[2024-01-24 13:32:55,741] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:55,747] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:55,747] [INFO] DQC Reference Directory: /var/lib/cwl/stg01b2df0c-2f23-4515-98f0-ce3a9aa8a844/dqc_reference
[2024-01-24 13:32:57,113] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:57,114] [INFO] Task started: Prodigal
[2024-01-24 13:32:57,114] [INFO] Running command: gunzip -c /var/lib/cwl/stgfcbf1d03-83a7-4ef6-aa75-ab523da1c844/GCF_000342045.1_MagSO-1_1.0_genomic.fna.gz | prodigal -d GCF_000342045.1_MagSO-1_1.0_genomic.fna/cds.fna -a GCF_000342045.1_MagSO-1_1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:12,721] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:12,721] [INFO] Task started: HMMsearch
[2024-01-24 13:33:12,721] [INFO] Running command: hmmsearch --tblout GCF_000342045.1_MagSO-1_1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01b2df0c-2f23-4515-98f0-ce3a9aa8a844/dqc_reference/reference_markers.hmm GCF_000342045.1_MagSO-1_1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:12,998] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:13,000] [INFO] Found 6/6 markers.
[2024-01-24 13:33:13,055] [INFO] Query marker FASTA was written to GCF_000342045.1_MagSO-1_1.0_genomic.fna/markers.fasta
[2024-01-24 13:33:13,056] [INFO] Task started: Blastn
[2024-01-24 13:33:13,056] [INFO] Running command: blastn -query GCF_000342045.1_MagSO-1_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg01b2df0c-2f23-4515-98f0-ce3a9aa8a844/dqc_reference/reference_markers.fasta -out GCF_000342045.1_MagSO-1_1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:14,049] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:14,051] [INFO] Selected 19 target genomes.
[2024-01-24 13:33:14,052] [INFO] Target genome list was writen to GCF_000342045.1_MagSO-1_1.0_genomic.fna/target_genomes.txt
[2024-01-24 13:33:14,078] [INFO] Task started: fastANI
[2024-01-24 13:33:14,078] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcbf1d03-83a7-4ef6-aa75-ab523da1c844/GCF_000342045.1_MagSO-1_1.0_genomic.fna.gz --refList GCF_000342045.1_MagSO-1_1.0_genomic.fna/target_genomes.txt --output GCF_000342045.1_MagSO-1_1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:32,192] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:32,193] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01b2df0c-2f23-4515-98f0-ce3a9aa8a844/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:32,193] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01b2df0c-2f23-4515-98f0-ce3a9aa8a844/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:32,208] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:32,208] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:32,208] [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 caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	100.0	1520	1530	95	conclusive
Magnetospirillum magnetotacticum	strain=MS-1	GCA_000829825.1	188	188	type	True	87.1528	1030	1530	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	84.0699	884	1530	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	83.5042	857	1530	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	81.3526	706	1530	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	80.6389	678	1530	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	80.4879	658	1530	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	80.166	594	1530	95	below_threshold
Magnetospirillum molischianum	strain=DSM 120	GCA_000294655.1	1083	1083	type	True	78.2637	347	1530	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	77.4588	463	1530	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	77.4582	464	1530	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	77.2409	270	1530	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	76.8158	166	1530	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.5134	319	1530	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	76.4853	173	1530	95	below_threshold
Aureimonas populi	strain=KCTC 42087	GCA_017815515.1	1701758	1701758	type	True	76.4208	167	1530	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	76.3848	256	1530	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.3416	290	1530	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.2058	158	1530	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:32,213] [INFO] DFAST Taxonomy check result was written to GCF_000342045.1_MagSO-1_1.0_genomic.fna/tc_result.tsv
[2024-01-24 13:33:32,214] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:32,214] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:32,214] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01b2df0c-2f23-4515-98f0-ce3a9aa8a844/dqc_reference/checkm_data
[2024-01-24 13:33:32,215] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:32,259] [INFO] Task started: CheckM
[2024-01-24 13:33:32,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000342045.1_MagSO-1_1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000342045.1_MagSO-1_1.0_genomic.fna/checkm_input GCF_000342045.1_MagSO-1_1.0_genomic.fna/checkm_result
[2024-01-24 13:34:16,446] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:16,447] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:16,465] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:16,465] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:16,465] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000342045.1_MagSO-1_1.0_genomic.fna/markers.fasta)
[2024-01-24 13:34:16,465] [INFO] Task started: Blastn
[2024-01-24 13:34:16,465] [INFO] Running command: blastn -query GCF_000342045.1_MagSO-1_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg01b2df0c-2f23-4515-98f0-ce3a9aa8a844/dqc_reference/reference_markers_gtdb.fasta -out GCF_000342045.1_MagSO-1_1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:18,024] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:18,027] [INFO] Selected 11 target genomes.
[2024-01-24 13:34:18,027] [INFO] Target genome list was writen to GCF_000342045.1_MagSO-1_1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:18,044] [INFO] Task started: fastANI
[2024-01-24 13:34:18,044] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcbf1d03-83a7-4ef6-aa75-ab523da1c844/GCF_000342045.1_MagSO-1_1.0_genomic.fna.gz --refList GCF_000342045.1_MagSO-1_1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000342045.1_MagSO-1_1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:31,489] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:31,498] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:31,499] [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_000342045.1	s__Phaeospirillum caucaseum	100.0	1520	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900184795.1	s__Phaeospirillum sp900184795	90.1423	1103	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105535.1	s__Phaeospirillum sp002105535	89.9507	1072	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001511835.1	s__Phaeospirillum sp001511835	89.9258	1123	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000009985.1	s__Phaeospirillum magneticum	89.1258	1108	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000829825.1	s__Phaeospirillum magnetotacticum	87.1671	1029	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650715.1	s__Phaeospirillum marisnigri	84.0862	880	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902729415.1	s__Phaeospirillum magnetica_A	82.3622	835	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003119195.2	s__Azospirillum baldaniorum	77.5101	456	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	97.20	95.48	0.90	0.83	11	-
GCA_016869675.1	s__VGDP01 sp016869675	76.7774	224	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SP197;f__SP197;g__VGDP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002429315.1	s__Rhizomicrobium sp002429315	75.9536	77	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	99.86	99.86	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:31,500] [INFO] GTDB search result was written to GCF_000342045.1_MagSO-1_1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:31,501] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:31,504] [INFO] DFAST_QC result json was written to GCF_000342045.1_MagSO-1_1.0_genomic.fna/dqc_result.json
[2024-01-24 13:34:31,504] [INFO] DFAST_QC completed!
[2024-01-24 13:34:31,504] [INFO] Total running time: 0h1m36s