[2023-06-05 18:05:12,444] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:05:12,467] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:05:12,468] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b5cdf21-2e2f-4796-a8d4-51e9532cdc9d/dqc_reference
[2023-06-05 18:05:13,887] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:05:13,888] [INFO] Task started: Prodigal
[2023-06-05 18:05:13,888] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f210d84-8f5c-4efa-bbe0-1aae99fa392e/GCA_004018175.1_ASM401817v1_genomic.fna.gz | prodigal -d GCA_004018175.1_ASM401817v1_genomic.fna/cds.fna -a GCA_004018175.1_ASM401817v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:06:01,305] [INFO] Task succeeded: Prodigal
[2023-06-05 18:06:01,306] [INFO] Task started: HMMsearch
[2023-06-05 18:06:01,306] [INFO] Running command: hmmsearch --tblout GCA_004018175.1_ASM401817v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b5cdf21-2e2f-4796-a8d4-51e9532cdc9d/dqc_reference/reference_markers.hmm GCA_004018175.1_ASM401817v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:06:01,714] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:06:01,716] [INFO] Found 6/6 markers.
[2023-06-05 18:06:01,772] [INFO] Query marker FASTA was written to GCA_004018175.1_ASM401817v1_genomic.fna/markers.fasta
[2023-06-05 18:06:01,772] [INFO] Task started: Blastn
[2023-06-05 18:06:01,773] [INFO] Running command: blastn -query GCA_004018175.1_ASM401817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b5cdf21-2e2f-4796-a8d4-51e9532cdc9d/dqc_reference/reference_markers.fasta -out GCA_004018175.1_ASM401817v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:06:03,447] [INFO] Task succeeded: Blastn
[2023-06-05 18:06:03,470] [INFO] Selected 11 target genomes.
[2023-06-05 18:06:03,474] [INFO] Target genome list was writen to GCA_004018175.1_ASM401817v1_genomic.fna/target_genomes.txt
[2023-06-05 18:06:03,486] [INFO] Task started: fastANI
[2023-06-05 18:06:03,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f210d84-8f5c-4efa-bbe0-1aae99fa392e/GCA_004018175.1_ASM401817v1_genomic.fna.gz --refList GCA_004018175.1_ASM401817v1_genomic.fna/target_genomes.txt --output GCA_004018175.1_ASM401817v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:06:28,167] [INFO] Task succeeded: fastANI
[2023-06-05 18:06:28,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b5cdf21-2e2f-4796-a8d4-51e9532cdc9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:06:28,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b5cdf21-2e2f-4796-a8d4-51e9532cdc9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:06:28,179] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-06-05 18:06:28,179] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 18:06:28,180] [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 wenxiniae	strain=WYCCWR 10195	GCA_002284535.1	2014805	2014805	type	True	95.5948	1777	2193	95	conclusive
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	93.1984	1770	2193	95	below_threshold
Mesorhizobium temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	93.146	1751	2193	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	92.2256	1712	2193	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	87.4875	1390	2193	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	87.0967	1433	2193	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	87.0181	1295	2193	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	83.7832	1222	2193	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.009	633	2193	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	78.9826	686	2193	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.9724	687	2193	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:06:28,182] [INFO] DFAST Taxonomy check result was written to GCA_004018175.1_ASM401817v1_genomic.fna/tc_result.tsv
[2023-06-05 18:06:28,183] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:06:28,183] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:06:28,183] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b5cdf21-2e2f-4796-a8d4-51e9532cdc9d/dqc_reference/checkm_data
[2023-06-05 18:06:28,185] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:06:28,389] [INFO] Task started: CheckM
[2023-06-05 18:06:28,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004018175.1_ASM401817v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004018175.1_ASM401817v1_genomic.fna/checkm_input GCA_004018175.1_ASM401817v1_genomic.fna/checkm_result
[2023-06-05 18:07:53,032] [INFO] Task succeeded: CheckM
[2023-06-05 18:07:53,033] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:07:53,057] [INFO] ===== Completeness check finished =====
[2023-06-05 18:07:53,058] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:07:53,058] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004018175.1_ASM401817v1_genomic.fna/markers.fasta)
[2023-06-05 18:07:53,058] [INFO] Task started: Blastn
[2023-06-05 18:07:53,059] [INFO] Running command: blastn -query GCA_004018175.1_ASM401817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b5cdf21-2e2f-4796-a8d4-51e9532cdc9d/dqc_reference/reference_markers_gtdb.fasta -out GCA_004018175.1_ASM401817v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:07:55,257] [INFO] Task succeeded: Blastn
[2023-06-05 18:07:55,262] [INFO] Selected 10 target genomes.
[2023-06-05 18:07:55,262] [INFO] Target genome list was writen to GCA_004018175.1_ASM401817v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:07:55,263] [INFO] Task started: fastANI
[2023-06-05 18:07:55,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f210d84-8f5c-4efa-bbe0-1aae99fa392e/GCA_004018175.1_ASM401817v1_genomic.fna.gz --refList GCA_004018175.1_ASM401817v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004018175.1_ASM401817v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:08:13,102] [INFO] Task succeeded: fastANI
[2023-06-05 18:08:13,111] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:08:13,111] [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_002284535.1	s__Mesorhizobium wenxiniae	95.6052	1776	2193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.50	95.53	0.83	0.79	62	conclusive
GCA_004020645.1	s__Mesorhizobium sp004020645	93.9412	1864	2193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.46	97.82	0.90	0.85	20	-
GCF_002284575.1	s__Mesorhizobium temperatum	93.146	1751	2193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	95.74	95.09	0.81	0.81	3	-
GCA_004020315.1	s__Mesorhizobium sp004020315	92.9624	1710	2193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.08	99.08	0.89	0.89	2	-
GCF_900099905.1	s__Mesorhizobium muleiense	92.2358	1711	2193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.77	96.33	0.85	0.80	57	-
GCF_900156895.1	s__Mesorhizobium prunaredense	92.2171	1645	2193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004020365.1	s__Mesorhizobium sp004020365	92.1481	1691	2193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.10	96.06	0.82	0.80	8	-
GCF_002284565.1	s__Mesorhizobium mediterraneum_A	92.0351	1701	2193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.16	97.72	0.92	0.89	20	-
GCF_016756595.1	s__Mesorhizobium sp004020105	91.7398	1715	2193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.38	95.83	0.84	0.81	7	-
GCA_004962925.1	s__Mesorhizobium sp004962925	91.6983	1534	2193	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 18:08:13,113] [INFO] GTDB search result was written to GCA_004018175.1_ASM401817v1_genomic.fna/result_gtdb.tsv
[2023-06-05 18:08:13,114] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:08:13,118] [INFO] DFAST_QC result json was written to GCA_004018175.1_ASM401817v1_genomic.fna/dqc_result.json
[2023-06-05 18:08:13,118] [INFO] DFAST_QC completed!
[2023-06-05 18:08:13,118] [INFO] Total running time: 0h3m1s