[2023-06-04 21:25:23,717] [INFO] DFAST_QC pipeline started.
[2023-06-04 21:25:23,721] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 21:25:23,721] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0330f59-54d6-4199-932b-f0d266e1eb05/dqc_reference
[2023-06-04 21:25:26,944] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 21:25:26,945] [INFO] Task started: Prodigal
[2023-06-04 21:25:26,945] [INFO] Running command: gunzip -c /var/lib/cwl/stgcdba7ccc-e8bc-4649-96ba-a967f7c75b0f/GCA_004962995.1_ASM496299v1_genomic.fna.gz | prodigal -d GCA_004962995.1_ASM496299v1_genomic.fna/cds.fna -a GCA_004962995.1_ASM496299v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 21:25:48,533] [INFO] Task succeeded: Prodigal
[2023-06-04 21:25:48,534] [INFO] Task started: HMMsearch
[2023-06-04 21:25:48,534] [INFO] Running command: hmmsearch --tblout GCA_004962995.1_ASM496299v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0330f59-54d6-4199-932b-f0d266e1eb05/dqc_reference/reference_markers.hmm GCA_004962995.1_ASM496299v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 21:25:48,880] [INFO] Task succeeded: HMMsearch
[2023-06-04 21:25:48,881] [INFO] Found 6/6 markers.
[2023-06-04 21:25:48,944] [INFO] Query marker FASTA was written to GCA_004962995.1_ASM496299v1_genomic.fna/markers.fasta
[2023-06-04 21:25:48,944] [INFO] Task started: Blastn
[2023-06-04 21:25:48,944] [INFO] Running command: blastn -query GCA_004962995.1_ASM496299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0330f59-54d6-4199-932b-f0d266e1eb05/dqc_reference/reference_markers.fasta -out GCA_004962995.1_ASM496299v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:25:50,005] [INFO] Task succeeded: Blastn
[2023-06-04 21:25:50,009] [INFO] Selected 11 target genomes.
[2023-06-04 21:25:50,010] [INFO] Target genome list was writen to GCA_004962995.1_ASM496299v1_genomic.fna/target_genomes.txt
[2023-06-04 21:25:50,013] [INFO] Task started: fastANI
[2023-06-04 21:25:50,014] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdba7ccc-e8bc-4649-96ba-a967f7c75b0f/GCA_004962995.1_ASM496299v1_genomic.fna.gz --refList GCA_004962995.1_ASM496299v1_genomic.fna/target_genomes.txt --output GCA_004962995.1_ASM496299v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 21:26:07,588] [INFO] Task succeeded: fastANI
[2023-06-04 21:26:07,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0330f59-54d6-4199-932b-f0d266e1eb05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 21:26:07,589] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0330f59-54d6-4199-932b-f0d266e1eb05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 21:26:07,603] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 21:26:07,603] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 21:26:07,603] [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 muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	94.7359	1821	2362	95	below_threshold
Mesorhizobium wenxiniae	strain=WYCCWR 10195	GCA_002284535.1	2014805	2014805	type	True	92.529	1716	2362	95	below_threshold
Mesorhizobium temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	92.3816	1722	2362	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	92.0063	1735	2362	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	87.0973	1347	2362	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	86.7781	1381	2362	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	86.6615	1254	2362	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	83.8026	1174	2362	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.2165	640	2362	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.0162	704	2362	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.0025	705	2362	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 21:26:07,606] [INFO] DFAST Taxonomy check result was written to GCA_004962995.1_ASM496299v1_genomic.fna/tc_result.tsv
[2023-06-04 21:26:07,606] [INFO] ===== Taxonomy check completed =====
[2023-06-04 21:26:07,606] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 21:26:07,607] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0330f59-54d6-4199-932b-f0d266e1eb05/dqc_reference/checkm_data
[2023-06-04 21:26:07,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 21:26:07,680] [INFO] Task started: CheckM
[2023-06-04 21:26:07,681] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004962995.1_ASM496299v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004962995.1_ASM496299v1_genomic.fna/checkm_input GCA_004962995.1_ASM496299v1_genomic.fna/checkm_result
[2023-06-04 21:27:08,986] [INFO] Task succeeded: CheckM
[2023-06-04 21:27:08,987] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.50%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-04 21:27:09,015] [INFO] ===== Completeness check finished =====
[2023-06-04 21:27:09,015] [INFO] ===== Start GTDB Search =====
[2023-06-04 21:27:09,016] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004962995.1_ASM496299v1_genomic.fna/markers.fasta)
[2023-06-04 21:27:09,016] [INFO] Task started: Blastn
[2023-06-04 21:27:09,016] [INFO] Running command: blastn -query GCA_004962995.1_ASM496299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0330f59-54d6-4199-932b-f0d266e1eb05/dqc_reference/reference_markers_gtdb.fasta -out GCA_004962995.1_ASM496299v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:27:11,126] [INFO] Task succeeded: Blastn
[2023-06-04 21:27:11,131] [INFO] Selected 9 target genomes.
[2023-06-04 21:27:11,132] [INFO] Target genome list was writen to GCA_004962995.1_ASM496299v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 21:27:11,136] [INFO] Task started: fastANI
[2023-06-04 21:27:11,136] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdba7ccc-e8bc-4649-96ba-a967f7c75b0f/GCA_004962995.1_ASM496299v1_genomic.fna.gz --refList GCA_004962995.1_ASM496299v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004962995.1_ASM496299v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 21:27:28,847] [INFO] Task succeeded: fastANI
[2023-06-04 21:27:28,861] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 21:27:28,861] [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_016756595.1	s__Mesorhizobium sp004020105	98.0578	1991	2362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.38	95.83	0.84	0.81	7	conclusive
GCF_900099905.1	s__Mesorhizobium muleiense	94.7488	1819	2362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.77	96.33	0.85	0.80	57	-
GCA_004020365.1	s__Mesorhizobium sp004020365	94.7323	1835	2362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.10	96.06	0.82	0.80	8	-
GCF_900156895.1	s__Mesorhizobium prunaredense	93.9764	1723	2362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004020315.1	s__Mesorhizobium sp004020315	92.805	1748	2362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.08	99.08	0.89	0.89	2	-
GCA_004020645.1	s__Mesorhizobium sp004020645	92.7758	1814	2362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.46	97.82	0.90	0.85	20	-
GCF_002284535.1	s__Mesorhizobium wenxiniae	92.5429	1715	2362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.50	95.53	0.83	0.79	62	-
GCF_002284575.1	s__Mesorhizobium temperatum	92.3876	1720	2362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	95.74	95.09	0.81	0.81	3	-
GCF_002284565.1	s__Mesorhizobium mediterraneum_A	91.4817	1659	2362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.16	97.72	0.92	0.89	20	-
--------------------------------------------------------------------------------
[2023-06-04 21:27:28,864] [INFO] GTDB search result was written to GCA_004962995.1_ASM496299v1_genomic.fna/result_gtdb.tsv
[2023-06-04 21:27:28,865] [INFO] ===== GTDB Search completed =====
[2023-06-04 21:27:28,871] [INFO] DFAST_QC result json was written to GCA_004962995.1_ASM496299v1_genomic.fna/dqc_result.json
[2023-06-04 21:27:28,872] [INFO] DFAST_QC completed!
[2023-06-04 21:27:28,872] [INFO] Total running time: 0h2m5s