[2024-01-24 14:11:49,353] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:49,355] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:49,355] [INFO] DQC Reference Directory: /var/lib/cwl/stgda6b13fa-4a05-403c-9720-ea11d1dbc661/dqc_reference
[2024-01-24 14:11:50,827] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:50,828] [INFO] Task started: Prodigal
[2024-01-24 14:11:50,828] [INFO] Running command: gunzip -c /var/lib/cwl/stg87665765-308e-4366-a62d-69991808fcd5/GCF_003601975.1_ASM360197v1_genomic.fna.gz | prodigal -d GCF_003601975.1_ASM360197v1_genomic.fna/cds.fna -a GCF_003601975.1_ASM360197v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:16,059] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:16,060] [INFO] Task started: HMMsearch
[2024-01-24 14:12:16,060] [INFO] Running command: hmmsearch --tblout GCF_003601975.1_ASM360197v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda6b13fa-4a05-403c-9720-ea11d1dbc661/dqc_reference/reference_markers.hmm GCF_003601975.1_ASM360197v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:16,495] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:16,496] [INFO] Found 6/6 markers.
[2024-01-24 14:12:16,568] [INFO] Query marker FASTA was written to GCF_003601975.1_ASM360197v1_genomic.fna/markers.fasta
[2024-01-24 14:12:16,568] [INFO] Task started: Blastn
[2024-01-24 14:12:16,568] [INFO] Running command: blastn -query GCF_003601975.1_ASM360197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda6b13fa-4a05-403c-9720-ea11d1dbc661/dqc_reference/reference_markers.fasta -out GCF_003601975.1_ASM360197v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:17,850] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:17,853] [INFO] Selected 19 target genomes.
[2024-01-24 14:12:17,853] [INFO] Target genome list was writen to GCF_003601975.1_ASM360197v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:17,864] [INFO] Task started: fastANI
[2024-01-24 14:12:17,864] [INFO] Running command: fastANI --query /var/lib/cwl/stg87665765-308e-4366-a62d-69991808fcd5/GCF_003601975.1_ASM360197v1_genomic.fna.gz --refList GCF_003601975.1_ASM360197v1_genomic.fna/target_genomes.txt --output GCF_003601975.1_ASM360197v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:51,660] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:51,661] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda6b13fa-4a05-403c-9720-ea11d1dbc661/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:51,662] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda6b13fa-4a05-403c-9720-ea11d1dbc661/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:51,743] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:51,744] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:51,744] [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	100.0	2612	2620	95	conclusive
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	86.9043	1698	2620	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	86.8519	1427	2620	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	86.7257	1495	2620	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	86.4132	1349	2620	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	86.3641	1634	2620	95	below_threshold
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	86.3418	1590	2620	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	86.0277	1581	2620	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	86.0044	1711	2620	95	below_threshold
Mesorhizobium sangaii	strain=DSM 100039	GCA_014207355.1	505389	505389	type	True	85.96	1575	2620	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	85.8295	1549	2620	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	85.8145	1480	2620	95	below_threshold
Mesorhizobium qingshengii	strain=CGMCC 1.12097	GCA_900103325.1	1165689	1165689	type	True	85.8118	1515	2620	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	85.7626	1475	2620	95	below_threshold
Mesorhizobium japonicum	strain=MAFF 303099	GCA_000009625.1	2066070	2066070	type	True	85.6904	1589	2620	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	84.7937	1400	2620	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.0695	674	2620	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.0651	724	2620	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.0606	726	2620	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:51,745] [INFO] DFAST Taxonomy check result was written to GCF_003601975.1_ASM360197v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:51,746] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:51,746] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:51,746] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda6b13fa-4a05-403c-9720-ea11d1dbc661/dqc_reference/checkm_data
[2024-01-24 14:12:51,752] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:51,831] [INFO] Task started: CheckM
[2024-01-24 14:12:51,831] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003601975.1_ASM360197v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003601975.1_ASM360197v1_genomic.fna/checkm_input GCF_003601975.1_ASM360197v1_genomic.fna/checkm_result
[2024-01-24 14:14:12,108] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:12,110] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:12,133] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:12,134] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:12,134] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003601975.1_ASM360197v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:12,135] [INFO] Task started: Blastn
[2024-01-24 14:14:12,135] [INFO] Running command: blastn -query GCF_003601975.1_ASM360197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda6b13fa-4a05-403c-9720-ea11d1dbc661/dqc_reference/reference_markers_gtdb.fasta -out GCF_003601975.1_ASM360197v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:16,948] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:16,953] [INFO] Selected 16 target genomes.
[2024-01-24 14:14:16,953] [INFO] Target genome list was writen to GCF_003601975.1_ASM360197v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:16,977] [INFO] Task started: fastANI
[2024-01-24 14:14:16,977] [INFO] Running command: fastANI --query /var/lib/cwl/stg87665765-308e-4366-a62d-69991808fcd5/GCF_003601975.1_ASM360197v1_genomic.fna.gz --refList GCF_003601975.1_ASM360197v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003601975.1_ASM360197v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:48,330] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:48,433] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:48,434] [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_003601975.1	s__Mesorhizobium waimense	100.0	2612	2620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014843845.1	s__Mesorhizobium amorphae_A	92.7353	1884	2620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0866	97.39	97.39	0.88	0.88	2	-
GCF_001686985.1	s__Mesorhizobium amorphae_B	92.5915	1877	2620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0866	99.99	99.99	1.00	1.00	2	-
GCF_016756535.1	s__Mesorhizobium sp016756535	87.3264	1674	2620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791025.1	s__Mesorhizobium sp004791025	87.2743	1648	2620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.99	98.05	0.93	0.88	18	-
GCF_003952505.1	s__Mesorhizobium sp003952505	87.0344	1626	2620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.46	98.78	0.92	0.87	11	-
GCF_000350085.1	s__Mesorhizobium metallidurans	86.8507	1426	2620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000359125.1	s__Mesorhizobium sp000359125	86.8378	1449	2620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004010325.2	s__Mesorhizobium sp004010325	86.3644	1509	2620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.05	98.94	0.91	0.90	4	-
GCF_016836705.1	s__Mesorhizobium caraganae	86.3628	1634	2620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.40	96.20	0.88	0.86	3	-
GCF_000502715.1	s__Mesorhizobium sp000502715	86.3277	1442	2620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.12	97.73	0.92	0.90	39	-
GCF_003253745.1	s__Mesorhizobium kowhaii	86.2908	1689	2620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003353565.1	s__Mesorhizobium sp003353565	86.0635	1566	2620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103325.1	s__Mesorhizobium qingshengii	85.8208	1513	2620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013170825.1	s__Mesorhizobium sp013170825	85.3635	1472	2620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	95.36	95.35	0.82	0.81	3	-
GCF_006439515.1	s__Mesorhizobium sp006439515	85.323	1414	2620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.05	98.05	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:48,437] [INFO] GTDB search result was written to GCF_003601975.1_ASM360197v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:48,438] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:48,443] [INFO] DFAST_QC result json was written to GCF_003601975.1_ASM360197v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:48,444] [INFO] DFAST_QC completed!
[2024-01-24 14:14:48,444] [INFO] Total running time: 0h2m59s