[2024-01-24 11:34:40,791] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:40,796] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:40,797] [INFO] DQC Reference Directory: /var/lib/cwl/stg50289a19-1b54-439b-999c-eda289a263ed/dqc_reference
[2024-01-24 11:34:42,062] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,064] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,064] [INFO] Running command: gunzip -c /var/lib/cwl/stgd04d2191-cf70-4934-9caa-ee7ef40a8d45/GCF_013240295.1_ASM1324029v1_genomic.fna.gz | prodigal -d GCF_013240295.1_ASM1324029v1_genomic.fna/cds.fna -a GCF_013240295.1_ASM1324029v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:01,527] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:01,527] [INFO] Task started: HMMsearch
[2024-01-24 11:35:01,527] [INFO] Running command: hmmsearch --tblout GCF_013240295.1_ASM1324029v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50289a19-1b54-439b-999c-eda289a263ed/dqc_reference/reference_markers.hmm GCF_013240295.1_ASM1324029v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:01,903] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:01,905] [INFO] Found 6/6 markers.
[2024-01-24 11:35:01,958] [INFO] Query marker FASTA was written to GCF_013240295.1_ASM1324029v1_genomic.fna/markers.fasta
[2024-01-24 11:35:01,959] [INFO] Task started: Blastn
[2024-01-24 11:35:01,959] [INFO] Running command: blastn -query GCF_013240295.1_ASM1324029v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50289a19-1b54-439b-999c-eda289a263ed/dqc_reference/reference_markers.fasta -out GCF_013240295.1_ASM1324029v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:03,018] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:03,020] [INFO] Selected 24 target genomes.
[2024-01-24 11:35:03,021] [INFO] Target genome list was writen to GCF_013240295.1_ASM1324029v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:03,029] [INFO] Task started: fastANI
[2024-01-24 11:35:03,029] [INFO] Running command: fastANI --query /var/lib/cwl/stgd04d2191-cf70-4934-9caa-ee7ef40a8d45/GCF_013240295.1_ASM1324029v1_genomic.fna.gz --refList GCF_013240295.1_ASM1324029v1_genomic.fna/target_genomes.txt --output GCF_013240295.1_ASM1324029v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:31,997] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:31,998] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50289a19-1b54-439b-999c-eda289a263ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:31,999] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50289a19-1b54-439b-999c-eda289a263ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:32,017] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:32,017] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:32,017] [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 sediminum	strain=KCTC 42205	GCA_013240295.1	1849104	1849104	type	True	100.0	2038	2041	95	conclusive
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	79.69	672	2041	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	79.6267	704	2041	95	below_threshold
Aquibium carbonis	strain=B2.3	GCA_003970795.1	2495581	2495581	type	True	79.5968	622	2041	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	79.3061	635	2041	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	79.264	670	2041	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	79.2364	676	2041	95	below_threshold
Aminobacter aminovorans	strain=DSM 7048	GCA_004341645.1	83263	83263	type	True	79.2284	647	2041	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	79.2239	607	2041	95	below_threshold
Aquibium oceanicum	strain=B7	GCA_001889605.1	1670800	1670800	type	True	79.1729	645	2041	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	79.1712	591	2041	95	below_threshold
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	79.1017	529	2041	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	79.0962	684	2041	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	79.0862	675	2041	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	79.0716	663	2041	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	79.0326	601	2041	95	below_threshold
Aquamicrobium lusatiense	strain=DSM 11099	GCA_014201615.1	89772	89772	type	True	79.0155	485	2041	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	79.0122	647	2041	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	78.9705	665	2041	95	below_threshold
Mesorhizobium sangaii	strain=DSM 100039	GCA_014207355.1	505389	505389	type	True	78.8441	646	2041	95	below_threshold
Mesorhizobium camelthorni	strain=CCNWXJ 40-4	GCA_011045125.1	475069	475069	type	True	78.8321	690	2041	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.5434	524	2041	95	below_threshold
Zhengella mangrovi	strain=X9-2-2	GCA_002727065.1	1982044	1982044	type	True	78.4605	467	2041	95	below_threshold
Aquamicrobium zhengzhouense	strain=cd-1	GCA_016124105.1	2781738	2781738	type	True	78.2706	423	2041	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:32,019] [INFO] DFAST Taxonomy check result was written to GCF_013240295.1_ASM1324029v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:32,019] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:32,019] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:32,020] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50289a19-1b54-439b-999c-eda289a263ed/dqc_reference/checkm_data
[2024-01-24 11:35:32,021] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:32,077] [INFO] Task started: CheckM
[2024-01-24 11:35:32,077] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013240295.1_ASM1324029v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013240295.1_ASM1324029v1_genomic.fna/checkm_input GCF_013240295.1_ASM1324029v1_genomic.fna/checkm_result
[2024-01-24 11:36:25,765] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:25,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:25,787] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:25,788] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:25,788] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013240295.1_ASM1324029v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:25,789] [INFO] Task started: Blastn
[2024-01-24 11:36:25,789] [INFO] Running command: blastn -query GCF_013240295.1_ASM1324029v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50289a19-1b54-439b-999c-eda289a263ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_013240295.1_ASM1324029v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:27,819] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:27,824] [INFO] Selected 21 target genomes.
[2024-01-24 11:36:27,824] [INFO] Target genome list was writen to GCF_013240295.1_ASM1324029v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:27,860] [INFO] Task started: fastANI
[2024-01-24 11:36:27,860] [INFO] Running command: fastANI --query /var/lib/cwl/stgd04d2191-cf70-4934-9caa-ee7ef40a8d45/GCF_013240295.1_ASM1324029v1_genomic.fna.gz --refList GCF_013240295.1_ASM1324029v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013240295.1_ASM1324029v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:51,022] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:51,041] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:51,042] [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_013240295.1	s__Aquamicrobium_A sediminum	100.0	2038	2041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008180155.1	s__Aquamicrobium_A microcysteis	81.7901	1006	2041	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_003577315.1	s__Aquamicrobium_A sp003577315	81.0625	645	2041	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_014860725.1	s__Aquamicrobium_A sp014860725	80.6338	406	2041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014615.2	s__Aquamicrobium_A sp001014615	80.2571	830	2041	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_017305835.1	s__RCIO01 sp017305835	80.0732	687	2041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014495845.1	s__Mesorhizobium_E sp014495845	79.6227	705	2041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003666685.1	s__RCIZ01 sp003666685	79.4603	649	2041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339215.1	s__DUSC01 sp008933895	79.3271	655	2041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	99.82	99.82	0.93	0.93	2	-
GCF_011045115.1	s__Pseudaminobacter zhangyensis	79.2709	668	2041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791585.1	s__Mesorhizobium sp004791585	79.2708	658	2041	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	79.2392	675	2041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019091085.1	s__Mesorhizobium sp019091085	79.1926	642	2041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889605.1	s__Mesorhizobium_E oceanicum	79.1845	645	2041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439355.1	s__Mesorhizobium sp006439355	79.1689	653	2041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012705.1	s__Pseudaminobacter soli	79.1662	638	2041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000350085.1	s__Mesorhizobium metallidurans	79.1656	615	2041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113935.1	s__Aquamicrobium_A aerolatum	79.109	509	2041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756495.1	s__Mesorhizobium sp016756495	79.0817	685	2041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363725.1	s__Mesorhizobium defluvii	79.0649	532	2041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.28	99.28	0.87	0.87	2	-
GCA_017306585.1	s__Mesorhizobium sp017306585	78.8162	633	2041	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 11:36:51,044] [INFO] GTDB search result was written to GCF_013240295.1_ASM1324029v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:51,044] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:51,051] [INFO] DFAST_QC result json was written to GCF_013240295.1_ASM1324029v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:51,051] [INFO] DFAST_QC completed!
[2024-01-24 11:36:51,051] [INFO] Total running time: 0h2m10s