[2024-01-24 11:35:34,597] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:34,599] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:34,599] [INFO] DQC Reference Directory: /var/lib/cwl/stge4dc6424-0589-482e-8709-7b81b092caea/dqc_reference
[2024-01-24 11:35:35,834] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:35,835] [INFO] Task started: Prodigal
[2024-01-24 11:35:35,835] [INFO] Running command: gunzip -c /var/lib/cwl/stg929d776d-7603-4778-9026-a8e4d61202f7/GCF_003034915.1_ASM303491v1_genomic.fna.gz | prodigal -d GCF_003034915.1_ASM303491v1_genomic.fna/cds.fna -a GCF_003034915.1_ASM303491v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:56,285] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:56,285] [INFO] Task started: HMMsearch
[2024-01-24 11:35:56,285] [INFO] Running command: hmmsearch --tblout GCF_003034915.1_ASM303491v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4dc6424-0589-482e-8709-7b81b092caea/dqc_reference/reference_markers.hmm GCF_003034915.1_ASM303491v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:56,615] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:56,616] [INFO] Found 6/6 markers.
[2024-01-24 11:35:56,670] [INFO] Query marker FASTA was written to GCF_003034915.1_ASM303491v1_genomic.fna/markers.fasta
[2024-01-24 11:35:56,671] [INFO] Task started: Blastn
[2024-01-24 11:35:56,671] [INFO] Running command: blastn -query GCF_003034915.1_ASM303491v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4dc6424-0589-482e-8709-7b81b092caea/dqc_reference/reference_markers.fasta -out GCF_003034915.1_ASM303491v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:57,700] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:57,703] [INFO] Selected 15 target genomes.
[2024-01-24 11:35:57,704] [INFO] Target genome list was writen to GCF_003034915.1_ASM303491v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:57,709] [INFO] Task started: fastANI
[2024-01-24 11:35:57,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg929d776d-7603-4778-9026-a8e4d61202f7/GCF_003034915.1_ASM303491v1_genomic.fna.gz --refList GCF_003034915.1_ASM303491v1_genomic.fna/target_genomes.txt --output GCF_003034915.1_ASM303491v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:21,555] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:21,555] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4dc6424-0589-482e-8709-7b81b092caea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:21,556] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4dc6424-0589-482e-8709-7b81b092caea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:21,571] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:36:21,571] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:36:21,571] [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 helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	100.0	2234	2237	95	conclusive
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	94.9474	1693	2237	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	92.1702	1540	2237	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	87.5024	1460	2237	95	below_threshold
Mesorhizobium temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	87.4048	1433	2237	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	87.0731	1403	2237	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	86.7743	1499	2237	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	85.9311	1442	2237	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	85.8279	1465	2237	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	85.7286	1493	2237	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	85.066	1378	2237	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	84.7446	1343	2237	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	79.031	605	2237	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	78.9986	693	2237	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.9896	695	2237	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:21,572] [INFO] DFAST Taxonomy check result was written to GCF_003034915.1_ASM303491v1_genomic.fna/tc_result.tsv
[2024-01-24 11:36:21,574] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:21,574] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:21,574] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4dc6424-0589-482e-8709-7b81b092caea/dqc_reference/checkm_data
[2024-01-24 11:36:21,575] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:21,636] [INFO] Task started: CheckM
[2024-01-24 11:36:21,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003034915.1_ASM303491v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003034915.1_ASM303491v1_genomic.fna/checkm_input GCF_003034915.1_ASM303491v1_genomic.fna/checkm_result
[2024-01-24 11:37:19,231] [INFO] Task succeeded: CheckM
[2024-01-24 11:37:19,233] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:37:19,254] [INFO] ===== Completeness check finished =====
[2024-01-24 11:37:19,255] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:37:19,255] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003034915.1_ASM303491v1_genomic.fna/markers.fasta)
[2024-01-24 11:37:19,256] [INFO] Task started: Blastn
[2024-01-24 11:37:19,256] [INFO] Running command: blastn -query GCF_003034915.1_ASM303491v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4dc6424-0589-482e-8709-7b81b092caea/dqc_reference/reference_markers_gtdb.fasta -out GCF_003034915.1_ASM303491v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:21,363] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:21,366] [INFO] Selected 15 target genomes.
[2024-01-24 11:37:21,367] [INFO] Target genome list was writen to GCF_003034915.1_ASM303491v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:21,394] [INFO] Task started: fastANI
[2024-01-24 11:37:21,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg929d776d-7603-4778-9026-a8e4d61202f7/GCF_003034915.1_ASM303491v1_genomic.fna.gz --refList GCF_003034915.1_ASM303491v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003034915.1_ASM303491v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:46,636] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:46,651] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:46,652] [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_003034915.1	s__Mesorhizobium helmanticense	100.0	2234	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	95.01	95.01	0.86	0.86	2	conclusive
GCF_000350085.1	s__Mesorhizobium metallidurans	92.1702	1540	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000359125.1	s__Mesorhizobium sp000359125	92.1669	1614	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830515.1	s__Mesorhizobium tianshanense	87.7731	1498	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952365.1	s__Mesorhizobium sp003952365	87.7011	1484	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002284565.1	s__Mesorhizobium mediterraneum_A	87.4856	1547	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.16	97.72	0.92	0.89	20	-
GCF_900156895.1	s__Mesorhizobium prunaredense	87.2059	1393	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001686985.1	s__Mesorhizobium amorphae_B	87.0199	1476	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0866	99.99	99.99	1.00	1.00	2	-
GCF_014843845.1	s__Mesorhizobium amorphae_A	87.016	1474	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0866	97.39	97.39	0.88	0.88	2	-
GCA_004020365.1	s__Mesorhizobium sp004020365	86.8813	1361	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.10	96.06	0.82	0.80	8	-
GCF_003253745.1	s__Mesorhizobium kowhaii	86.3262	1477	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007003975.1	s__Mesorhizobium sp007003975	85.8995	1384	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.98	99.98	0.98	0.98	2	-
GCA_004017275.1	s__Mesorhizobium sp004017275	85.7593	1374	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.13	97.50	0.90	0.85	4	-
GCF_000519305.1	s__Mesorhizobium ciceri_B	85.6037	1427	2237	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	85.083	1375	2237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:46,653] [INFO] GTDB search result was written to GCF_003034915.1_ASM303491v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:46,654] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:46,659] [INFO] DFAST_QC result json was written to GCF_003034915.1_ASM303491v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:46,660] [INFO] DFAST_QC completed!
[2024-01-24 11:37:46,660] [INFO] Total running time: 0h2m12s