[2023-06-28 22:25:18,042] [INFO] DFAST_QC pipeline started.
[2023-06-28 22:25:18,044] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 22:25:18,044] [INFO] DQC Reference Directory: /var/lib/cwl/stg523c5c35-124d-4c96-9a7c-315db5f851c3/dqc_reference
[2023-06-28 22:25:20,124] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 22:25:20,125] [INFO] Task started: Prodigal
[2023-06-28 22:25:20,126] [INFO] Running command: gunzip -c /var/lib/cwl/stgc08e20e8-faa3-4b49-a20e-abd75f3af593/GCA_005063105.1_ASM506310v1_genomic.fna.gz | prodigal -d GCA_005063105.1_ASM506310v1_genomic.fna/cds.fna -a GCA_005063105.1_ASM506310v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 22:25:38,118] [INFO] Task succeeded: Prodigal
[2023-06-28 22:25:38,118] [INFO] Task started: HMMsearch
[2023-06-28 22:25:38,118] [INFO] Running command: hmmsearch --tblout GCA_005063105.1_ASM506310v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg523c5c35-124d-4c96-9a7c-315db5f851c3/dqc_reference/reference_markers.hmm GCA_005063105.1_ASM506310v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 22:25:38,426] [INFO] Task succeeded: HMMsearch
[2023-06-28 22:25:38,427] [INFO] Found 6/6 markers.
[2023-06-28 22:25:38,478] [INFO] Query marker FASTA was written to GCA_005063105.1_ASM506310v1_genomic.fna/markers.fasta
[2023-06-28 22:25:38,478] [INFO] Task started: Blastn
[2023-06-28 22:25:38,479] [INFO] Running command: blastn -query GCA_005063105.1_ASM506310v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg523c5c35-124d-4c96-9a7c-315db5f851c3/dqc_reference/reference_markers.fasta -out GCA_005063105.1_ASM506310v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:25:39,556] [INFO] Task succeeded: Blastn
[2023-06-28 22:25:39,561] [INFO] Selected 15 target genomes.
[2023-06-28 22:25:39,562] [INFO] Target genome list was writen to GCA_005063105.1_ASM506310v1_genomic.fna/target_genomes.txt
[2023-06-28 22:25:39,567] [INFO] Task started: fastANI
[2023-06-28 22:25:39,568] [INFO] Running command: fastANI --query /var/lib/cwl/stgc08e20e8-faa3-4b49-a20e-abd75f3af593/GCA_005063105.1_ASM506310v1_genomic.fna.gz --refList GCA_005063105.1_ASM506310v1_genomic.fna/target_genomes.txt --output GCA_005063105.1_ASM506310v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 22:26:01,978] [INFO] Task succeeded: fastANI
[2023-06-28 22:26:01,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg523c5c35-124d-4c96-9a7c-315db5f851c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 22:26:01,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg523c5c35-124d-4c96-9a7c-315db5f851c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 22:26:01,996] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 22:26:01,996] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 22:26:01,996] [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 waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	87.0291	1493	2006	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	86.5207	1406	2006	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	86.4354	1345	2006	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	86.1128	1423	2006	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	85.9746	1396	2006	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	85.9245	1357	2006	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	85.7585	1231	2006	95	below_threshold
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	85.7578	1382	2006	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	85.6866	1282	2006	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	85.5257	1156	2006	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	84.9765	1278	2006	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	84.7439	1246	2006	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.4155	676	2006	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.4128	676	2006	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.2186	631	2006	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 22:26:01,998] [INFO] DFAST Taxonomy check result was written to GCA_005063105.1_ASM506310v1_genomic.fna/tc_result.tsv
[2023-06-28 22:26:01,998] [INFO] ===== Taxonomy check completed =====
[2023-06-28 22:26:01,998] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 22:26:01,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg523c5c35-124d-4c96-9a7c-315db5f851c3/dqc_reference/checkm_data
[2023-06-28 22:26:02,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 22:26:02,059] [INFO] Task started: CheckM
[2023-06-28 22:26:02,059] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005063105.1_ASM506310v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005063105.1_ASM506310v1_genomic.fna/checkm_input GCA_005063105.1_ASM506310v1_genomic.fna/checkm_result
[2023-06-28 22:26:54,558] [INFO] Task succeeded: CheckM
[2023-06-28 22:26:54,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 22:26:54,582] [INFO] ===== Completeness check finished =====
[2023-06-28 22:26:54,582] [INFO] ===== Start GTDB Search =====
[2023-06-28 22:26:54,583] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005063105.1_ASM506310v1_genomic.fna/markers.fasta)
[2023-06-28 22:26:54,583] [INFO] Task started: Blastn
[2023-06-28 22:26:54,583] [INFO] Running command: blastn -query GCA_005063105.1_ASM506310v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg523c5c35-124d-4c96-9a7c-315db5f851c3/dqc_reference/reference_markers_gtdb.fasta -out GCA_005063105.1_ASM506310v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:26:56,723] [INFO] Task succeeded: Blastn
[2023-06-28 22:26:56,728] [INFO] Selected 14 target genomes.
[2023-06-28 22:26:56,728] [INFO] Target genome list was writen to GCA_005063105.1_ASM506310v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 22:26:56,740] [INFO] Task started: fastANI
[2023-06-28 22:26:56,740] [INFO] Running command: fastANI --query /var/lib/cwl/stgc08e20e8-faa3-4b49-a20e-abd75f3af593/GCA_005063105.1_ASM506310v1_genomic.fna.gz --refList GCA_005063105.1_ASM506310v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005063105.1_ASM506310v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 22:27:20,213] [INFO] Task succeeded: fastANI
[2023-06-28 22:27:20,232] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 22:27:20,232] [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_003952505.1	s__Mesorhizobium sp003952505	99.7641	1836	2006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.46	98.78	0.92	0.87	11	conclusive
GCF_004791025.1	s__Mesorhizobium sp004791025	93.1299	1675	2006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.99	98.05	0.93	0.88	18	-
GCF_016756535.1	s__Mesorhizobium sp016756535	91.7147	1593	2006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952385.1	s__Mesorhizobium sp003952385	87.6084	1519	2006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.01	97.50	0.89	0.87	7	-
GCA_004963905.1	s__Mesorhizobium sp004963905	87.3991	1419	2006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952465.1	s__Mesorhizobium sp003952465	87.3719	1520	2006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.37	98.09	0.92	0.88	6	-
GCF_003952485.1	s__Mesorhizobium sp003952485	87.3585	1502	2006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.38	98.21	0.91	0.89	5	-
GCF_014843845.1	s__Mesorhizobium amorphae_A	87.1092	1473	2006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0866	97.39	97.39	0.88	0.88	2	-
GCF_003601975.1	s__Mesorhizobium waimense	87.0321	1493	2006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004016445.2	s__Mesorhizobium sp004016445	86.7492	1495	2006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	96.92	0.94	0.90	3	-
GCF_003863365.1	s__Mesorhizobium tamadayense	86.5344	1404	2006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001510895.1	s__Mesorhizobium loti_A	86.2214	1404	2006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439355.1	s__Mesorhizobium sp006439355	85.6774	1251	2006	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	84.9869	1279	2006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.67	99.16	0.95	0.91	4	-
--------------------------------------------------------------------------------
[2023-06-28 22:27:20,234] [INFO] GTDB search result was written to GCA_005063105.1_ASM506310v1_genomic.fna/result_gtdb.tsv
[2023-06-28 22:27:20,235] [INFO] ===== GTDB Search completed =====
[2023-06-28 22:27:20,242] [INFO] DFAST_QC result json was written to GCA_005063105.1_ASM506310v1_genomic.fna/dqc_result.json
[2023-06-28 22:27:20,242] [INFO] DFAST_QC completed!
[2023-06-28 22:27:20,242] [INFO] Total running time: 0h2m2s