[2024-01-24 14:22:33,369] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:33,371] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:33,372] [INFO] DQC Reference Directory: /var/lib/cwl/stgee5a9350-17b6-4b61-a2db-8ec70493fe42/dqc_reference
[2024-01-24 14:22:34,633] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:34,634] [INFO] Task started: Prodigal
[2024-01-24 14:22:34,634] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a4baa90-e3eb-49e6-b3b6-71a20b119c16/GCF_002148795.1_ASM214879v1_genomic.fna.gz | prodigal -d GCF_002148795.1_ASM214879v1_genomic.fna/cds.fna -a GCF_002148795.1_ASM214879v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:45,836] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:45,836] [INFO] Task started: HMMsearch
[2024-01-24 14:22:45,837] [INFO] Running command: hmmsearch --tblout GCF_002148795.1_ASM214879v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee5a9350-17b6-4b61-a2db-8ec70493fe42/dqc_reference/reference_markers.hmm GCF_002148795.1_ASM214879v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:46,150] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:46,151] [INFO] Found 6/6 markers.
[2024-01-24 14:22:46,187] [INFO] Query marker FASTA was written to GCF_002148795.1_ASM214879v1_genomic.fna/markers.fasta
[2024-01-24 14:22:46,187] [INFO] Task started: Blastn
[2024-01-24 14:22:46,188] [INFO] Running command: blastn -query GCF_002148795.1_ASM214879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee5a9350-17b6-4b61-a2db-8ec70493fe42/dqc_reference/reference_markers.fasta -out GCF_002148795.1_ASM214879v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:47,565] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:47,569] [INFO] Selected 18 target genomes.
[2024-01-24 14:22:47,569] [INFO] Target genome list was writen to GCF_002148795.1_ASM214879v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:47,576] [INFO] Task started: fastANI
[2024-01-24 14:22:47,576] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a4baa90-e3eb-49e6-b3b6-71a20b119c16/GCF_002148795.1_ASM214879v1_genomic.fna.gz --refList GCF_002148795.1_ASM214879v1_genomic.fna/target_genomes.txt --output GCF_002148795.1_ASM214879v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:05,565] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:05,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee5a9350-17b6-4b61-a2db-8ec70493fe42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:05,566] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee5a9350-17b6-4b61-a2db-8ec70493fe42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:05,586] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:05,586] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:05,586] [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
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	100.0	1262	1263	95	conclusive
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	90.2662	1090	1263	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	84.125	774	1263	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	77.5708	434	1263	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	77.5261	375	1263	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	77.5196	379	1263	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	77.4701	375	1263	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	77.4004	283	1263	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	77.3832	262	1263	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	77.3626	371	1263	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	77.3479	423	1263	95	below_threshold
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	77.1874	411	1263	95	below_threshold
Marivibrio halodurans	strain=CGMCC 1.15697	GCA_017963645.1	2039722	2039722	type	True	77.0922	262	1263	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	77.0625	405	1263	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.7144	269	1263	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.7128	276	1263	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.155	243	1263	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	76.0238	154	1263	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:05,588] [INFO] DFAST Taxonomy check result was written to GCF_002148795.1_ASM214879v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:05,588] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:05,589] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:05,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee5a9350-17b6-4b61-a2db-8ec70493fe42/dqc_reference/checkm_data
[2024-01-24 14:23:05,590] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:05,629] [INFO] Task started: CheckM
[2024-01-24 14:23:05,630] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002148795.1_ASM214879v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002148795.1_ASM214879v1_genomic.fna/checkm_input GCF_002148795.1_ASM214879v1_genomic.fna/checkm_result
[2024-01-24 14:23:41,506] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:41,507] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:41,537] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:41,538] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:41,538] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002148795.1_ASM214879v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:41,538] [INFO] Task started: Blastn
[2024-01-24 14:23:41,538] [INFO] Running command: blastn -query GCF_002148795.1_ASM214879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee5a9350-17b6-4b61-a2db-8ec70493fe42/dqc_reference/reference_markers_gtdb.fasta -out GCF_002148795.1_ASM214879v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:43,506] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:43,510] [INFO] Selected 11 target genomes.
[2024-01-24 14:23:43,510] [INFO] Target genome list was writen to GCF_002148795.1_ASM214879v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:43,521] [INFO] Task started: fastANI
[2024-01-24 14:23:43,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a4baa90-e3eb-49e6-b3b6-71a20b119c16/GCF_002148795.1_ASM214879v1_genomic.fna.gz --refList GCF_002148795.1_ASM214879v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002148795.1_ASM214879v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:56,145] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:56,156] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:56,156] [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_002148795.1	s__Oceanibaculum nanhaiense	100.0	1262	1263	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000299935.1	s__Oceanibaculum indicum	90.2662	1090	1263	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	97.37	97.37	0.93	0.93	2	-
GCA_018823745.1	s__Oceanibaculum sp018823745	84.5875	861	1263	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	99.98	99.98	1.00	1.00	4	-
GCF_001618175.1	s__Oceanibaculum pacificum	84.1095	776	1263	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359905.1	s__Hoeflea sp014359905	78.2772	199	1263	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401495.1	s__Thalassobaculum_A sp018401495	77.5891	368	1263	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001315015.1	s__Azospirillum brasilense	77.5423	364	1263	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	99.35	95.17	0.92	0.83	16	-
GCF_007827795.1	s__Azospirillum brasilense_E	77.5107	368	1263	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.90	98.81	0.89	0.86	3	-
GCF_002195995.1	s__Inquilinus limosus_C	77.472	407	1263	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876095.1	s__Azospirillum agricola	77.3194	428	1263	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	96.88	96.88	0.87	0.87	2	-
GCA_000171835.1	s__Thalassobaculum_A sp000171835	77.2929	258	1263	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:56,167] [INFO] GTDB search result was written to GCF_002148795.1_ASM214879v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:56,168] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:56,176] [INFO] DFAST_QC result json was written to GCF_002148795.1_ASM214879v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:56,176] [INFO] DFAST_QC completed!
[2024-01-24 14:23:56,176] [INFO] Total running time: 0h1m23s