[2023-06-29 03:47:03,815] [INFO] DFAST_QC pipeline started.
[2023-06-29 03:47:03,818] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 03:47:03,818] [INFO] DQC Reference Directory: /var/lib/cwl/stgbeb1933e-a5a5-490a-bc60-7cc144aa1b83/dqc_reference
[2023-06-29 03:47:05,118] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 03:47:05,119] [INFO] Task started: Prodigal
[2023-06-29 03:47:05,119] [INFO] Running command: gunzip -c /var/lib/cwl/stg91e24332-07c6-4e01-aa09-df0ee474ecf0/GCA_027310685.1_ASM2731068v1_genomic.fna.gz | prodigal -d GCA_027310685.1_ASM2731068v1_genomic.fna/cds.fna -a GCA_027310685.1_ASM2731068v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 03:47:13,636] [INFO] Task succeeded: Prodigal
[2023-06-29 03:47:13,637] [INFO] Task started: HMMsearch
[2023-06-29 03:47:13,637] [INFO] Running command: hmmsearch --tblout GCA_027310685.1_ASM2731068v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbeb1933e-a5a5-490a-bc60-7cc144aa1b83/dqc_reference/reference_markers.hmm GCA_027310685.1_ASM2731068v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 03:47:13,921] [INFO] Task succeeded: HMMsearch
[2023-06-29 03:47:13,922] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg91e24332-07c6-4e01-aa09-df0ee474ecf0/GCA_027310685.1_ASM2731068v1_genomic.fna.gz]
[2023-06-29 03:47:13,953] [INFO] Query marker FASTA was written to GCA_027310685.1_ASM2731068v1_genomic.fna/markers.fasta
[2023-06-29 03:47:13,953] [INFO] Task started: Blastn
[2023-06-29 03:47:13,953] [INFO] Running command: blastn -query GCA_027310685.1_ASM2731068v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbeb1933e-a5a5-490a-bc60-7cc144aa1b83/dqc_reference/reference_markers.fasta -out GCA_027310685.1_ASM2731068v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:47:14,835] [INFO] Task succeeded: Blastn
[2023-06-29 03:47:14,839] [INFO] Selected 18 target genomes.
[2023-06-29 03:47:14,839] [INFO] Target genome list was writen to GCA_027310685.1_ASM2731068v1_genomic.fna/target_genomes.txt
[2023-06-29 03:47:14,843] [INFO] Task started: fastANI
[2023-06-29 03:47:14,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg91e24332-07c6-4e01-aa09-df0ee474ecf0/GCA_027310685.1_ASM2731068v1_genomic.fna.gz --refList GCA_027310685.1_ASM2731068v1_genomic.fna/target_genomes.txt --output GCA_027310685.1_ASM2731068v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 03:47:31,040] [INFO] Task succeeded: fastANI
[2023-06-29 03:47:31,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbeb1933e-a5a5-490a-bc60-7cc144aa1b83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 03:47:31,041] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbeb1933e-a5a5-490a-bc60-7cc144aa1b83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 03:47:31,057] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 03:47:31,057] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 03:47:31,057] [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 marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	79.305	357	769	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	79.2196	370	769	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	79.1678	332	769	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	79.1377	319	769	95	below_threshold
Magnetospirillum magnetotacticum	strain=MS-1	GCA_000829825.1	188	188	type	True	78.8724	296	769	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	78.8086	313	769	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	78.7029	326	769	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	78.6952	316	769	95	below_threshold
Telmatospirillum siberiense	strain=26-4b1	GCA_002845745.1	382514	382514	type	True	78.4615	305	769	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	77.5487	238	769	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	77.3852	257	769	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	77.3383	294	769	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	77.0852	192	769	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.8186	78	769	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	76.5675	117	769	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.455	217	769	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.4423	177	769	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.1874	132	769	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 03:47:31,059] [INFO] DFAST Taxonomy check result was written to GCA_027310685.1_ASM2731068v1_genomic.fna/tc_result.tsv
[2023-06-29 03:47:31,059] [INFO] ===== Taxonomy check completed =====
[2023-06-29 03:47:31,059] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 03:47:31,060] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbeb1933e-a5a5-490a-bc60-7cc144aa1b83/dqc_reference/checkm_data
[2023-06-29 03:47:31,061] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 03:47:31,098] [INFO] Task started: CheckM
[2023-06-29 03:47:31,098] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027310685.1_ASM2731068v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027310685.1_ASM2731068v1_genomic.fna/checkm_input GCA_027310685.1_ASM2731068v1_genomic.fna/checkm_result
[2023-06-29 03:48:00,910] [INFO] Task succeeded: CheckM
[2023-06-29 03:48:00,912] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 1.50%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 03:48:00,943] [INFO] ===== Completeness check finished =====
[2023-06-29 03:48:00,943] [INFO] ===== Start GTDB Search =====
[2023-06-29 03:48:00,944] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027310685.1_ASM2731068v1_genomic.fna/markers.fasta)
[2023-06-29 03:48:00,944] [INFO] Task started: Blastn
[2023-06-29 03:48:00,945] [INFO] Running command: blastn -query GCA_027310685.1_ASM2731068v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbeb1933e-a5a5-490a-bc60-7cc144aa1b83/dqc_reference/reference_markers_gtdb.fasta -out GCA_027310685.1_ASM2731068v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:48:02,616] [INFO] Task succeeded: Blastn
[2023-06-29 03:48:02,621] [INFO] Selected 19 target genomes.
[2023-06-29 03:48:02,622] [INFO] Target genome list was writen to GCA_027310685.1_ASM2731068v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 03:48:02,630] [INFO] Task started: fastANI
[2023-06-29 03:48:02,630] [INFO] Running command: fastANI --query /var/lib/cwl/stg91e24332-07c6-4e01-aa09-df0ee474ecf0/GCA_027310685.1_ASM2731068v1_genomic.fna.gz --refList GCA_027310685.1_ASM2731068v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027310685.1_ASM2731068v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 03:48:17,868] [INFO] Task succeeded: fastANI
[2023-06-29 03:48:17,884] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 03:48:17,884] [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_902729435.1	s__Magnetospirillum sp902729435	79.3458	332	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105535.1	s__Phaeospirillum sp002105535	79.3363	365	769	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	79.3256	355	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000342045.1	s__Phaeospirillum caucaseum	79.2266	370	769	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	79.1847	332	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013349665.1	s__Telmatospirillum sp013349665	79.138	277	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001511835.1	s__Phaeospirillum sp001511835	79.0947	369	769	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	79.017	361	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898825.1	s__Magnetospirillum sp001898825	78.8561	321	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	95.98	95.98	0.88	0.88	2	-
GCF_006980715.1	s__Oleiliquidispirillum nitrogeniifigens	78.7968	295	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Oleiliquidispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232485.1	s__JADFZP01 sp015232485	78.7444	236	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	96.70	95.97	0.70	0.69	3	-
GCA_903858635.1	s__Telmatospirillum sp903858635	78.692	333	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	99.88	99.86	0.92	0.90	3	-
GCF_011022235.1	s__Magnetospirillum aberrantis	78.6756	318	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902729415.1	s__Phaeospirillum magnetica_A	78.6658	288	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654615.1	s__Telmatospirillum sp015654615	78.6179	296	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014380005.1	s__Magnetospirillum sp014380005	78.475	280	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002845745.1	s__Telmatospirillum siberiense	78.4209	307	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009712185.1	s__Telmatospirillum sp009712185	78.2021	287	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232025.1	s__JADFZP01 sp015232025	78.0984	209	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 03:48:17,886] [INFO] GTDB search result was written to GCA_027310685.1_ASM2731068v1_genomic.fna/result_gtdb.tsv
[2023-06-29 03:48:17,887] [INFO] ===== GTDB Search completed =====
[2023-06-29 03:48:17,891] [INFO] DFAST_QC result json was written to GCA_027310685.1_ASM2731068v1_genomic.fna/dqc_result.json
[2023-06-29 03:48:17,891] [INFO] DFAST_QC completed!
[2023-06-29 03:48:17,891] [INFO] Total running time: 0h1m14s