[2024-01-24 11:05:34,608] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:34,610] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:34,610] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbff268d-89d1-4273-a0a6-24618c913845/dqc_reference
[2024-01-24 11:05:35,789] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:35,789] [INFO] Task started: Prodigal
[2024-01-24 11:05:35,790] [INFO] Running command: gunzip -c /var/lib/cwl/stgd53628bd-ea9e-4228-a7d5-9666a34d42d1/GCF_004216635.1_ASM421663v1_genomic.fna.gz | prodigal -d GCF_004216635.1_ASM421663v1_genomic.fna/cds.fna -a GCF_004216635.1_ASM421663v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:49,310] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:49,311] [INFO] Task started: HMMsearch
[2024-01-24 11:05:49,311] [INFO] Running command: hmmsearch --tblout GCF_004216635.1_ASM421663v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbff268d-89d1-4273-a0a6-24618c913845/dqc_reference/reference_markers.hmm GCF_004216635.1_ASM421663v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:49,714] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:49,716] [INFO] Found 6/6 markers.
[2024-01-24 11:05:49,757] [INFO] Query marker FASTA was written to GCF_004216635.1_ASM421663v1_genomic.fna/markers.fasta
[2024-01-24 11:05:49,758] [INFO] Task started: Blastn
[2024-01-24 11:05:49,758] [INFO] Running command: blastn -query GCF_004216635.1_ASM421663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbff268d-89d1-4273-a0a6-24618c913845/dqc_reference/reference_markers.fasta -out GCF_004216635.1_ASM421663v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:50,766] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:50,770] [INFO] Selected 18 target genomes.
[2024-01-24 11:05:50,771] [INFO] Target genome list was writen to GCF_004216635.1_ASM421663v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:50,794] [INFO] Task started: fastANI
[2024-01-24 11:05:50,794] [INFO] Running command: fastANI --query /var/lib/cwl/stgd53628bd-ea9e-4228-a7d5-9666a34d42d1/GCF_004216635.1_ASM421663v1_genomic.fna.gz --refList GCF_004216635.1_ASM421663v1_genomic.fna/target_genomes.txt --output GCF_004216635.1_ASM421663v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:10,828] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:10,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbff268d-89d1-4273-a0a6-24618c913845/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:10,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbff268d-89d1-4273-a0a6-24618c913845/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:10,849] [INFO] Found 18 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:06:10,849] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:10,849] [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
Variibacter gotjawalensis	strain=DSM 29671	GCA_004216635.1	1333996	1333996	type	True	100.0	1527	1527	95	conclusive
Variibacter gotjawalensis	strain=GJW-30	GCA_002355335.1	1333996	1333996	type	True	99.9998	1526	1527	95	conclusive
Variibacter gotjawalensis	strain=CECT 8514	GCA_011761465.1	1333996	1333996	type	True	99.9997	1527	1527	95	conclusive
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	77.7564	385	1527	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	77.7427	381	1527	95	below_threshold
Rhodopseudomonas pseudopalustris	strain=DSM 123	GCA_900110435.1	1513892	1513892	type	True	77.694	341	1527	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	77.5871	399	1527	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	77.5687	349	1527	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	77.5051	350	1527	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	77.4663	398	1527	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	77.4586	318	1527	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	77.4152	382	1527	95	below_threshold
Bradyrhizobium embrapense	strain=SEMIA 6208	GCA_001189235.2	630921	630921	type	True	77.4109	420	1527	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	77.4035	378	1527	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	77.2685	307	1527	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	77.2349	414	1527	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	77.1625	197	1527	95	below_threshold
Rhizobium rhizolycopersici	strain=DBTS2	GCA_013378445.1	2746702	2746702	type	True	76.8972	163	1527	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:10,851] [INFO] DFAST Taxonomy check result was written to GCF_004216635.1_ASM421663v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:10,851] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:10,852] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:10,852] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbff268d-89d1-4273-a0a6-24618c913845/dqc_reference/checkm_data
[2024-01-24 11:06:10,853] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:10,896] [INFO] Task started: CheckM
[2024-01-24 11:06:10,896] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004216635.1_ASM421663v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004216635.1_ASM421663v1_genomic.fna/checkm_input GCF_004216635.1_ASM421663v1_genomic.fna/checkm_result
[2024-01-24 11:06:52,103] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:52,104] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:52,127] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:52,128] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:52,128] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004216635.1_ASM421663v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:52,129] [INFO] Task started: Blastn
[2024-01-24 11:06:52,129] [INFO] Running command: blastn -query GCF_004216635.1_ASM421663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbff268d-89d1-4273-a0a6-24618c913845/dqc_reference/reference_markers_gtdb.fasta -out GCF_004216635.1_ASM421663v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:53,991] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:53,996] [INFO] Selected 25 target genomes.
[2024-01-24 11:06:53,996] [INFO] Target genome list was writen to GCF_004216635.1_ASM421663v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:54,021] [INFO] Task started: fastANI
[2024-01-24 11:06:54,021] [INFO] Running command: fastANI --query /var/lib/cwl/stgd53628bd-ea9e-4228-a7d5-9666a34d42d1/GCF_004216635.1_ASM421663v1_genomic.fna.gz --refList GCF_004216635.1_ASM421663v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004216635.1_ASM421663v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:19,543] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:19,566] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:19,566] [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_002355335.1	s__Variibacter gotjawalensis	99.9998	1526	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Variibacter	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCA_018240595.1	s__Pseudolabrys sp018240595	78.043	367	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304555.1	s__JAFKKS01 sp017304555	77.9725	371	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__JAFKKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242205.1	s__Pseudolabrys sp018242205	77.8645	352	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011365.1	s__Bradyrhizobium diazoefficiens	77.7425	381	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.15	98.13	0.93	0.84	23	-
GCF_003367395.1	s__Pseudolabrys taiwanensis	77.7314	396	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884685.1	s__PALSA-894 sp005884685	77.7066	454	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__PALSA-894	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004571025.1	s__Bradyrhizobium niftali	77.6738	389	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.00	95.49	0.80	0.80	3	-
GCA_001899285.1	s__Pseudolabrys sp001899285	77.6612	363	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.99	99.99	1.00	1.00	2	-
GCA_003105195.1	s__FEB-22 sp003105195	77.6572	331	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__FEB-22	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258865.1	s__Rhodoplanes roseus	77.5947	346	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570865.1	s__Bradyrhizobium frederickii	77.5861	394	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.35	97.32	0.89	0.89	3	-
GCF_016653355.1	s__Rhodoplanes elegans	77.585	394	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	99.89	99.89	0.96	0.96	2	-
GCF_018130695.1	s__Bradyrhizobium jicamae_B	77.5703	407	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011602485.1	s__Bradyrhizobium sp011602485	77.5377	391	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.68	97.67	0.91	0.90	3	-
GCA_019187085.1	s__Pseudorhodoplanes sp019187085	77.5182	336	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudorhodoplanes	95.0	98.90	98.90	0.85	0.85	2	-
GCF_003020115.1	s__Bradyrhizobium sp003020115	77.4785	361	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114915.1	s__Bradyrhizobium sp900114915	77.4628	396	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.76	97.31	0.89	0.88	8	-
GCA_903885555.1	s__Pseudolabrys sp903885555	77.4264	297	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.81	99.81	0.96	0.96	2	-
GCA_009694215.1	s__Z2-YC6860 sp009694215	77.4017	239	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Z2-YC6860	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185205.1	s__Pseudolabrys sp016185205	77.3759	324	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899255.1	s__62-47 sp001899255	77.3519	284	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__62-47	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000472925.1	s__Bradyrhizobium sp000472925	77.2834	371	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003140315.1	s__PALSA-894 sp003140315	77.2262	414	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__PALSA-894	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793595.1	s__Phreatobacter sp016793595	77.0176	290	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:19,568] [INFO] GTDB search result was written to GCF_004216635.1_ASM421663v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:19,568] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:19,573] [INFO] DFAST_QC result json was written to GCF_004216635.1_ASM421663v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:19,573] [INFO] DFAST_QC completed!
[2024-01-24 11:07:19,573] [INFO] Total running time: 0h1m45s