[2023-06-04 22:02:53,712] [INFO] DFAST_QC pipeline started.
[2023-06-04 22:02:53,717] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 22:02:53,718] [INFO] DQC Reference Directory: /var/lib/cwl/stgc76b5f03-ed7a-498e-8c93-49e47abf5de3/dqc_reference
[2023-06-04 22:02:56,011] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 22:02:56,012] [INFO] Task started: Prodigal
[2023-06-04 22:02:56,012] [INFO] Running command: gunzip -c /var/lib/cwl/stg57b5b9b7-cc3e-432c-9044-fdd694c078f5/GCA_004018595.1_ASM401859v1_genomic.fna.gz | prodigal -d GCA_004018595.1_ASM401859v1_genomic.fna/cds.fna -a GCA_004018595.1_ASM401859v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 22:03:16,490] [INFO] Task succeeded: Prodigal
[2023-06-04 22:03:16,490] [INFO] Task started: HMMsearch
[2023-06-04 22:03:16,490] [INFO] Running command: hmmsearch --tblout GCA_004018595.1_ASM401859v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc76b5f03-ed7a-498e-8c93-49e47abf5de3/dqc_reference/reference_markers.hmm GCA_004018595.1_ASM401859v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 22:03:16,859] [INFO] Task succeeded: HMMsearch
[2023-06-04 22:03:16,860] [INFO] Found 6/6 markers.
[2023-06-04 22:03:16,924] [INFO] Query marker FASTA was written to GCA_004018595.1_ASM401859v1_genomic.fna/markers.fasta
[2023-06-04 22:03:16,925] [INFO] Task started: Blastn
[2023-06-04 22:03:16,925] [INFO] Running command: blastn -query GCA_004018595.1_ASM401859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc76b5f03-ed7a-498e-8c93-49e47abf5de3/dqc_reference/reference_markers.fasta -out GCA_004018595.1_ASM401859v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:03:18,027] [INFO] Task succeeded: Blastn
[2023-06-04 22:03:18,030] [INFO] Selected 15 target genomes.
[2023-06-04 22:03:18,031] [INFO] Target genome list was writen to GCA_004018595.1_ASM401859v1_genomic.fna/target_genomes.txt
[2023-06-04 22:03:18,032] [INFO] Task started: fastANI
[2023-06-04 22:03:18,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg57b5b9b7-cc3e-432c-9044-fdd694c078f5/GCA_004018595.1_ASM401859v1_genomic.fna.gz --refList GCA_004018595.1_ASM401859v1_genomic.fna/target_genomes.txt --output GCA_004018595.1_ASM401859v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 22:03:41,479] [INFO] Task succeeded: fastANI
[2023-06-04 22:03:41,480] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc76b5f03-ed7a-498e-8c93-49e47abf5de3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 22:03:41,481] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc76b5f03-ed7a-498e-8c93-49e47abf5de3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 22:03:41,496] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 22:03:41,496] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 22:03:41,496] [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 silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	89.9531	1593	2205	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	89.5656	1700	2205	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	87.341	1592	2205	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	87.3093	1653	2205	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	85.553	1585	2205	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	85.2988	1337	2205	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	84.9191	1280	2205	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	84.6497	1351	2205	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	84.6331	1498	2205	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	84.3327	1312	2205	95	below_threshold
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	84.2104	1438	2205	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	84.0996	1388	2205	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.5937	666	2205	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.5222	718	2205	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.5023	720	2205	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 22:03:41,499] [INFO] DFAST Taxonomy check result was written to GCA_004018595.1_ASM401859v1_genomic.fna/tc_result.tsv
[2023-06-04 22:03:41,499] [INFO] ===== Taxonomy check completed =====
[2023-06-04 22:03:41,499] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 22:03:41,500] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc76b5f03-ed7a-498e-8c93-49e47abf5de3/dqc_reference/checkm_data
[2023-06-04 22:03:41,501] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 22:03:41,566] [INFO] Task started: CheckM
[2023-06-04 22:03:41,566] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004018595.1_ASM401859v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004018595.1_ASM401859v1_genomic.fna/checkm_input GCA_004018595.1_ASM401859v1_genomic.fna/checkm_result
[2023-06-04 22:04:38,449] [INFO] Task succeeded: CheckM
[2023-06-04 22:04:38,451] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 22:04:38,478] [INFO] ===== Completeness check finished =====
[2023-06-04 22:04:38,478] [INFO] ===== Start GTDB Search =====
[2023-06-04 22:04:38,479] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004018595.1_ASM401859v1_genomic.fna/markers.fasta)
[2023-06-04 22:04:38,479] [INFO] Task started: Blastn
[2023-06-04 22:04:38,479] [INFO] Running command: blastn -query GCA_004018595.1_ASM401859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc76b5f03-ed7a-498e-8c93-49e47abf5de3/dqc_reference/reference_markers_gtdb.fasta -out GCA_004018595.1_ASM401859v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:04:40,628] [INFO] Task succeeded: Blastn
[2023-06-04 22:04:40,633] [INFO] Selected 11 target genomes.
[2023-06-04 22:04:40,633] [INFO] Target genome list was writen to GCA_004018595.1_ASM401859v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 22:04:40,635] [INFO] Task started: fastANI
[2023-06-04 22:04:40,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg57b5b9b7-cc3e-432c-9044-fdd694c078f5/GCA_004018595.1_ASM401859v1_genomic.fna.gz --refList GCA_004018595.1_ASM401859v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004018595.1_ASM401859v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 22:05:00,530] [INFO] Task succeeded: fastANI
[2023-06-04 22:05:00,543] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 22:05:00,544] [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_004791585.1	s__Mesorhizobium sp004791585	98.2084	1990	2205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.07	98.11	0.95	0.89	24	conclusive
GCF_003952385.1	s__Mesorhizobium sp003952385	91.4088	1760	2205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.01	97.50	0.89	0.87	7	-
GCA_004020545.1	s__Mesorhizobium sp004020545	90.744	1748	2205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	97.54	0.89	0.86	9	-
GCF_003952465.1	s__Mesorhizobium sp003952465	90.4973	1796	2205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.37	98.09	0.92	0.88	6	-
GCF_003952485.1	s__Mesorhizobium sp003952485	90.3836	1814	2205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.38	98.21	0.91	0.89	5	-
GCA_004963905.1	s__Mesorhizobium sp004963905	90.2962	1718	2205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014843825.1	s__Mesorhizobium silamurunense	89.9533	1592	2205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.52	99.52	0.90	0.90	2	-
GCA_001510895.1	s__Mesorhizobium loti_A	89.8844	1646	2205	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	89.5711	1700	2205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002294995.1	s__Mesorhizobium sp002294995	88.8961	1581	2205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004016445.2	s__Mesorhizobium sp004016445	88.0223	1669	2205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	96.92	0.94	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-04 22:05:00,546] [INFO] GTDB search result was written to GCA_004018595.1_ASM401859v1_genomic.fna/result_gtdb.tsv
[2023-06-04 22:05:00,547] [INFO] ===== GTDB Search completed =====
[2023-06-04 22:05:00,550] [INFO] DFAST_QC result json was written to GCA_004018595.1_ASM401859v1_genomic.fna/dqc_result.json
[2023-06-04 22:05:00,550] [INFO] DFAST_QC completed!
[2023-06-04 22:05:00,550] [INFO] Total running time: 0h2m7s