[2024-01-25 18:04:50,583] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:04:50,588] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:04:50,589] [INFO] DQC Reference Directory: /var/lib/cwl/stgcbe394a6-4f87-42be-9447-22934001aecc/dqc_reference
[2024-01-25 18:04:51,709] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:04:51,709] [INFO] Task started: Prodigal
[2024-01-25 18:04:51,709] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d817386-7d07-45c7-9d63-6ab1ae394055/GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna/cds.fna -a GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:05:01,829] [INFO] Task succeeded: Prodigal
[2024-01-25 18:05:01,830] [INFO] Task started: HMMsearch
[2024-01-25 18:05:01,830] [INFO] Running command: hmmsearch --tblout GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcbe394a6-4f87-42be-9447-22934001aecc/dqc_reference/reference_markers.hmm GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:05:02,082] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:05:02,083] [INFO] Found 6/6 markers.
[2024-01-25 18:05:02,127] [INFO] Query marker FASTA was written to GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 18:05:02,127] [INFO] Task started: Blastn
[2024-01-25 18:05:02,127] [INFO] Running command: blastn -query GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbe394a6-4f87-42be-9447-22934001aecc/dqc_reference/reference_markers.fasta -out GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:03,043] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:03,046] [INFO] Selected 22 target genomes.
[2024-01-25 18:05:03,046] [INFO] Target genome list was writen to GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 18:05:03,055] [INFO] Task started: fastANI
[2024-01-25 18:05:03,055] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d817386-7d07-45c7-9d63-6ab1ae394055/GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna.gz --refList GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:05:25,081] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:25,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcbe394a6-4f87-42be-9447-22934001aecc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:05:25,082] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcbe394a6-4f87-42be-9447-22934001aecc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:05:25,094] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:05:25,095] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:05:25,095] [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
Aquamicrobium zhengzhouense	strain=cd-1	GCA_016124105.1	2781738	2781738	type	True	79.3232	365	1189	95	below_threshold
Mesorhizobium sediminum	strain=KCTC 42205	GCA_013240295.1	1849104	1849104	type	True	79.2814	503	1189	95	below_threshold
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	78.7909	396	1189	95	below_threshold
Aminobacter aminovorans	strain=NCTC10684	GCA_900445235.1	83263	83263	type	True	78.7526	394	1189	95	below_threshold
Aminobacter ciceronei	strain=DSM 17455	GCA_014138635.1	150723	150723	type	True	78.7409	404	1189	95	below_threshold
Aminobacter aminovorans	strain=DSM 7048	GCA_004341645.1	83263	83263	type	True	78.6929	396	1189	95	below_threshold
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	78.6779	408	1189	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	78.5993	362	1189	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	78.5529	373	1189	95	below_threshold
Mesorhizobium australicum	strain=WSM2073	GCA_000230995.3	536018	536018	type	True	78.5389	340	1189	95	below_threshold
Mesorhizobium intechi	strain=BD68	GCA_002879535.2	537601	537601	type	True	78.4623	358	1189	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	78.4338	345	1189	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	78.3523	395	1189	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	78.3494	336	1189	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	78.3016	356	1189	95	below_threshold
Mesorhizobium camelthorni	strain=CCNWXJ 40-4	GCA_011045125.1	475069	475069	type	True	78.1403	384	1189	95	below_threshold
Mesorhizobium alhagi	strain=CCNWXJ12-2	GCA_000236565.2	475067	475067	type	True	78.069	372	1189	95	below_threshold
Rhizobium subbaraonis	strain=JC85	GCA_900220975.1	908946	908946	type	True	77.8435	259	1189	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	77.6705	276	1189	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	77.5271	215	1189	95	below_threshold
Rhizobium tubonense	strain=CCBAU 85046	GCA_003240585.1	484088	484088	type	True	77.0927	190	1189	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	76.7098	153	1189	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:05:25,096] [INFO] DFAST Taxonomy check result was written to GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 18:05:25,097] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:05:25,097] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:05:25,097] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcbe394a6-4f87-42be-9447-22934001aecc/dqc_reference/checkm_data
[2024-01-25 18:05:25,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:05:25,134] [INFO] Task started: CheckM
[2024-01-25 18:05:25,134] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna/checkm_input GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 18:05:57,780] [INFO] Task succeeded: CheckM
[2024-01-25 18:05:57,781] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:05:57,797] [INFO] ===== Completeness check finished =====
[2024-01-25 18:05:57,797] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:05:57,797] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 18:05:57,798] [INFO] Task started: Blastn
[2024-01-25 18:05:57,798] [INFO] Running command: blastn -query GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbe394a6-4f87-42be-9447-22934001aecc/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:59,537] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:59,540] [INFO] Selected 21 target genomes.
[2024-01-25 18:05:59,540] [INFO] Target genome list was writen to GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:05:59,561] [INFO] Task started: fastANI
[2024-01-25 18:05:59,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d817386-7d07-45c7-9d63-6ab1ae394055/GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna.gz --refList GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:06:19,714] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:19,726] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:06:19,726] [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_900113935.1	s__Aquamicrobium_A aerolatum	100.0	1187	1189	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	79.4493	518	1189	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_000526635.1	s__Aquamicrobium_A sp000526635	79.3263	480	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	99.33	98.68	0.94	0.89	3	-
GCF_016124105.1	s__Aquamicrobium_A sp016124105	79.3225	365	1189	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_013240295.1	s__Aquamicrobium_A sediminum	79.2821	503	1189	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	79.1885	442	1189	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	79.148	442	1189	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_018555685.1	s__Aminobacter anthyllidis	78.8597	403	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000497755.1	s__Aliihoeflea sp000497755	78.8578	410	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aliihoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874015.1	s__Pseudaminobacter sp017874015	78.7328	390	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467435.1	s__Mesorhizobium sp016467435	78.6785	369	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.58	98.58	0.95	0.95	2	-
GCF_014863355.1	s__Aminobacter carboxidus	78.6663	402	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.38	98.38	0.89	0.89	2	-
GCF_001686985.1	s__Mesorhizobium amorphae_B	78.617	387	1189	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	78.5167	392	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0866	97.39	97.39	0.88	0.88	2	-
GCA_004962245.1	s__Mesorhizobium sp004962245	78.5078	355	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.59	99.49	0.95	0.95	3	-
GCF_008727715.1	s__Mesorhizobium terrae	78.477	387	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.80	99.17	0.95	0.89	9	-
GCF_013170825.1	s__Mesorhizobium sp013170825	78.4728	366	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	95.36	95.35	0.82	0.81	3	-
GCF_015500075.1	s__Mesorhizobium sp015500075	78.4561	338	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008520305.1	s__Mesorhizobium sp008520305	78.4098	337	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305835.1	s__RCIO01 sp017305835	78.3631	403	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724355.1	s__Aminobacter sp001724355	78.3006	313	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:06:19,727] [INFO] GTDB search result was written to GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 18:06:19,728] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:06:19,731] [INFO] DFAST_QC result json was written to GCF_900113935.1_IMG-taxon_2595699008_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 18:06:19,732] [INFO] DFAST_QC completed!
[2024-01-25 18:06:19,732] [INFO] Total running time: 0h1m29s