference/reference_markers.fasta -out GCA_020161665.1_ASM2016166v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:39:14,974] [INFO] Task succeeded: Blastn
[2023-06-29 00:39:14,979] [INFO] Selected 33 target genomes.
[2023-06-29 00:39:14,980] [INFO] Target genome list was writen to GCA_020161665.1_ASM2016166v1_genomic.fna/target_genomes.txt
[2023-06-29 00:39:14,989] [INFO] Task started: fastANI
[2023-06-29 00:39:14,990] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0e73afd-cf9f-4609-af32-96022833ae3c/GCA_020161665.1_ASM2016166v1_genomic.fna.gz --refList GCA_020161665.1_ASM2016166v1_genomic.fna/target_genomes.txt --output GCA_020161665.1_ASM2016166v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:39:49,471] [INFO] Task succeeded: fastANI
[2023-06-29 00:39:49,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5700da3-59f1-4677-97d7-ff842d382b6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:39:49,472] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5700da3-59f1-4677-97d7-ff842d382b6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:39:49,498] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:39:49,498] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 00:39:49,498] [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
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	79.2876	490	1105	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.0239	460	1105	95	below_threshold
Rhizobium rosettiformans	strain=DSM 26376	GCA_014202175.1	1368430	1368430	type	True	78.8618	420	1105	95	below_threshold
Rhizobium pseudoryzae	strain=DSM 19479	GCA_011046245.1	379684	379684	type	True	78.857	480	1105	95	below_threshold
Rhizobium oryzihabitans	strain=M15	GCA_010669145.1	2267833	2267833	type	True	78.8225	489	1105	95	below_threshold
Agrobacterium salinitolerans	strain=YIC 5082	GCA_002008225.1	1183413	1183413	type	True	78.8188	470	1105	95	below_threshold
Rhizobium pusense	strain=LMG 25623	GCA_900102105.1	648995	648995	type	True	78.723	437	1105	95	below_threshold
Rhizobium pusense	strain=NRCPB10	GCA_002008275.1	648995	648995	type	True	78.7086	435	1105	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	78.708	467	1105	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	78.7007	468	1105	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	78.6985	451	1105	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	78.6852	474	1105	95	below_threshold
Rhizobium wenxiniae	strain=CGMCC 1.15279	GCA_014641515.1	1737357	1737357	type	True	78.6763	391	1105	95	below_threshold
Rhizobium wuzhouense	strain=W44	GCA_003205195.1	1986026	1986026	type	True	78.6651	421	1105	95	below_threshold
Rhizobium metallidurans	strain=DSM 26575	GCA_014196505.1	1265931	1265931	type	True	78.6628	423	1105	95	below_threshold
Rhizobium wenxiniae	strain=DSM 100734	GCA_014201355.1	1737357	1737357	type	True	78.5899	403	1105	95	below_threshold
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	78.5448	394	1105	95	below_threshold
Rhizobium chutanense	strain=C5	GCA_002531935.1	2035448	2035448	type	True	78.5412	439	1105	95	below_threshold
Neorhizobium galegae	strain=HAMBI 540	GCA_000731315.1	399	399	suspected-type	True	78.4509	431	1105	95	below_threshold
Rhizobium binae	strain=BLR195	GCA_017357225.1	1138190	1138190	type	True	78.4416	418	1105	95	below_threshold
Rhizobium indicum	strain=JKLM 12A2	GCA_005862305.2	2583231	2583231	type	True	78.4382	446	1105	95	below_threshold
Rhizobium glycinendophyticum	strain=CL12	GCA_006443685.1	2589807	2589807	type	True	78.4179	411	1105	95	below_threshold
Rhizobium ecuadorense	strain=CNPSO 671	GCA_001187535.1	1671795	1671795	type	True	78.416	447	1105	95	below_threshold
Rhizobium ruizarguesonis	strain=UPM1133	GCA_012349115.1	2081791	2081791	type	True	78.3947	441	1105	95	below_threshold
Rhizobium binae	strain=BLR195	GCA_019684455.1	1138190	1138190	type	True	78.3835	427	1105	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	78.3396	418	1105	95	below_threshold
Rhizobium rhizophilum	strain=7209-2	GCA_004912145.1	1850373	1850373	type	True	78.3394	420	1105	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	78.3348	373	1105	95	below_threshold
Rhizobium multihospitium	strain=HAMBI 2975	GCA_900094585.1	410764	410764	type	True	78.276	432	1105	95	below_threshold
Rhizobium grahamii	strain=CCGE 502	GCA_000298315.2	1120045	1120045	type	True	78.2397	328	1105	95	below_threshold
Rhizobium fabae	strain=CCBAU 33202	GCA_003985135.1	573179	573179	type	True	78.2262	445	1105	95	below_threshold
Rhizobium vallis	strain=CCBAU 65647	GCA_003985155.1	634290	634290	type	True	78.1634	435	1105	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	77.9411	366	1105	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 00:39:49,500] [INFO] DFAST Taxonomy check result was written to GCA_020161665.1_ASM2016166v1_genomic.fna/tc_result.tsv
[2023-06-29 00:39:49,501] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:39:49,501] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:39:49,501] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5700da3-59f1-4677-97d7-ff842d382b6e/dqc_reference/checkm_data
[2023-06-29 00:39:49,502] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:39:49,541] [INFO] Task started: CheckM
[2023-06-29 00:39:49,541] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020161665.1_ASM2016166v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020161665.1_ASM2016166v1_genomic.fna/checkm_input GCA_020161665.1_ASM2016166v1_genomic.fna/checkm_result
[2023-06-29 00:40:25,410] [INFO] Task succeeded: CheckM
[2023-06-29 00:40:25,412] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 00:40:25,438] [INFO] ===== Completeness check finished =====
[2023-06-29 00:40:25,439] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:40:25,439] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020161665.1_ASM2016166v1_genomic.fna/markers.fasta)
[2023-06-29 00:40:25,439] [INFO] Task started: Blastn
[2023-06-29 00:40:25,440] [INFO] Running command: blastn -query GCA_020161665.1_ASM2016166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5700da3-59f1-4677-97d7-ff842d382b6e/dqc_reference/reference_markers_gtdb.fasta -out GCA_020161665.1_ASM2016166v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:40:27,169] [INFO] Task succeeded: Blastn
[2023-06-29 00:40:27,179] [INFO] Selected 30 target genomes.
[2023-06-29 00:40:27,179] [INFO] Target genome list was writen to GCA_020161665.1_ASM2016166v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:40:27,227] [INFO] Task started: fastANI
[2023-06-29 00:40:27,227] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0e73afd-cf9f-4609-af32-96022833ae3c/GCA_020161665.1_ASM2016166v1_genomic.fna.gz --refList GCA_020161665.1_ASM2016166v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020161665.1_ASM2016166v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:40:57,661] [INFO] Task succeeded: fastANI
[2023-06-29 00:40:57,686] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 00:40:57,687] [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_014196535.1	s__Rhizobium_B borbori	81.3069	756	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_B	95.0	98.16	98.16	0.88	0.88	2	-
GCA_017744915.1	s__Agrobacterium tumefaciens_I	79.1448	480	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005205.3	s__Agrobacterium rhizogenes_A	79.0278	505	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.60	97.88	0.94	0.88	11	-
GCF_007004135.1	s__Rhizobium_A straminoryzae	78.9845	487	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	98.62	98.62	0.94	0.94	2	-
GCF_900492205.1	s__Allorhizobium naphthalenivorans_A	78.9749	483	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	95.27	95.27	0.88	0.88	2	-
GCF_900012615.1	s__Agrobacterium sp900012615	78.9746	474	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.47	97.45	0.92	0.92	3	-
GCF_017877135.1	s__Rhizobium_A galegae_A	78.9393	480	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007002745.1	s__Agrobacterium rhizogenes_B	78.924	471	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829835.1	s__Neorhizobium sp002431175	78.8831	463	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	95.71	95.71	0.88	0.88	2	-
GCF_010669145.1	s__Agrobacterium oryzihabitans	78.828	488	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.96	97.17	0.87	0.79	9	-
GCF_002008225.1	s__Agrobacterium salinitolerans	78.8134	471	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.86	95.71	0.92	0.87	11	-
GCF_017877055.1	s__Neorhizobium galegae_D	78.7409	443	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102105.1	s__Agrobacterium pusense	78.7325	436	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.39	97.95	0.91	0.74	79	-
GCF_000732195.1	s__Neorhizobium vignae	78.7167	449	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900466875.1	s__Neorhizobium sp900466875	78.6814	412	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196505.1	s__Rhizobium metallidurans	78.6814	421	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001713475.1	s__Allorhizobium sp001713475	78.6351	411	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	98.17	97.98	0.95	0.89	6	-
GCA_017305935.1	s__Rhizobium sp017305935	78.5982	508	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002211285.1	s__Rhizobium sp002211285	78.5969	449	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300855.1	s__Allorhizobium albertimagni	78.5839	426	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222845.1	s__Rhizobium_A sp005222845	78.5797	473	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241215.1	s__Agrobacterium fabrum_A	78.5788	358	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013390595.1	s__Agrobacterium sp005938205	78.5556	355	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003491345.1	s__Neorhizobium sp003491345	78.5379	389	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002531935.1	s__Rhizobium chutanense	78.5366	440	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.76	96.76	0.89	0.89	2	-
GCF_003597675.1	s__Neorhizobium sp003597675	78.5272	454	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016806065.1	s__Allorhizobium sp001724035	78.4131	413	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.77	96.77	0.91	0.91	2	-
GCF_001692325.1	s__Rhizobium sp001692325	78.3017	429	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.36	95.29	0.93	0.90	3	-
GCF_000621665.1	s__Allorhizobium undicola	78.2613	415	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003985155.1	s__Rhizobium vallis	78.1723	434	1105	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 00:40:57,693] [INFO] GTDB search result was written to GCA_020161665.1_ASM2016166v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:40:57,694] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:40:57,707] [INFO] DFAST_QC result json was written to GCA_020161665.1_ASM2016166v1_genomic.fna/dqc_result.json
[2023-06-29 00:40:57,708] [INFO] DFAST_QC completed!
[2023-06-29 00:40:57,708] [INFO] Total running time: 0h1m56s