[2024-01-24 13:40:55,628] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,639] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,639] [INFO] DQC Reference Directory: /var/lib/cwl/stg05310e78-2274-4c51-9407-16b7218c3b41/dqc_reference
[2024-01-24 13:40:56,826] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,827] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,827] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c4fa825-d8c1-46e3-8126-8f619335395a/GCF_002995515.1_ASM299551v1_genomic.fna.gz | prodigal -d GCF_002995515.1_ASM299551v1_genomic.fna/cds.fna -a GCF_002995515.1_ASM299551v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:11,780] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:11,780] [INFO] Task started: HMMsearch
[2024-01-24 13:41:11,780] [INFO] Running command: hmmsearch --tblout GCF_002995515.1_ASM299551v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05310e78-2274-4c51-9407-16b7218c3b41/dqc_reference/reference_markers.hmm GCF_002995515.1_ASM299551v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:12,067] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:12,068] [INFO] Found 6/6 markers.
[2024-01-24 13:41:12,103] [INFO] Query marker FASTA was written to GCF_002995515.1_ASM299551v1_genomic.fna/markers.fasta
[2024-01-24 13:41:12,103] [INFO] Task started: Blastn
[2024-01-24 13:41:12,103] [INFO] Running command: blastn -query GCF_002995515.1_ASM299551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05310e78-2274-4c51-9407-16b7218c3b41/dqc_reference/reference_markers.fasta -out GCF_002995515.1_ASM299551v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:13,018] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:13,021] [INFO] Selected 12 target genomes.
[2024-01-24 13:41:13,022] [INFO] Target genome list was writen to GCF_002995515.1_ASM299551v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:13,025] [INFO] Task started: fastANI
[2024-01-24 13:41:13,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c4fa825-d8c1-46e3-8126-8f619335395a/GCF_002995515.1_ASM299551v1_genomic.fna.gz --refList GCF_002995515.1_ASM299551v1_genomic.fna/target_genomes.txt --output GCF_002995515.1_ASM299551v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:24,390] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:24,390] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05310e78-2274-4c51-9407-16b7218c3b41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:24,391] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05310e78-2274-4c51-9407-16b7218c3b41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:24,399] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:24,399] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:24,399] [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
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	100.0	1385	1385	95	conclusive
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	97.8385	1253	1385	95	conclusive
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	81.9701	747	1385	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	80.8207	670	1385	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	80.4735	662	1385	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	80.2573	646	1385	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	80.0221	597	1385	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.5486	240	1385	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	76.0203	92	1385	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	76.011	155	1385	95	below_threshold
Methylobacterium adhaesivum	strain=DSM 17169	GCA_022179065.1	333297	333297	type	True	75.8788	112	1385	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	75.752	95	1385	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:24,406] [INFO] DFAST Taxonomy check result was written to GCF_002995515.1_ASM299551v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:24,407] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:24,407] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:24,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05310e78-2274-4c51-9407-16b7218c3b41/dqc_reference/checkm_data
[2024-01-24 13:41:24,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:24,454] [INFO] Task started: CheckM
[2024-01-24 13:41:24,454] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002995515.1_ASM299551v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002995515.1_ASM299551v1_genomic.fna/checkm_input GCF_002995515.1_ASM299551v1_genomic.fna/checkm_result
[2024-01-24 13:42:15,527] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:15,528] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:15,544] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:15,544] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:15,544] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002995515.1_ASM299551v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:15,544] [INFO] Task started: Blastn
[2024-01-24 13:42:15,544] [INFO] Running command: blastn -query GCF_002995515.1_ASM299551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05310e78-2274-4c51-9407-16b7218c3b41/dqc_reference/reference_markers_gtdb.fasta -out GCF_002995515.1_ASM299551v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:17,255] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:17,258] [INFO] Selected 7 target genomes.
[2024-01-24 13:42:17,258] [INFO] Target genome list was writen to GCF_002995515.1_ASM299551v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:17,262] [INFO] Task started: fastANI
[2024-01-24 13:42:17,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c4fa825-d8c1-46e3-8126-8f619335395a/GCF_002995515.1_ASM299551v1_genomic.fna.gz --refList GCF_002995515.1_ASM299551v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002995515.1_ASM299551v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:25,093] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:25,099] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:25,099] [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_000513295.1	s__Magnetospirillum gryphiswaldense	97.811	1254	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	97.87	97.87	0.91	0.91	3	conclusive
GCA_006218045.1	s__Magnetospirillum sp006218045	92.3946	1101	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	99.95	99.95	0.98	0.98	2	-
GCA_001898825.1	s__Magnetospirillum sp001898825	84.7814	948	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	95.98	95.98	0.88	0.88	2	-
GCF_018224925.1	s__Magnetospirillum sp018224925	84.7753	943	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002435715.1	s__Magnetospirillum sp002435715	84.2293	924	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184795.1	s__Phaeospirillum sp900184795	80.1516	633	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284725.1	s__Phaeospirillum kuznetsovii	79.9877	600	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:25,100] [INFO] GTDB search result was written to GCF_002995515.1_ASM299551v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:25,101] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:25,103] [INFO] DFAST_QC result json was written to GCF_002995515.1_ASM299551v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:25,104] [INFO] DFAST_QC completed!
[2024-01-24 13:42:25,104] [INFO] Total running time: 0h1m29s