[2024-01-24 13:01:26,391] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:26,394] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:26,394] [INFO] DQC Reference Directory: /var/lib/cwl/stgb55eef55-4ff7-4455-97c8-2694928232df/dqc_reference
[2024-01-24 13:01:27,835] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:27,836] [INFO] Task started: Prodigal
[2024-01-24 13:01:27,836] [INFO] Running command: gunzip -c /var/lib/cwl/stge0740d06-2616-4fc9-af40-b8e26b67250d/GCF_000236565.1_ASM23656v2_genomic.fna.gz | prodigal -d GCF_000236565.1_ASM23656v2_genomic.fna/cds.fna -a GCF_000236565.1_ASM23656v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:49,525] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:49,526] [INFO] Task started: HMMsearch
[2024-01-24 13:01:49,526] [INFO] Running command: hmmsearch --tblout GCF_000236565.1_ASM23656v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb55eef55-4ff7-4455-97c8-2694928232df/dqc_reference/reference_markers.hmm GCF_000236565.1_ASM23656v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:49,876] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:49,878] [INFO] Found 6/6 markers.
[2024-01-24 13:01:49,937] [INFO] Query marker FASTA was written to GCF_000236565.1_ASM23656v2_genomic.fna/markers.fasta
[2024-01-24 13:01:49,937] [INFO] Task started: Blastn
[2024-01-24 13:01:49,938] [INFO] Running command: blastn -query GCF_000236565.1_ASM23656v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb55eef55-4ff7-4455-97c8-2694928232df/dqc_reference/reference_markers.fasta -out GCF_000236565.1_ASM23656v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:50,992] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:50,996] [INFO] Selected 21 target genomes.
[2024-01-24 13:01:50,996] [INFO] Target genome list was writen to GCF_000236565.1_ASM23656v2_genomic.fna/target_genomes.txt
[2024-01-24 13:01:51,025] [INFO] Task started: fastANI
[2024-01-24 13:01:51,025] [INFO] Running command: fastANI --query /var/lib/cwl/stge0740d06-2616-4fc9-af40-b8e26b67250d/GCF_000236565.1_ASM23656v2_genomic.fna.gz --refList GCF_000236565.1_ASM23656v2_genomic.fna/target_genomes.txt --output GCF_000236565.1_ASM23656v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:19,481] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:19,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb55eef55-4ff7-4455-97c8-2694928232df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:19,481] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb55eef55-4ff7-4455-97c8-2694928232df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:19,497] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:19,497] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:19,497] [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 alhagi	strain=CCNWXJ12-2	GCA_000236565.2	475067	475067	type	True	100.0	2134	2150	95	conclusive
Mesorhizobium camelthorni	strain=CCNWXJ 40-4	GCA_011045125.1	475069	475069	type	True	91.287	1481	2150	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	81.0389	934	2150	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	80.935	982	2150	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	80.9128	887	2150	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	80.9113	929	2150	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	80.8601	964	2150	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	80.8541	932	2150	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	80.7778	988	2150	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	80.7402	938	2150	95	below_threshold
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	80.7254	923	2150	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	80.5987	917	2150	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	80.5719	953	2150	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	80.5202	932	2150	95	below_threshold
Mesorhizobium albiziae	strain=DSM 21822	GCA_900114255.1	335020	335020	type	True	80.4994	934	2150	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	80.4576	862	2150	95	below_threshold
Aminobacter aminovorans	strain=DSM 7048	GCA_004341645.1	83263	83263	type	True	80.2944	794	2150	95	below_threshold
Aminobacter aminovorans	strain=NCTC10684	GCA_900445235.1	83263	83263	type	True	80.2714	788	2150	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	79.576	704	2150	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.2475	700	2150	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.2474	699	2150	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:19,499] [INFO] DFAST Taxonomy check result was written to GCF_000236565.1_ASM23656v2_genomic.fna/tc_result.tsv
[2024-01-24 13:02:19,500] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:19,500] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:19,500] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb55eef55-4ff7-4455-97c8-2694928232df/dqc_reference/checkm_data
[2024-01-24 13:02:19,501] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:19,570] [INFO] Task started: CheckM
[2024-01-24 13:02:19,570] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000236565.1_ASM23656v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000236565.1_ASM23656v2_genomic.fna/checkm_input GCF_000236565.1_ASM23656v2_genomic.fna/checkm_result
[2024-01-24 13:03:17,440] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:17,442] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:17,472] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:17,472] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:17,472] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000236565.1_ASM23656v2_genomic.fna/markers.fasta)
[2024-01-24 13:03:17,473] [INFO] Task started: Blastn
[2024-01-24 13:03:17,473] [INFO] Running command: blastn -query GCF_000236565.1_ASM23656v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb55eef55-4ff7-4455-97c8-2694928232df/dqc_reference/reference_markers_gtdb.fasta -out GCF_000236565.1_ASM23656v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:19,574] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:19,578] [INFO] Selected 20 target genomes.
[2024-01-24 13:03:19,579] [INFO] Target genome list was writen to GCF_000236565.1_ASM23656v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:19,615] [INFO] Task started: fastANI
[2024-01-24 13:03:19,615] [INFO] Running command: fastANI --query /var/lib/cwl/stge0740d06-2616-4fc9-af40-b8e26b67250d/GCF_000236565.1_ASM23656v2_genomic.fna.gz --refList GCF_000236565.1_ASM23656v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000236565.1_ASM23656v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:47,982] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:48,005] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:48,005] [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_000236565.1	s__Pseudaminobacter alhagi	100.0	2134	2150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011045125.1	s__Pseudaminobacter camelthorni	91.3077	1479	2150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830515.1	s__Mesorhizobium tianshanense	81.1917	1020	2150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590645.1	s__Pseudaminobacter sp900116595	81.1203	884	2150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	98.40	97.54	0.93	0.88	4	-
GCF_017874015.1	s__Pseudaminobacter sp017874015	81.0513	776	2150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045115.1	s__Pseudaminobacter zhangyensis	81.0341	936	2150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756535.1	s__Mesorhizobium sp016756535	80.9834	960	2150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156895.1	s__Mesorhizobium prunaredense	80.9406	950	2150	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	80.8119	921	2150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791585.1	s__Mesorhizobium sp004791585	80.7203	927	2150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.07	98.11	0.95	0.89	24	-
GCF_016756495.1	s__Mesorhizobium sp016756495	80.7081	949	2150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006442965.1	s__Mesorhizobium sp006442965	80.6968	872	2150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.99	99.99	1.00	1.00	2	-
GCA_018823835.1	s__RCIZ01 sp018823835	80.67	808	2150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIZ01	95.0	99.96	99.89	0.99	0.96	11	-
GCF_007003975.1	s__Mesorhizobium sp007003975	80.5875	906	2150	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	80.5665	911	2150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.13	97.50	0.90	0.85	4	-
GCF_900114255.1	s__Mesorhizobium_F albiziae	80.5364	927	2150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003289945.1	s__Mesorhizobium hawassense	80.5115	934	2150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014615.2	s__Aquamicrobium_A sp001014615	79.6804	714	2150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016742175.1	s__Aliihoeflea sp016742175	79.577	614	2150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aliihoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000497755.1	s__Aliihoeflea sp000497755	79.3039	574	2150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aliihoeflea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:48,007] [INFO] GTDB search result was written to GCF_000236565.1_ASM23656v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:48,007] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:48,011] [INFO] DFAST_QC result json was written to GCF_000236565.1_ASM23656v2_genomic.fna/dqc_result.json
[2024-01-24 13:03:48,011] [INFO] DFAST_QC completed!
[2024-01-24 13:03:48,012] [INFO] Total running time: 0h2m22s