[2024-01-24 14:23:20,454] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:20,456] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:20,456] [INFO] DQC Reference Directory: /var/lib/cwl/stgec1d7c91-eec5-467f-a523-732e23131524/dqc_reference
[2024-01-24 14:23:21,761] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:21,762] [INFO] Task started: Prodigal
[2024-01-24 14:23:21,763] [INFO] Running command: gunzip -c /var/lib/cwl/stg47214b87-3e79-4cde-9ba4-7bdd8a31c3de/GCF_003863365.1_ASM386336v1_genomic.fna.gz | prodigal -d GCF_003863365.1_ASM386336v1_genomic.fna/cds.fna -a GCF_003863365.1_ASM386336v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:44,358] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:44,358] [INFO] Task started: HMMsearch
[2024-01-24 14:23:44,358] [INFO] Running command: hmmsearch --tblout GCF_003863365.1_ASM386336v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec1d7c91-eec5-467f-a523-732e23131524/dqc_reference/reference_markers.hmm GCF_003863365.1_ASM386336v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:44,818] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:44,819] [INFO] Found 6/6 markers.
[2024-01-24 14:23:44,884] [INFO] Query marker FASTA was written to GCF_003863365.1_ASM386336v1_genomic.fna/markers.fasta
[2024-01-24 14:23:44,884] [INFO] Task started: Blastn
[2024-01-24 14:23:44,884] [INFO] Running command: blastn -query GCF_003863365.1_ASM386336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec1d7c91-eec5-467f-a523-732e23131524/dqc_reference/reference_markers.fasta -out GCF_003863365.1_ASM386336v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:46,037] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:46,040] [INFO] Selected 15 target genomes.
[2024-01-24 14:23:46,041] [INFO] Target genome list was writen to GCF_003863365.1_ASM386336v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:46,049] [INFO] Task started: fastANI
[2024-01-24 14:23:46,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg47214b87-3e79-4cde-9ba4-7bdd8a31c3de/GCF_003863365.1_ASM386336v1_genomic.fna.gz --refList GCF_003863365.1_ASM386336v1_genomic.fna/target_genomes.txt --output GCF_003863365.1_ASM386336v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:24:12,178] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:12,179] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec1d7c91-eec5-467f-a523-732e23131524/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:24:12,179] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec1d7c91-eec5-467f-a523-732e23131524/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:24:12,191] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:24:12,191] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:24:12,192] [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 tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	100.0	2392	2396	95	conclusive
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	90.7558	1607	2396	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	87.3491	1583	2396	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	87.2181	1555	2396	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	85.862	1625	2396	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	85.1841	1346	2396	95	below_threshold
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	84.9895	1505	2396	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	84.9477	1392	2396	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	84.7465	1233	2396	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	84.4576	1435	2396	95	below_threshold
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	84.4269	1474	2396	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	84.3965	1323	2396	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.4014	738	2396	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.1409	683	2396	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	78.6732	548	2396	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:24:12,193] [INFO] DFAST Taxonomy check result was written to GCF_003863365.1_ASM386336v1_genomic.fna/tc_result.tsv
[2024-01-24 14:24:12,194] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:24:12,194] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:24:12,194] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec1d7c91-eec5-467f-a523-732e23131524/dqc_reference/checkm_data
[2024-01-24 14:24:12,195] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:24:12,269] [INFO] Task started: CheckM
[2024-01-24 14:24:12,269] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003863365.1_ASM386336v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003863365.1_ASM386336v1_genomic.fna/checkm_input GCF_003863365.1_ASM386336v1_genomic.fna/checkm_result
[2024-01-24 14:25:13,447] [INFO] Task succeeded: CheckM
[2024-01-24 14:25:13,449] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:25:13,473] [INFO] ===== Completeness check finished =====
[2024-01-24 14:25:13,473] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:25:13,474] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003863365.1_ASM386336v1_genomic.fna/markers.fasta)
[2024-01-24 14:25:13,474] [INFO] Task started: Blastn
[2024-01-24 14:25:13,474] [INFO] Running command: blastn -query GCF_003863365.1_ASM386336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec1d7c91-eec5-467f-a523-732e23131524/dqc_reference/reference_markers_gtdb.fasta -out GCF_003863365.1_ASM386336v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:25:15,691] [INFO] Task succeeded: Blastn
[2024-01-24 14:25:15,696] [INFO] Selected 12 target genomes.
[2024-01-24 14:25:15,696] [INFO] Target genome list was writen to GCF_003863365.1_ASM386336v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:25:15,714] [INFO] Task started: fastANI
[2024-01-24 14:25:15,715] [INFO] Running command: fastANI --query /var/lib/cwl/stg47214b87-3e79-4cde-9ba4-7bdd8a31c3de/GCF_003863365.1_ASM386336v1_genomic.fna.gz --refList GCF_003863365.1_ASM386336v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003863365.1_ASM386336v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:25:40,532] [INFO] Task succeeded: fastANI
[2024-01-24 14:25:40,547] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:25:40,547] [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_003863365.1	s__Mesorhizobium tamadayense	100.0	2392	2396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014843825.1	s__Mesorhizobium silamurunense	90.7533	1607	2396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.52	99.52	0.90	0.90	2	-
GCF_003952385.1	s__Mesorhizobium sp003952385	90.0132	1679	2396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.01	97.50	0.89	0.87	7	-
GCA_004963905.1	s__Mesorhizobium sp004963905	89.937	1667	2396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004020545.1	s__Mesorhizobium sp004020545	89.7122	1672	2396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	97.54	0.89	0.86	9	-
GCF_004791585.1	s__Mesorhizobium sp004791585	89.6742	1690	2396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.07	98.11	0.95	0.89	24	-
GCF_003952485.1	s__Mesorhizobium sp003952485	89.6528	1718	2396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.38	98.21	0.91	0.89	5	-
GCA_001510895.1	s__Mesorhizobium loti_A	89.5929	1699	2396	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	89.5592	1581	2396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002294985.1	s__Mesorhizobium sp002294985	89.4341	1546	2396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.32	96.92	0.87	0.76	62	-
GCA_000824825.2	s__Mesorhizobium sp000824825	89.111	1631	2396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427725.1	s__Mesorhizobium sp000427725	87.8286	1629	2396	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 14:25:40,548] [INFO] GTDB search result was written to GCF_003863365.1_ASM386336v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:25:40,549] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:25:40,553] [INFO] DFAST_QC result json was written to GCF_003863365.1_ASM386336v1_genomic.fna/dqc_result.json
[2024-01-24 14:25:40,553] [INFO] DFAST_QC completed!
[2024-01-24 14:25:40,553] [INFO] Total running time: 0h2m20s