[2024-01-24 12:45:10,416] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:10,421] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:10,421] [INFO] DQC Reference Directory: /var/lib/cwl/stgb21af7c0-cc4f-4b3a-9842-614002e0853b/dqc_reference
[2024-01-24 12:45:13,084] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,085] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,085] [INFO] Running command: gunzip -c /var/lib/cwl/stg507e1326-58a8-4759-8317-0416c516d6c4/GCF_024662015.1_ASM2466201v1_genomic.fna.gz | prodigal -d GCF_024662015.1_ASM2466201v1_genomic.fna/cds.fna -a GCF_024662015.1_ASM2466201v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:26,519] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:26,519] [INFO] Task started: HMMsearch
[2024-01-24 12:45:26,520] [INFO] Running command: hmmsearch --tblout GCF_024662015.1_ASM2466201v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb21af7c0-cc4f-4b3a-9842-614002e0853b/dqc_reference/reference_markers.hmm GCF_024662015.1_ASM2466201v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:26,798] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:26,799] [INFO] Found 6/6 markers.
[2024-01-24 12:45:26,839] [INFO] Query marker FASTA was written to GCF_024662015.1_ASM2466201v1_genomic.fna/markers.fasta
[2024-01-24 12:45:26,839] [INFO] Task started: Blastn
[2024-01-24 12:45:26,839] [INFO] Running command: blastn -query GCF_024662015.1_ASM2466201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb21af7c0-cc4f-4b3a-9842-614002e0853b/dqc_reference/reference_markers.fasta -out GCF_024662015.1_ASM2466201v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:27,804] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:27,808] [INFO] Selected 12 target genomes.
[2024-01-24 12:45:27,809] [INFO] Target genome list was writen to GCF_024662015.1_ASM2466201v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:27,816] [INFO] Task started: fastANI
[2024-01-24 12:45:27,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg507e1326-58a8-4759-8317-0416c516d6c4/GCF_024662015.1_ASM2466201v1_genomic.fna.gz --refList GCF_024662015.1_ASM2466201v1_genomic.fna/target_genomes.txt --output GCF_024662015.1_ASM2466201v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:39,312] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:39,313] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb21af7c0-cc4f-4b3a-9842-614002e0853b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:39,313] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb21af7c0-cc4f-4b3a-9842-614002e0853b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:39,326] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:39,326] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:39,326] [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
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	100.0	1581	1582	95	conclusive
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	84.6803	1206	1582	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	81.0816	948	1582	95	below_threshold
Nisaea denitrificans	strain=DSM 18348	GCA_000426505.1	390877	390877	type	True	81.0304	966	1582	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	77.9278	491	1582	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	77.5106	292	1582	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	77.2327	269	1582	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.9587	162	1582	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.6242	134	1582	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.4106	243	1582	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.3814	156	1582	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.3057	232	1582	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:39,327] [INFO] DFAST Taxonomy check result was written to GCF_024662015.1_ASM2466201v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:39,328] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:39,328] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:39,328] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb21af7c0-cc4f-4b3a-9842-614002e0853b/dqc_reference/checkm_data
[2024-01-24 12:45:39,329] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:39,375] [INFO] Task started: CheckM
[2024-01-24 12:45:39,375] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024662015.1_ASM2466201v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024662015.1_ASM2466201v1_genomic.fna/checkm_input GCF_024662015.1_ASM2466201v1_genomic.fna/checkm_result
[2024-01-24 12:46:19,567] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:19,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:19,591] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:19,591] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:19,592] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024662015.1_ASM2466201v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:19,592] [INFO] Task started: Blastn
[2024-01-24 12:46:19,592] [INFO] Running command: blastn -query GCF_024662015.1_ASM2466201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb21af7c0-cc4f-4b3a-9842-614002e0853b/dqc_reference/reference_markers_gtdb.fasta -out GCF_024662015.1_ASM2466201v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:21,425] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:21,429] [INFO] Selected 10 target genomes.
[2024-01-24 12:46:21,429] [INFO] Target genome list was writen to GCF_024662015.1_ASM2466201v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:21,484] [INFO] Task started: fastANI
[2024-01-24 12:46:21,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg507e1326-58a8-4759-8317-0416c516d6c4/GCF_024662015.1_ASM2466201v1_genomic.fna.gz --refList GCF_024662015.1_ASM2466201v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024662015.1_ASM2466201v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:31,431] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:31,444] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:46:31,445] [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
GCA_017640745.1	s__Nisaea sp017640745	84.8228	1152	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904705.1	s__Nisaea sp014904705	84.7051	1204	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904795.1	s__Nisaea nitritireducens	81.0886	947	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426505.1	s__Nisaea denitrificans	81.0561	962	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102465.1	s__Thalassobaculum litoreum	78.2347	462	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	77.9213	489	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401495.1	s__Thalassobaculum_A sp018401495	77.8314	380	1582	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_000342045.1	s__Phaeospirillum caucaseum	76.9876	160	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780745.1	s__JADHLJ01 sp016780745	76.9772	217	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__JADHLJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876095.1	s__Azospirillum agricola	76.7985	296	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	96.88	96.88	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:31,447] [INFO] GTDB search result was written to GCF_024662015.1_ASM2466201v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:31,447] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:31,451] [INFO] DFAST_QC result json was written to GCF_024662015.1_ASM2466201v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:31,451] [INFO] DFAST_QC completed!
[2024-01-24 12:46:31,452] [INFO] Total running time: 0h1m21s