[2023-06-04 19:18:19,409] [INFO] DFAST_QC pipeline started.
[2023-06-04 19:18:19,414] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 19:18:19,414] [INFO] DQC Reference Directory: /var/lib/cwl/stg44fe8804-7d3b-45c0-bfb4-19b439539bfa/dqc_reference
[2023-06-04 19:18:20,768] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 19:18:20,769] [INFO] Task started: Prodigal
[2023-06-04 19:18:20,769] [INFO] Running command: gunzip -c /var/lib/cwl/stgba4589e5-fb2c-45a2-b413-960f4e85f58a/GCA_004964035.1_ASM496403v1_genomic.fna.gz | prodigal -d GCA_004964035.1_ASM496403v1_genomic.fna/cds.fna -a GCA_004964035.1_ASM496403v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 19:18:28,482] [INFO] Task succeeded: Prodigal
[2023-06-04 19:18:28,483] [INFO] Task started: HMMsearch
[2023-06-04 19:18:28,483] [INFO] Running command: hmmsearch --tblout GCA_004964035.1_ASM496403v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44fe8804-7d3b-45c0-bfb4-19b439539bfa/dqc_reference/reference_markers.hmm GCA_004964035.1_ASM496403v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 19:18:28,714] [INFO] Task succeeded: HMMsearch
[2023-06-04 19:18:28,716] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgba4589e5-fb2c-45a2-b413-960f4e85f58a/GCA_004964035.1_ASM496403v1_genomic.fna.gz]
[2023-06-04 19:18:28,758] [INFO] Query marker FASTA was written to GCA_004964035.1_ASM496403v1_genomic.fna/markers.fasta
[2023-06-04 19:18:28,759] [INFO] Task started: Blastn
[2023-06-04 19:18:28,759] [INFO] Running command: blastn -query GCA_004964035.1_ASM496403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44fe8804-7d3b-45c0-bfb4-19b439539bfa/dqc_reference/reference_markers.fasta -out GCA_004964035.1_ASM496403v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:18:29,395] [INFO] Task succeeded: Blastn
[2023-06-04 19:18:29,400] [INFO] Selected 9 target genomes.
[2023-06-04 19:18:29,400] [INFO] Target genome list was writen to GCA_004964035.1_ASM496403v1_genomic.fna/target_genomes.txt
[2023-06-04 19:18:29,402] [INFO] Task started: fastANI
[2023-06-04 19:18:29,403] [INFO] Running command: fastANI --query /var/lib/cwl/stgba4589e5-fb2c-45a2-b413-960f4e85f58a/GCA_004964035.1_ASM496403v1_genomic.fna.gz --refList GCA_004964035.1_ASM496403v1_genomic.fna/target_genomes.txt --output GCA_004964035.1_ASM496403v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 19:18:38,363] [INFO] Task succeeded: fastANI
[2023-06-04 19:18:38,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44fe8804-7d3b-45c0-bfb4-19b439539bfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 19:18:38,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44fe8804-7d3b-45c0-bfb4-19b439539bfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 19:18:38,380] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 19:18:38,381] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 19:18:38,381] [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 atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	89.6468	102	169	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	87.241	106	169	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	85.5544	101	169	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	85.2144	99	169	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	84.5377	83	169	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	84.0726	97	169	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	84.0523	96	169	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	83.4358	102	169	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	83.4022	99	169	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 19:18:38,384] [INFO] DFAST Taxonomy check result was written to GCA_004964035.1_ASM496403v1_genomic.fna/tc_result.tsv
[2023-06-04 19:18:38,384] [INFO] ===== Taxonomy check completed =====
[2023-06-04 19:18:38,385] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 19:18:38,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44fe8804-7d3b-45c0-bfb4-19b439539bfa/dqc_reference/checkm_data
[2023-06-04 19:18:38,386] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 19:18:38,426] [INFO] Task started: CheckM
[2023-06-04 19:18:38,427] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004964035.1_ASM496403v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004964035.1_ASM496403v1_genomic.fna/checkm_input GCA_004964035.1_ASM496403v1_genomic.fna/checkm_result
[2023-06-04 19:19:06,789] [INFO] Task succeeded: CheckM
[2023-06-04 19:19:06,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.76%
Contamintation: 3.01%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 19:19:06,818] [INFO] ===== Completeness check finished =====
[2023-06-04 19:19:06,819] [INFO] ===== Start GTDB Search =====
[2023-06-04 19:19:06,819] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004964035.1_ASM496403v1_genomic.fna/markers.fasta)
[2023-06-04 19:19:06,820] [INFO] Task started: Blastn
[2023-06-04 19:19:06,820] [INFO] Running command: blastn -query GCA_004964035.1_ASM496403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44fe8804-7d3b-45c0-bfb4-19b439539bfa/dqc_reference/reference_markers_gtdb.fasta -out GCA_004964035.1_ASM496403v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:19:07,672] [INFO] Task succeeded: Blastn
[2023-06-04 19:19:07,677] [INFO] Selected 10 target genomes.
[2023-06-04 19:19:07,677] [INFO] Target genome list was writen to GCA_004964035.1_ASM496403v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 19:19:07,721] [INFO] Task started: fastANI
[2023-06-04 19:19:07,722] [INFO] Running command: fastANI --query /var/lib/cwl/stgba4589e5-fb2c-45a2-b413-960f4e85f58a/GCA_004964035.1_ASM496403v1_genomic.fna.gz --refList GCA_004964035.1_ASM496403v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004964035.1_ASM496403v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 19:19:16,317] [INFO] Task succeeded: fastANI
[2023-06-04 19:19:16,331] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-04 19:19:16,332] [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_003952425.1	s__Mesorhizobium sp003952425	94.7856	139	169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.51	95.02	0.90	0.84	19	-
GCA_004017535.1	s__Mesorhizobium sp004017535	93.8541	137	169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.05	98.03	0.89	0.85	7	-
GCF_004016445.2	s__Mesorhizobium sp004016445	93.6371	145	169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	96.92	0.94	0.90	3	-
GCA_000824845.1	s__Mesorhizobium sp000824845	93.6225	113	169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004020875.1	s__Mesorhizobium sp004020875	91.3014	122	169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.89	99.01	0.98	0.89	11	-
GCF_003289965.1	s__Mesorhizobium atlanticum	89.6468	102	169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006440735.1	s__Mesorhizobium sp006440735	88.9855	93	169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000824785.1	s__Mesorhizobium plurifarium	88.811	101	169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.23	96.62	0.87	0.84	6	-
GCA_003963455.1	s__Mesorhizobium sp003963455	87.075	86	169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002294985.1	s__Mesorhizobium sp002294985	85.0386	92	169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.32	96.92	0.87	0.76	62	-
--------------------------------------------------------------------------------
[2023-06-04 19:19:16,334] [INFO] GTDB search result was written to GCA_004964035.1_ASM496403v1_genomic.fna/result_gtdb.tsv
[2023-06-04 19:19:16,334] [INFO] ===== GTDB Search completed =====
[2023-06-04 19:19:16,337] [INFO] DFAST_QC result json was written to GCA_004964035.1_ASM496403v1_genomic.fna/dqc_result.json
[2023-06-04 19:19:16,338] [INFO] DFAST_QC completed!
[2023-06-04 19:19:16,338] [INFO] Total running time: 0h0m57s