[2024-01-24 12:44:10,073] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:10,075] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:10,075] [INFO] DQC Reference Directory: /var/lib/cwl/stgf324871c-e20f-47ff-b6c1-ee201680a77a/dqc_reference
[2024-01-24 12:44:11,585] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:11,586] [INFO] Task started: Prodigal
[2024-01-24 12:44:11,586] [INFO] Running command: gunzip -c /var/lib/cwl/stg8efc801f-6a52-4ab1-9934-5d3126981fe2/GCF_014641695.1_ASM1464169v1_genomic.fna.gz | prodigal -d GCF_014641695.1_ASM1464169v1_genomic.fna/cds.fna -a GCF_014641695.1_ASM1464169v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:24,939] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:24,939] [INFO] Task started: HMMsearch
[2024-01-24 12:44:24,939] [INFO] Running command: hmmsearch --tblout GCF_014641695.1_ASM1464169v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf324871c-e20f-47ff-b6c1-ee201680a77a/dqc_reference/reference_markers.hmm GCF_014641695.1_ASM1464169v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:25,303] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:25,304] [INFO] Found 6/6 markers.
[2024-01-24 12:44:25,344] [INFO] Query marker FASTA was written to GCF_014641695.1_ASM1464169v1_genomic.fna/markers.fasta
[2024-01-24 12:44:25,344] [INFO] Task started: Blastn
[2024-01-24 12:44:25,344] [INFO] Running command: blastn -query GCF_014641695.1_ASM1464169v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf324871c-e20f-47ff-b6c1-ee201680a77a/dqc_reference/reference_markers.fasta -out GCF_014641695.1_ASM1464169v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:26,289] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:26,293] [INFO] Selected 24 target genomes.
[2024-01-24 12:44:26,293] [INFO] Target genome list was writen to GCF_014641695.1_ASM1464169v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:26,306] [INFO] Task started: fastANI
[2024-01-24 12:44:26,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg8efc801f-6a52-4ab1-9934-5d3126981fe2/GCF_014641695.1_ASM1464169v1_genomic.fna.gz --refList GCF_014641695.1_ASM1464169v1_genomic.fna/target_genomes.txt --output GCF_014641695.1_ASM1464169v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:48,411] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:48,411] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf324871c-e20f-47ff-b6c1-ee201680a77a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:48,412] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf324871c-e20f-47ff-b6c1-ee201680a77a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:48,441] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:48,441] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:48,441] [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
Nitratireductor aestuarii	strain=CGMCC 1.15320	GCA_014641695.1	1735103	1735103	type	True	100.0	1478	1479	95	conclusive
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	78.4127	327	1479	95	below_threshold
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	78.0897	353	1479	95	below_threshold
Chelativorans xinjiangense	strain=lm93	GCA_009812055.1	2681485	2681485	type	True	77.9824	377	1479	95	below_threshold
Aminobacter ciceronei	strain=DSM 17455	GCA_014138635.1	150723	150723	type	True	77.9145	360	1479	95	below_threshold
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	77.9143	357	1479	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	77.8925	320	1479	95	below_threshold
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	77.8754	336	1479	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	77.8501	347	1479	95	below_threshold
Aquamicrobium lusatiense	strain=DSM 11099	GCA_014201615.1	89772	89772	type	True	77.8439	302	1479	95	below_threshold
Chelativorans alearense	strain=UJN715	GCA_010993735.1	2681495	2681495	type	True	77.8224	391	1479	95	below_threshold
Mesorhizobium sediminum	strain=KCTC 42205	GCA_013240295.1	1849104	1849104	type	True	77.8112	327	1479	95	below_threshold
Nitratireductor indicus	strain=C115	GCA_000300515.1	721133	721133	type	True	77.7851	255	1479	95	below_threshold
Zhengella mangrovi	strain=X9-2-2	GCA_002727065.1	1982044	1982044	type	True	77.7686	283	1479	95	below_threshold
Mesorhizobium albiziae	strain=DSM 21822	GCA_900114255.1	335020	335020	type	True	77.7387	316	1479	95	below_threshold
Nitratireductor aquibiodomus	strain=JCM 21793	GCA_000615975.1	204799	204799	type	True	77.6689	273	1479	95	below_threshold
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	77.667	314	1479	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	77.6448	316	1479	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	77.435	320	1479	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	77.4211	325	1479	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.3974	286	1479	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	77.3868	287	1479	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.372	283	1479	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	77.252	328	1479	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:48,443] [INFO] DFAST Taxonomy check result was written to GCF_014641695.1_ASM1464169v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:48,444] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:48,444] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:48,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf324871c-e20f-47ff-b6c1-ee201680a77a/dqc_reference/checkm_data
[2024-01-24 12:44:48,445] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:48,489] [INFO] Task started: CheckM
[2024-01-24 12:44:48,489] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014641695.1_ASM1464169v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014641695.1_ASM1464169v1_genomic.fna/checkm_input GCF_014641695.1_ASM1464169v1_genomic.fna/checkm_result
[2024-01-24 12:45:30,928] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:30,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:30,947] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:30,948] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:30,948] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014641695.1_ASM1464169v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:30,949] [INFO] Task started: Blastn
[2024-01-24 12:45:30,949] [INFO] Running command: blastn -query GCF_014641695.1_ASM1464169v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf324871c-e20f-47ff-b6c1-ee201680a77a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014641695.1_ASM1464169v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:32,793] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:32,796] [INFO] Selected 25 target genomes.
[2024-01-24 12:45:32,796] [INFO] Target genome list was writen to GCF_014641695.1_ASM1464169v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:32,834] [INFO] Task started: fastANI
[2024-01-24 12:45:32,835] [INFO] Running command: fastANI --query /var/lib/cwl/stg8efc801f-6a52-4ab1-9934-5d3126981fe2/GCF_014641695.1_ASM1464169v1_genomic.fna.gz --refList GCF_014641695.1_ASM1464169v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014641695.1_ASM1464169v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:54,229] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:54,262] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:54,263] [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_014641695.1	s__Nitratireductor_C aestuarii	100.0	1478	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000300335.1	s__Nitratireductor pacificus	78.4248	326	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255295.1	s__Nitratireductor aquimarinus	78.1887	346	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	98.42	98.07	0.93	0.92	7	-
GCF_014206975.1	s__Aminobacter aganoensis	78.1204	350	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.80	98.79	0.89	0.89	3	-
GCF_000372965.1	s__Aminobacter sp000372965	78.0923	352	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050155.1	s__Nitratireductor soli	77.9781	341	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009812055.1	s__Chelativorans xinjiangense	77.9613	378	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000497755.1	s__Aliihoeflea sp000497755	77.9393	319	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aliihoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733725.1	s__Nitratireductor_A basaltis	77.9074	263	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016742175.1	s__Aliihoeflea sp016742175	77.8969	341	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aliihoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555685.1	s__Aminobacter anthyllidis	77.8749	353	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200015.1	s__Aminobacter niigataensis	77.8709	335	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.01	98.00	0.90	0.90	3	-
GCA_001724355.1	s__Aminobacter sp001724355	77.8595	261	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590645.1	s__Pseudaminobacter sp900116595	77.842	321	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	98.40	97.54	0.93	0.88	4	-
GCF_014201615.1	s__Mesorhizobium lusatiense	77.8297	304	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013240295.1	s__Aquamicrobium_A sediminum	77.8212	326	1479	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_017794765.1	s__Nitratireductor sp017794765	77.8059	230	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002727065.1	s__Zhengella mangrovi	77.7574	284	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Zhengella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114255.1	s__Mesorhizobium_F albiziae	77.7387	316	1479	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_004801285.1	s__Mesorhizobium composti	77.6348	317	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.99	96.99	0.90	0.90	2	-
GCF_011317445.1	s__Chelativorans multitrophicus	77.5997	250	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	99.92	99.90	0.98	0.98	3	-
GCF_900115245.1	s__Mesorhizobium sp900115245	77.562	302	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518985.1	s__Chelativorans sp000518985	77.4231	287	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305925.1	s__JAFKJW01 sp017305925	77.1959	294	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__JAFKJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963455.1	s__Mesorhizobium sp003963455	77.0038	236	1479	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 12:45:54,265] [INFO] GTDB search result was written to GCF_014641695.1_ASM1464169v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:54,266] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:54,273] [INFO] DFAST_QC result json was written to GCF_014641695.1_ASM1464169v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:54,273] [INFO] DFAST_QC completed!
[2024-01-24 12:45:54,273] [INFO] Total running time: 0h1m44s