[2024-01-24 13:49:19,042] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:19,044] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:19,045] [INFO] DQC Reference Directory: /var/lib/cwl/stg99a425a8-bb22-49ff-a1a8-81cc97e2e317/dqc_reference
[2024-01-24 13:49:20,399] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:20,400] [INFO] Task started: Prodigal
[2024-01-24 13:49:20,400] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d2d8159-452f-4755-ae58-46616918dfc4/GCF_000013085.1_ASM1308v1_genomic.fna.gz | prodigal -d GCF_000013085.1_ASM1308v1_genomic.fna/cds.fna -a GCF_000013085.1_ASM1308v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:34,019] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:34,019] [INFO] Task started: HMMsearch
[2024-01-24 13:49:34,019] [INFO] Running command: hmmsearch --tblout GCF_000013085.1_ASM1308v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99a425a8-bb22-49ff-a1a8-81cc97e2e317/dqc_reference/reference_markers.hmm GCF_000013085.1_ASM1308v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:34,340] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:34,344] [INFO] Found 6/6 markers.
[2024-01-24 13:49:34,406] [INFO] Query marker FASTA was written to GCF_000013085.1_ASM1308v1_genomic.fna/markers.fasta
[2024-01-24 13:49:34,406] [INFO] Task started: Blastn
[2024-01-24 13:49:34,407] [INFO] Running command: blastn -query GCF_000013085.1_ASM1308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99a425a8-bb22-49ff-a1a8-81cc97e2e317/dqc_reference/reference_markers.fasta -out GCF_000013085.1_ASM1308v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:35,464] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:35,468] [INFO] Selected 15 target genomes.
[2024-01-24 13:49:35,468] [INFO] Target genome list was writen to GCF_000013085.1_ASM1308v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:35,473] [INFO] Task started: fastANI
[2024-01-24 13:49:35,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d2d8159-452f-4755-ae58-46616918dfc4/GCF_000013085.1_ASM1308v1_genomic.fna.gz --refList GCF_000013085.1_ASM1308v1_genomic.fna/target_genomes.txt --output GCF_000013085.1_ASM1308v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:47,595] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:47,595] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99a425a8-bb22-49ff-a1a8-81cc97e2e317/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:47,596] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99a425a8-bb22-49ff-a1a8-81cc97e2e317/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:47,608] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:47,608] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:47,608] [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
Rhodospirillum rubrum	strain=ATCC 11170	GCA_000013085.1	1085	1085	type	True	100.0	1467	1467	95	conclusive
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	99.9988	1464	1467	95	conclusive
Pararhodospirillum photometricum	strain=DSM 122	GCA_000284415.2	1084	1084	type	True	78.089	360	1467	95	below_threshold
Pararhodospirillum oryzae	strain=NBRC 107573	GCA_007992075.1	478448	478448	type	True	78.0345	389	1467	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	77.3777	332	1467	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	77.093	280	1467	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014203135.1	140057	140057	type	True	77.0505	264	1467	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	77.0055	303	1467	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	76.8595	298	1467	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.76	239	1467	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	76.1839	135	1467	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.1368	126	1467	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	75.9786	98	1467	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	75.8915	186	1467	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.8175	189	1467	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:47,611] [INFO] DFAST Taxonomy check result was written to GCF_000013085.1_ASM1308v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:47,612] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:47,613] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:47,613] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99a425a8-bb22-49ff-a1a8-81cc97e2e317/dqc_reference/checkm_data
[2024-01-24 13:49:47,614] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:47,660] [INFO] Task started: CheckM
[2024-01-24 13:49:47,660] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000013085.1_ASM1308v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000013085.1_ASM1308v1_genomic.fna/checkm_input GCF_000013085.1_ASM1308v1_genomic.fna/checkm_result
[2024-01-24 13:50:28,491] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:28,492] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:28,508] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:28,508] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:28,509] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000013085.1_ASM1308v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:28,509] [INFO] Task started: Blastn
[2024-01-24 13:50:28,509] [INFO] Running command: blastn -query GCF_000013085.1_ASM1308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99a425a8-bb22-49ff-a1a8-81cc97e2e317/dqc_reference/reference_markers_gtdb.fasta -out GCF_000013085.1_ASM1308v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:30,473] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:30,476] [INFO] Selected 18 target genomes.
[2024-01-24 13:50:30,476] [INFO] Target genome list was writen to GCF_000013085.1_ASM1308v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:30,488] [INFO] Task started: fastANI
[2024-01-24 13:50:30,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d2d8159-452f-4755-ae58-46616918dfc4/GCF_000013085.1_ASM1308v1_genomic.fna.gz --refList GCF_000013085.1_ASM1308v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000013085.1_ASM1308v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:45,457] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:45,480] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:45,480] [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_000013085.1	s__Rhodospirillum rubrum	100.0	1466	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospirillum	95.0	98.74	96.31	0.98	0.96	7	conclusive
GCF_000284415.1	s__Pararhodospirillum photometricum	78.0606	357	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Pararhodospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992075.1	s__Pararhodospirillum oryzae	78.0079	392	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Pararhodospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006980715.1	s__Oleiliquidispirillum nitrogeniifigens	77.3668	312	1467	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	77.3391	272	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	96.70	95.97	0.70	0.69	3	-
GCF_001650635.1	s__Magnetospirillum moscoviense	77.3311	315	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	96.81	95.25	0.84	0.84	3	-
GCF_900230255.1	s__Caenispirillum bisanense	77.1434	369	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108475.1	s__Phaeospirillum fulvum_A	77.122	285	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729425.1	s__Phaeospirillum sp902729425	77.1217	320	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197915.1	s__Rhodospira visakhapatnamensis	77.1037	331	1467	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	77.0967	335	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442515.1	s__Phaeospirillum fulvum_B	77.0625	241	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197855.1	s__Rhodospira marina	77.0064	263	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	100.00	99.99	1.00	1.00	3	-
GCA_015232025.1	s__JADFZP01 sp015232025	76.9737	225	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009601025.1	s__Rhodospira navarrensis	76.8692	297	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858635.1	s__Telmatospirillum sp903858635	76.6841	279	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	99.88	99.86	0.92	0.90	3	-
GCF_014205675.1	s__Novispirillum itersonii_A	76.5432	250	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Novispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002195995.1	s__Inquilinus limosus_C	76.319	310	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:45,482] [INFO] GTDB search result was written to GCF_000013085.1_ASM1308v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:45,482] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:45,486] [INFO] DFAST_QC result json was written to GCF_000013085.1_ASM1308v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:45,486] [INFO] DFAST_QC completed!
[2024-01-24 13:50:45,486] [INFO] Total running time: 0h1m26s