[2023-06-05 19:00:28,458] [INFO] DFAST_QC pipeline started.
[2023-06-05 19:00:28,462] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 19:00:28,462] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ae7ba62-7acd-4edd-bbe6-077fc1e99e19/dqc_reference
[2023-06-05 19:00:29,574] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 19:00:29,575] [INFO] Task started: Prodigal
[2023-06-05 19:00:29,575] [INFO] Running command: gunzip -c /var/lib/cwl/stgf088cf65-916f-4404-b4f3-77fb7ac08dc1/GCA_004965335.1_ASM496533v1_genomic.fna.gz | prodigal -d GCA_004965335.1_ASM496533v1_genomic.fna/cds.fna -a GCA_004965335.1_ASM496533v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 19:00:45,865] [INFO] Task succeeded: Prodigal
[2023-06-05 19:00:45,866] [INFO] Task started: HMMsearch
[2023-06-05 19:00:45,866] [INFO] Running command: hmmsearch --tblout GCA_004965335.1_ASM496533v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ae7ba62-7acd-4edd-bbe6-077fc1e99e19/dqc_reference/reference_markers.hmm GCA_004965335.1_ASM496533v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 19:00:46,139] [INFO] Task succeeded: HMMsearch
[2023-06-05 19:00:46,141] [INFO] Found 6/6 markers.
[2023-06-05 19:00:46,204] [INFO] Query marker FASTA was written to GCA_004965335.1_ASM496533v1_genomic.fna/markers.fasta
[2023-06-05 19:00:46,204] [INFO] Task started: Blastn
[2023-06-05 19:00:46,204] [INFO] Running command: blastn -query GCA_004965335.1_ASM496533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ae7ba62-7acd-4edd-bbe6-077fc1e99e19/dqc_reference/reference_markers.fasta -out GCA_004965335.1_ASM496533v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 19:00:47,280] [INFO] Task succeeded: Blastn
[2023-06-05 19:00:47,288] [INFO] Selected 16 target genomes.
[2023-06-05 19:00:47,289] [INFO] Target genome list was writen to GCA_004965335.1_ASM496533v1_genomic.fna/target_genomes.txt
[2023-06-05 19:00:47,290] [INFO] Task started: fastANI
[2023-06-05 19:00:47,290] [INFO] Running command: fastANI --query /var/lib/cwl/stgf088cf65-916f-4404-b4f3-77fb7ac08dc1/GCA_004965335.1_ASM496533v1_genomic.fna.gz --refList GCA_004965335.1_ASM496533v1_genomic.fna/target_genomes.txt --output GCA_004965335.1_ASM496533v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 19:01:11,889] [INFO] Task succeeded: fastANI
[2023-06-05 19:01:11,890] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ae7ba62-7acd-4edd-bbe6-077fc1e99e19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 19:01:11,893] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ae7ba62-7acd-4edd-bbe6-077fc1e99e19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 19:01:11,904] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 19:01:11,904] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 19:01:11,904] [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	87.3087	1454	1962	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	86.6738	1372	1962	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	86.5448	1299	1962	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	86.5076	1416	1962	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	86.2575	1397	1962	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	86.1018	1351	1962	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	86.0763	1206	1962	95	below_threshold
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	86.0387	1355	1962	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	85.7923	1158	1962	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	85.7273	1240	1962	95	below_threshold
Mesorhizobium intechi	strain=BD68	GCA_002879535.2	537601	537601	type	True	85.2936	1235	1962	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	85.1453	1222	1962	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	85.0018	1263	1962	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.5964	678	1962	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.5754	680	1962	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	79.2952	614	1962	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 19:01:11,906] [INFO] DFAST Taxonomy check result was written to GCA_004965335.1_ASM496533v1_genomic.fna/tc_result.tsv
[2023-06-05 19:01:11,906] [INFO] ===== Taxonomy check completed =====
[2023-06-05 19:01:11,906] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 19:01:11,906] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ae7ba62-7acd-4edd-bbe6-077fc1e99e19/dqc_reference/checkm_data
[2023-06-05 19:01:11,907] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 19:01:11,976] [INFO] Task started: CheckM
[2023-06-05 19:01:11,976] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004965335.1_ASM496533v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004965335.1_ASM496533v1_genomic.fna/checkm_input GCA_004965335.1_ASM496533v1_genomic.fna/checkm_result
[2023-06-05 19:01:59,694] [INFO] Task succeeded: CheckM
[2023-06-05 19:01:59,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 19:01:59,717] [INFO] ===== Completeness check finished =====
[2023-06-05 19:01:59,717] [INFO] ===== Start GTDB Search =====
[2023-06-05 19:01:59,718] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004965335.1_ASM496533v1_genomic.fna/markers.fasta)
[2023-06-05 19:01:59,719] [INFO] Task started: Blastn
[2023-06-05 19:01:59,719] [INFO] Running command: blastn -query GCA_004965335.1_ASM496533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ae7ba62-7acd-4edd-bbe6-077fc1e99e19/dqc_reference/reference_markers_gtdb.fasta -out GCA_004965335.1_ASM496533v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 19:02:01,994] [INFO] Task succeeded: Blastn
[2023-06-05 19:02:01,997] [INFO] Selected 16 target genomes.
[2023-06-05 19:02:01,997] [INFO] Target genome list was writen to GCA_004965335.1_ASM496533v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 19:02:02,010] [INFO] Task started: fastANI
[2023-06-05 19:02:02,011] [INFO] Running command: fastANI --query /var/lib/cwl/stgf088cf65-916f-4404-b4f3-77fb7ac08dc1/GCA_004965335.1_ASM496533v1_genomic.fna.gz --refList GCA_004965335.1_ASM496533v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004965335.1_ASM496533v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 19:02:29,441] [INFO] Task succeeded: fastANI
[2023-06-05 19:02:29,453] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 19:02:29,453] [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_004791025.1	s__Mesorhizobium sp004791025	99.6538	1881	1962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.99	98.05	0.93	0.88	18	conclusive
GCF_003952505.1	s__Mesorhizobium sp003952505	92.9618	1635	1962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.46	98.78	0.92	0.87	11	-
GCF_016756535.1	s__Mesorhizobium sp016756535	90.777	1578	1962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001686985.1	s__Mesorhizobium amorphae_B	87.7244	1474	1962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0866	99.99	99.99	1.00	1.00	2	-
GCF_004791585.1	s__Mesorhizobium sp004791585	87.6906	1476	1962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.07	98.11	0.95	0.89	24	-
GCF_003952465.1	s__Mesorhizobium sp003952465	87.5515	1483	1962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.37	98.09	0.92	0.88	6	-
GCF_014843845.1	s__Mesorhizobium amorphae_A	87.4634	1411	1962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0866	97.39	97.39	0.88	0.88	2	-
GCA_004963905.1	s__Mesorhizobium sp004963905	87.3888	1385	1962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952485.1	s__Mesorhizobium sp003952485	87.246	1492	1962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.38	98.21	0.91	0.89	5	-
GCF_004016445.2	s__Mesorhizobium sp004016445	87.1605	1461	1962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	96.92	0.94	0.90	3	-
GCF_003952525.1	s__Mesorhizobium sp002294945	86.968	1352	1962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.39	99.02	0.88	0.85	8	-
GCF_002294725.1	s__Mesorhizobium sp002294725	86.9374	1362	1962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.90	96.90	0.87	0.87	2	-
GCF_019091085.1	s__Mesorhizobium sp019091085	86.7282	1281	1962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003863365.1	s__Mesorhizobium tamadayense	86.6721	1371	1962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000350085.1	s__Mesorhizobium metallidurans	86.0666	1207	1962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000824805.1	s__Mesorhizobium sp000824805	86.017	1277	1962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 19:02:29,462] [INFO] GTDB search result was written to GCA_004965335.1_ASM496533v1_genomic.fna/result_gtdb.tsv
[2023-06-05 19:02:29,462] [INFO] ===== GTDB Search completed =====
[2023-06-05 19:02:29,466] [INFO] DFAST_QC result json was written to GCA_004965335.1_ASM496533v1_genomic.fna/dqc_result.json
[2023-06-05 19:02:29,466] [INFO] DFAST_QC completed!
[2023-06-05 19:02:29,466] [INFO] Total running time: 0h2m1s