[2024-01-24 15:26:35,783] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:35,786] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:35,786] [INFO] DQC Reference Directory: /var/lib/cwl/stg493e906e-f8cc-481e-9128-aaa3c7958779/dqc_reference
[2024-01-24 15:26:39,060] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:39,061] [INFO] Task started: Prodigal
[2024-01-24 15:26:39,062] [INFO] Running command: gunzip -c /var/lib/cwl/stg28345ac1-b8e4-45d3-94bd-4beee146b943/GCF_018224925.1_ASM1822492v1_genomic.fna.gz | prodigal -d GCF_018224925.1_ASM1822492v1_genomic.fna/cds.fna -a GCF_018224925.1_ASM1822492v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:54,275] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:54,276] [INFO] Task started: HMMsearch
[2024-01-24 15:26:54,276] [INFO] Running command: hmmsearch --tblout GCF_018224925.1_ASM1822492v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg493e906e-f8cc-481e-9128-aaa3c7958779/dqc_reference/reference_markers.hmm GCF_018224925.1_ASM1822492v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:54,578] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:54,579] [INFO] Found 6/6 markers.
[2024-01-24 15:26:54,621] [INFO] Query marker FASTA was written to GCF_018224925.1_ASM1822492v1_genomic.fna/markers.fasta
[2024-01-24 15:26:54,621] [INFO] Task started: Blastn
[2024-01-24 15:26:54,621] [INFO] Running command: blastn -query GCF_018224925.1_ASM1822492v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg493e906e-f8cc-481e-9128-aaa3c7958779/dqc_reference/reference_markers.fasta -out GCF_018224925.1_ASM1822492v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:55,491] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:55,494] [INFO] Selected 14 target genomes.
[2024-01-24 15:26:55,495] [INFO] Target genome list was writen to GCF_018224925.1_ASM1822492v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:55,501] [INFO] Task started: fastANI
[2024-01-24 15:26:55,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg28345ac1-b8e4-45d3-94bd-4beee146b943/GCF_018224925.1_ASM1822492v1_genomic.fna.gz --refList GCF_018224925.1_ASM1822492v1_genomic.fna/target_genomes.txt --output GCF_018224925.1_ASM1822492v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:07,658] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:07,658] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg493e906e-f8cc-481e-9128-aaa3c7958779/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:07,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg493e906e-f8cc-481e-9128-aaa3c7958779/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:07,671] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:27:07,671] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:27:07,671] [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	84.801	953	1347	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	84.7341	957	1347	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	80.5528	643	1347	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	80.1473	612	1347	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	78.8419	505	1347	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	78.7669	530	1347	95	below_threshold
Magnetospirillum magnetotacticum	strain=MS-1	GCA_000829825.1	188	188	type	True	78.7189	487	1347	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	78.7132	528	1347	95	below_threshold
Magnetospirillum molischianum	strain=DSM 120	GCA_000294655.1	1083	1083	type	True	77.7867	252	1347	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.948	192	1347	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.7875	122	1347	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	75.746	88	1347	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	75.7069	85	1347	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	75.665	115	1347	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:07,673] [INFO] DFAST Taxonomy check result was written to GCF_018224925.1_ASM1822492v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:07,674] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:07,674] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:07,674] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg493e906e-f8cc-481e-9128-aaa3c7958779/dqc_reference/checkm_data
[2024-01-24 15:27:07,676] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:07,720] [INFO] Task started: CheckM
[2024-01-24 15:27:07,720] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018224925.1_ASM1822492v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018224925.1_ASM1822492v1_genomic.fna/checkm_input GCF_018224925.1_ASM1822492v1_genomic.fna/checkm_result
[2024-01-24 15:27:54,079] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:54,081] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:54,103] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:54,104] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:54,104] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018224925.1_ASM1822492v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:54,105] [INFO] Task started: Blastn
[2024-01-24 15:27:54,105] [INFO] Running command: blastn -query GCF_018224925.1_ASM1822492v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg493e906e-f8cc-481e-9128-aaa3c7958779/dqc_reference/reference_markers_gtdb.fasta -out GCF_018224925.1_ASM1822492v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:55,758] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:55,762] [INFO] Selected 8 target genomes.
[2024-01-24 15:27:55,763] [INFO] Target genome list was writen to GCF_018224925.1_ASM1822492v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:55,770] [INFO] Task started: fastANI
[2024-01-24 15:27:55,770] [INFO] Running command: fastANI --query /var/lib/cwl/stg28345ac1-b8e4-45d3-94bd-4beee146b943/GCF_018224925.1_ASM1822492v1_genomic.fna.gz --refList GCF_018224925.1_ASM1822492v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018224925.1_ASM1822492v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:04,362] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:04,372] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:04,373] [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_018224925.1	s__Magnetospirillum sp018224925	100.0	1343	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000513295.1	s__Magnetospirillum gryphiswaldense	84.7133	959	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	97.87	97.87	0.91	0.91	3	-
GCA_006218045.1	s__Magnetospirillum sp006218045	84.576	958	1347	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	83.2433	934	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	95.98	95.98	0.88	0.88	2	-
GCA_002435715.1	s__Magnetospirillum sp002435715	83.1686	909	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011022235.1	s__Magnetospirillum aberrantis	80.152	611	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284725.1	s__Phaeospirillum kuznetsovii	78.8417	505	1347	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	78.7593	531	1347	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 15:28:04,374] [INFO] GTDB search result was written to GCF_018224925.1_ASM1822492v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:04,375] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:04,378] [INFO] DFAST_QC result json was written to GCF_018224925.1_ASM1822492v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:04,378] [INFO] DFAST_QC completed!
[2024-01-24 15:28:04,378] [INFO] Total running time: 0h1m29s