[2023-06-05 07:09:24,686] [INFO] DFAST_QC pipeline started.
[2023-06-05 07:09:24,693] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 07:09:24,693] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ec88105-6e02-4ea6-93c0-fd117d6e66cd/dqc_reference
[2023-06-05 07:09:26,307] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 07:09:26,308] [INFO] Task started: Prodigal
[2023-06-05 07:09:26,309] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe6404e7-b307-4f6b-b865-cb9821a03538/GCA_004019075.1_ASM401907v1_genomic.fna.gz | prodigal -d GCA_004019075.1_ASM401907v1_genomic.fna/cds.fna -a GCA_004019075.1_ASM401907v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 07:09:42,500] [INFO] Task succeeded: Prodigal
[2023-06-05 07:09:42,502] [INFO] Task started: HMMsearch
[2023-06-05 07:09:42,502] [INFO] Running command: hmmsearch --tblout GCA_004019075.1_ASM401907v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ec88105-6e02-4ea6-93c0-fd117d6e66cd/dqc_reference/reference_markers.hmm GCA_004019075.1_ASM401907v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 07:09:42,801] [INFO] Task succeeded: HMMsearch
[2023-06-05 07:09:42,803] [INFO] Found 6/6 markers.
[2023-06-05 07:09:42,868] [INFO] Query marker FASTA was written to GCA_004019075.1_ASM401907v1_genomic.fna/markers.fasta
[2023-06-05 07:09:42,869] [INFO] Task started: Blastn
[2023-06-05 07:09:42,869] [INFO] Running command: blastn -query GCA_004019075.1_ASM401907v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ec88105-6e02-4ea6-93c0-fd117d6e66cd/dqc_reference/reference_markers.fasta -out GCA_004019075.1_ASM401907v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:09:43,959] [INFO] Task succeeded: Blastn
[2023-06-05 07:09:43,964] [INFO] Selected 15 target genomes.
[2023-06-05 07:09:43,964] [INFO] Target genome list was writen to GCA_004019075.1_ASM401907v1_genomic.fna/target_genomes.txt
[2023-06-05 07:09:43,968] [INFO] Task started: fastANI
[2023-06-05 07:09:43,968] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe6404e7-b307-4f6b-b865-cb9821a03538/GCA_004019075.1_ASM401907v1_genomic.fna.gz --refList GCA_004019075.1_ASM401907v1_genomic.fna/target_genomes.txt --output GCA_004019075.1_ASM401907v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 07:10:05,832] [INFO] Task succeeded: fastANI
[2023-06-05 07:10:05,832] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ec88105-6e02-4ea6-93c0-fd117d6e66cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 07:10:05,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ec88105-6e02-4ea6-93c0-fd117d6e66cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 07:10:05,847] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 07:10:05,847] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 07:10:05,848] [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	89.6638	1315	1791	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	89.2389	1360	1791	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	86.9814	1332	1791	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	86.8431	1292	1791	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	85.048	1292	1791	95	below_threshold
Mesorhizobium japonicum	strain=MAFF 303099	GCA_000009625.1	2066070	2066070	type	True	84.5264	1232	1791	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	84.3688	1128	1791	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	84.2505	1268	1791	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	84.0631	1116	1791	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	83.9299	1213	1791	95	below_threshold
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	83.8885	1200	1791	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	83.7039	1139	1791	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.446	636	1791	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.2981	546	1791	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	78.993	534	1791	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 07:10:05,850] [INFO] DFAST Taxonomy check result was written to GCA_004019075.1_ASM401907v1_genomic.fna/tc_result.tsv
[2023-06-05 07:10:05,850] [INFO] ===== Taxonomy check completed =====
[2023-06-05 07:10:05,850] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 07:10:05,850] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ec88105-6e02-4ea6-93c0-fd117d6e66cd/dqc_reference/checkm_data
[2023-06-05 07:10:05,851] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 07:10:05,911] [INFO] Task started: CheckM
[2023-06-05 07:10:05,912] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004019075.1_ASM401907v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004019075.1_ASM401907v1_genomic.fna/checkm_input GCA_004019075.1_ASM401907v1_genomic.fna/checkm_result
[2023-06-05 07:10:53,781] [INFO] Task succeeded: CheckM
[2023-06-05 07:10:53,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 07:10:53,807] [INFO] ===== Completeness check finished =====
[2023-06-05 07:10:53,807] [INFO] ===== Start GTDB Search =====
[2023-06-05 07:10:53,807] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004019075.1_ASM401907v1_genomic.fna/markers.fasta)
[2023-06-05 07:10:53,808] [INFO] Task started: Blastn
[2023-06-05 07:10:53,808] [INFO] Running command: blastn -query GCA_004019075.1_ASM401907v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ec88105-6e02-4ea6-93c0-fd117d6e66cd/dqc_reference/reference_markers_gtdb.fasta -out GCA_004019075.1_ASM401907v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:10:55,931] [INFO] Task succeeded: Blastn
[2023-06-05 07:10:55,936] [INFO] Selected 12 target genomes.
[2023-06-05 07:10:55,936] [INFO] Target genome list was writen to GCA_004019075.1_ASM401907v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 07:10:55,943] [INFO] Task started: fastANI
[2023-06-05 07:10:55,943] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe6404e7-b307-4f6b-b865-cb9821a03538/GCA_004019075.1_ASM401907v1_genomic.fna.gz --refList GCA_004019075.1_ASM401907v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004019075.1_ASM401907v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 07:11:14,097] [INFO] Task succeeded: fastANI
[2023-06-05 07:11:14,114] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 07:11:14,114] [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_002294985.1	s__Mesorhizobium sp002294985	97.0436	1587	1791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.32	96.92	0.87	0.76	62	conclusive
GCF_002294995.1	s__Mesorhizobium sp002294995	94.0999	1554	1791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004963905.1	s__Mesorhizobium sp004963905	90.1583	1438	1791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952385.1	s__Mesorhizobium sp003952385	90.0224	1400	1791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.01	97.50	0.89	0.87	7	-
GCF_014843825.1	s__Mesorhizobium silamurunense	89.6524	1316	1791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.52	99.52	0.90	0.90	2	-
GCA_004020545.1	s__Mesorhizobium sp004020545	89.5641	1365	1791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	97.54	0.89	0.86	9	-
GCF_003952485.1	s__Mesorhizobium sp003952485	89.5433	1415	1791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.38	98.21	0.91	0.89	5	-
GCF_004791585.1	s__Mesorhizobium sp004791585	89.5279	1389	1791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.07	98.11	0.95	0.89	24	-
GCF_003863365.1	s__Mesorhizobium tamadayense	89.2231	1362	1791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001510895.1	s__Mesorhizobium loti_A	89.0795	1339	1791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000824825.2	s__Mesorhizobium sp000824825	88.62	1343	1791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001854785.1	s__Mesorhizobium sp001854785	88.0344	1327	1791	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 07:11:14,116] [INFO] GTDB search result was written to GCA_004019075.1_ASM401907v1_genomic.fna/result_gtdb.tsv
[2023-06-05 07:11:14,117] [INFO] ===== GTDB Search completed =====
[2023-06-05 07:11:14,120] [INFO] DFAST_QC result json was written to GCA_004019075.1_ASM401907v1_genomic.fna/dqc_result.json
[2023-06-05 07:11:14,120] [INFO] DFAST_QC completed!
[2023-06-05 07:11:14,121] [INFO] Total running time: 0h1m49s