[2024-01-24 14:05:36,453] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:36,456] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:36,456] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1847af1-4451-4ad7-a666-ddd932643ac9/dqc_reference
[2024-01-24 14:05:37,809] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:37,810] [INFO] Task started: Prodigal
[2024-01-24 14:05:37,810] [INFO] Running command: gunzip -c /var/lib/cwl/stgc97d01d2-0055-4694-85d6-92ee87cad499/GCF_007992075.1_ASM799207v1_genomic.fna.gz | prodigal -d GCF_007992075.1_ASM799207v1_genomic.fna/cds.fna -a GCF_007992075.1_ASM799207v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:49,314] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:49,314] [INFO] Task started: HMMsearch
[2024-01-24 14:05:49,314] [INFO] Running command: hmmsearch --tblout GCF_007992075.1_ASM799207v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1847af1-4451-4ad7-a666-ddd932643ac9/dqc_reference/reference_markers.hmm GCF_007992075.1_ASM799207v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:49,653] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:49,654] [INFO] Found 6/6 markers.
[2024-01-24 14:05:49,703] [INFO] Query marker FASTA was written to GCF_007992075.1_ASM799207v1_genomic.fna/markers.fasta
[2024-01-24 14:05:49,704] [INFO] Task started: Blastn
[2024-01-24 14:05:49,704] [INFO] Running command: blastn -query GCF_007992075.1_ASM799207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1847af1-4451-4ad7-a666-ddd932643ac9/dqc_reference/reference_markers.fasta -out GCF_007992075.1_ASM799207v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:50,629] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:50,632] [INFO] Selected 13 target genomes.
[2024-01-24 14:05:50,633] [INFO] Target genome list was writen to GCF_007992075.1_ASM799207v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:50,640] [INFO] Task started: fastANI
[2024-01-24 14:05:50,640] [INFO] Running command: fastANI --query /var/lib/cwl/stgc97d01d2-0055-4694-85d6-92ee87cad499/GCF_007992075.1_ASM799207v1_genomic.fna.gz --refList GCF_007992075.1_ASM799207v1_genomic.fna/target_genomes.txt --output GCF_007992075.1_ASM799207v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:02,696] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:02,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1847af1-4451-4ad7-a666-ddd932643ac9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:02,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1847af1-4451-4ad7-a666-ddd932643ac9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:02,712] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:02,713] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:02,713] [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
Pararhodospirillum oryzae	strain=NBRC 107573	GCA_007992075.1	478448	478448	type	True	100.0	1165	1176	95	conclusive
Pararhodospirillum photometricum	strain=DSM 122	GCA_000284415.2	1084	1084	type	True	79.7233	537	1176	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	77.8635	392	1176	95	below_threshold
Rhodospirillum rubrum	strain=ATCC 11170	GCA_000013085.1	1085	1085	type	True	77.8583	390	1176	95	below_threshold
Phaeovibrio sulfidiphilus	strain=DSM 23193	GCA_014861485.1	1220600	1220600	type	True	77.8285	196	1176	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	77.2019	304	1176	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	76.9312	228	1176	95	below_threshold
Magnetospirillum magnetotacticum	strain=MS-1	GCA_000829825.1	188	188	type	True	76.7248	206	1176	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.1935	186	1176	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	75.8942	114	1176	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.8105	87	1176	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.784	199	1176	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	75.6454	108	1176	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:02,715] [INFO] DFAST Taxonomy check result was written to GCF_007992075.1_ASM799207v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:02,715] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:02,716] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:02,716] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1847af1-4451-4ad7-a666-ddd932643ac9/dqc_reference/checkm_data
[2024-01-24 14:06:02,718] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:02,761] [INFO] Task started: CheckM
[2024-01-24 14:06:02,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007992075.1_ASM799207v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007992075.1_ASM799207v1_genomic.fna/checkm_input GCF_007992075.1_ASM799207v1_genomic.fna/checkm_result
[2024-01-24 14:06:44,020] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:44,022] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:44,044] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:44,045] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:44,045] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007992075.1_ASM799207v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:44,046] [INFO] Task started: Blastn
[2024-01-24 14:06:44,046] [INFO] Running command: blastn -query GCF_007992075.1_ASM799207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1847af1-4451-4ad7-a666-ddd932643ac9/dqc_reference/reference_markers_gtdb.fasta -out GCF_007992075.1_ASM799207v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:45,913] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:45,917] [INFO] Selected 13 target genomes.
[2024-01-24 14:06:45,918] [INFO] Target genome list was writen to GCF_007992075.1_ASM799207v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:45,930] [INFO] Task started: fastANI
[2024-01-24 14:06:45,931] [INFO] Running command: fastANI --query /var/lib/cwl/stgc97d01d2-0055-4694-85d6-92ee87cad499/GCF_007992075.1_ASM799207v1_genomic.fna.gz --refList GCF_007992075.1_ASM799207v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007992075.1_ASM799207v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:55,324] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:55,335] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:55,335] [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_007992075.1	s__Pararhodospirillum oryzae	100.0	1165	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Pararhodospirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000284415.1	s__Pararhodospirillum photometricum	79.7325	535	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Pararhodospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013085.1	s__Rhodospirillum rubrum	77.8455	391	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospirillum	95.0	98.74	96.31	0.98	0.96	7	-
GCF_014861485.1	s__Phaeovibrio sulfidiphilus	77.8285	196	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Phaeovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009601025.1	s__Rhodospira navarrensis	77.6197	285	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100455.1	s__Roseospirillum parvum	77.3835	335	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Roseospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961745.1	s__BRH-c57 sp000961745	77.2639	192	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__BRH-c57	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197915.1	s__Rhodospira visakhapatnamensis	77.2254	301	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197795.1	s__Rhodospira goensis	77.1684	308	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729435.1	s__Magnetospirillum sp902729435	77.0324	260	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001511835.1	s__Phaeospirillum sp001511835	77.0135	269	1176	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	76.7218	205	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003250275.1	s__Alpha-05 sp003250275	76.6157	152	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Alpha-05	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:55,337] [INFO] GTDB search result was written to GCF_007992075.1_ASM799207v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:55,338] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:55,341] [INFO] DFAST_QC result json was written to GCF_007992075.1_ASM799207v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:55,342] [INFO] DFAST_QC completed!
[2024-01-24 14:06:55,342] [INFO] Total running time: 0h1m19s