[2024-01-24 14:06:30,831] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:30,921] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:30,921] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6485fc2-6506-4ddc-8547-9ac859fd26f3/dqc_reference
[2024-01-24 14:06:32,390] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:32,397] [INFO] Task started: Prodigal
[2024-01-24 14:06:32,397] [INFO] Running command: gunzip -c /var/lib/cwl/stg772c1370-4ea6-4877-96ac-ddaf76402631/GCF_000299935.1_ASM29993v1_genomic.fna.gz | prodigal -d GCF_000299935.1_ASM29993v1_genomic.fna/cds.fna -a GCF_000299935.1_ASM29993v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:45,088] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:45,089] [INFO] Task started: HMMsearch
[2024-01-24 14:06:45,089] [INFO] Running command: hmmsearch --tblout GCF_000299935.1_ASM29993v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6485fc2-6506-4ddc-8547-9ac859fd26f3/dqc_reference/reference_markers.hmm GCF_000299935.1_ASM29993v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:45,399] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:45,401] [INFO] Found 6/6 markers.
[2024-01-24 14:06:45,456] [INFO] Query marker FASTA was written to GCF_000299935.1_ASM29993v1_genomic.fna/markers.fasta
[2024-01-24 14:06:45,457] [INFO] Task started: Blastn
[2024-01-24 14:06:45,458] [INFO] Running command: blastn -query GCF_000299935.1_ASM29993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6485fc2-6506-4ddc-8547-9ac859fd26f3/dqc_reference/reference_markers.fasta -out GCF_000299935.1_ASM29993v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:46,486] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:46,490] [INFO] Selected 20 target genomes.
[2024-01-24 14:06:46,491] [INFO] Target genome list was writen to GCF_000299935.1_ASM29993v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:46,625] [INFO] Task started: fastANI
[2024-01-24 14:06:46,625] [INFO] Running command: fastANI --query /var/lib/cwl/stg772c1370-4ea6-4877-96ac-ddaf76402631/GCF_000299935.1_ASM29993v1_genomic.fna.gz --refList GCF_000299935.1_ASM29993v1_genomic.fna/target_genomes.txt --output GCF_000299935.1_ASM29993v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:07,798] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:07,799] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6485fc2-6506-4ddc-8547-9ac859fd26f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:07,799] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6485fc2-6506-4ddc-8547-9ac859fd26f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:07,820] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:07,820] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:07,821] [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 indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	100.0	1280	1286	95	conclusive
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	90.2705	1089	1286	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	83.9175	754	1286	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	77.8825	423	1286	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	77.8422	302	1286	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	77.5921	376	1286	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	77.5742	404	1286	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	77.5447	375	1286	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	77.3052	367	1286	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	77.302	388	1286	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	77.27	416	1286	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	77.2242	413	1286	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	77.0978	325	1286	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	77.0947	309	1286	95	below_threshold
Nisaea denitrificans	strain=DSM 18348	GCA_000426505.1	390877	390877	type	True	76.9623	234	1286	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.8711	282	1286	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.5994	315	1286	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.4104	268	1286	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	76.1412	127	1286	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	76.1344	158	1286	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:07,822] [INFO] DFAST Taxonomy check result was written to GCF_000299935.1_ASM29993v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:07,823] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:07,823] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:07,823] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6485fc2-6506-4ddc-8547-9ac859fd26f3/dqc_reference/checkm_data
[2024-01-24 14:07:07,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:07,871] [INFO] Task started: CheckM
[2024-01-24 14:07:07,872] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000299935.1_ASM29993v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000299935.1_ASM29993v1_genomic.fna/checkm_input GCF_000299935.1_ASM29993v1_genomic.fna/checkm_result
[2024-01-24 14:07:48,182] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:48,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:48,203] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:48,203] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:48,204] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000299935.1_ASM29993v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:48,204] [INFO] Task started: Blastn
[2024-01-24 14:07:48,204] [INFO] Running command: blastn -query GCF_000299935.1_ASM29993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6485fc2-6506-4ddc-8547-9ac859fd26f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000299935.1_ASM29993v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:50,218] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:50,222] [INFO] Selected 11 target genomes.
[2024-01-24 14:07:50,222] [INFO] Target genome list was writen to GCF_000299935.1_ASM29993v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:50,230] [INFO] Task started: fastANI
[2024-01-24 14:07:50,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg772c1370-4ea6-4877-96ac-ddaf76402631/GCF_000299935.1_ASM29993v1_genomic.fna.gz --refList GCF_000299935.1_ASM29993v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000299935.1_ASM29993v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:02,475] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:02,492] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:02,492] [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_000299935.1	s__Oceanibaculum indicum	100.0	1280	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	97.37	97.37	0.93	0.93	2	conclusive
GCF_002148795.1	s__Oceanibaculum nanhaiense	90.2467	1091	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618175.1	s__Oceanibaculum pacificum	83.9076	755	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823745.1	s__Oceanibaculum sp018823745	83.708	876	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	99.98	99.98	1.00	1.00	4	-
GCA_017640745.1	s__Nisaea sp017640745	77.6655	305	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002195995.1	s__Inquilinus limosus_C	77.4079	441	1286	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_017876165.1	s__Azospirillum soli	77.3126	386	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003349955.1	s__Azospirillum brasilense_B	77.1092	407	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCA_016792585.1	s__SHVZ01 sp016792585	77.0613	286	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__SHVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590795.1	s__Azospirillum sp003590795	77.0591	314	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869645.1	s__SHVW01 sp016869645	76.9828	309	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:02,494] [INFO] GTDB search result was written to GCF_000299935.1_ASM29993v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:02,495] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:02,498] [INFO] DFAST_QC result json was written to GCF_000299935.1_ASM29993v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:02,499] [INFO] DFAST_QC completed!
[2024-01-24 14:08:02,499] [INFO] Total running time: 0h1m32s