[2024-01-24 14:14:47,165] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:47,184] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:47,185] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ec58ed7-25ea-4559-9288-392e57fdcac2/dqc_reference
[2024-01-24 14:14:49,421] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:49,422] [INFO] Task started: Prodigal
[2024-01-24 14:14:49,423] [INFO] Running command: gunzip -c /var/lib/cwl/stg0abdc140-e82e-44e5-8758-df39a888a492/GCF_011045155.1_ASM1104515v1_genomic.fna.gz | prodigal -d GCF_011045155.1_ASM1104515v1_genomic.fna/cds.fna -a GCF_011045155.1_ASM1104515v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:04,765] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:04,766] [INFO] Task started: HMMsearch
[2024-01-24 14:15:04,766] [INFO] Running command: hmmsearch --tblout GCF_011045155.1_ASM1104515v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ec58ed7-25ea-4559-9288-392e57fdcac2/dqc_reference/reference_markers.hmm GCF_011045155.1_ASM1104515v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:05,087] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:05,088] [INFO] Found 6/6 markers.
[2024-01-24 14:15:05,136] [INFO] Query marker FASTA was written to GCF_011045155.1_ASM1104515v1_genomic.fna/markers.fasta
[2024-01-24 14:15:05,137] [INFO] Task started: Blastn
[2024-01-24 14:15:05,137] [INFO] Running command: blastn -query GCF_011045155.1_ASM1104515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ec58ed7-25ea-4559-9288-392e57fdcac2/dqc_reference/reference_markers.fasta -out GCF_011045155.1_ASM1104515v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:06,167] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:06,173] [INFO] Selected 19 target genomes.
[2024-01-24 14:15:06,173] [INFO] Target genome list was writen to GCF_011045155.1_ASM1104515v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:06,184] [INFO] Task started: fastANI
[2024-01-24 14:15:06,184] [INFO] Running command: fastANI --query /var/lib/cwl/stg0abdc140-e82e-44e5-8758-df39a888a492/GCF_011045155.1_ASM1104515v1_genomic.fna.gz --refList GCF_011045155.1_ASM1104515v1_genomic.fna/target_genomes.txt --output GCF_011045155.1_ASM1104515v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:26,662] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:26,663] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ec58ed7-25ea-4559-9288-392e57fdcac2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:26,663] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ec58ed7-25ea-4559-9288-392e57fdcac2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:26,689] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:15:26,689] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:26,689] [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
Rhizobium daejeonense	strain=CCBAU10050	GCA_011045155.1	240521	240521	type	True	100.0	1693	1694	95	conclusive
Rhizobium daejeonense	strain=L61	GCA_014280875.1	240521	240521	type	True	99.9999	1689	1694	95	conclusive
Ciceribacter selenitireducens	strain=ATCC BAA-1503	GCA_000518785.1	448181	448181	type	True	81.6345	975	1694	95	below_threshold
Ciceribacter naphthalenivorans	strain=NBRC 107585	GCA_007992095.1	1118451	1118451	type	True	80.4726	789	1694	95	below_threshold
Ciceribacter lividus	strain=DSM 25528	GCA_003337715.1	1197950	1197950	type	True	80.3499	713	1694	95	below_threshold
Rhizobium rosettiformans	strain=DSM 26376	GCA_014202175.1	1368430	1368430	type	True	80.3147	740	1694	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	80.298	738	1694	95	below_threshold
Rhizobium rosettiformans	strain=W3	GCA_004912135.1	1368430	1368430	type	True	80.2453	746	1694	95	below_threshold
Rhizobium wuzhouense	strain=W44	GCA_003205195.1	1986026	1986026	type	True	80.2102	745	1694	95	below_threshold
Rhizobium glycinendophyticum	strain=CL12	GCA_006443685.1	2589807	2589807	type	True	80.1231	691	1694	95	below_threshold
Rhizobium rhizophilum	strain=7209-2	GCA_004912145.1	1850373	1850373	type	True	80.1011	711	1694	95	below_threshold
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	80.0985	720	1694	95	below_threshold
Rhizobium wenxiniae	strain=DSM 100734	GCA_014201355.1	1737357	1737357	type	True	79.2174	571	1694	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	79.2088	638	1694	95	below_threshold
Rhizobium wenxiniae	strain=CGMCC 1.15279	GCA_014641515.1	1737357	1737357	type	True	79.1919	578	1694	95	below_threshold
Rhizobium smilacinae	strain=PTYR-5	GCA_006335145.1	1395944	1395944	type	True	79.1537	586	1694	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	78.5262	540	1694	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	78.059	408	1694	95	below_threshold
Rhizobium skierniewicense	strain=DSM 26438	GCA_014196515.1	984260	984260	type	True	78.0193	398	1694	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:26,691] [INFO] DFAST Taxonomy check result was written to GCF_011045155.1_ASM1104515v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:26,692] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:26,692] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:26,692] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ec58ed7-25ea-4559-9288-392e57fdcac2/dqc_reference/checkm_data
[2024-01-24 14:15:26,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:26,744] [INFO] Task started: CheckM
[2024-01-24 14:15:26,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011045155.1_ASM1104515v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011045155.1_ASM1104515v1_genomic.fna/checkm_input GCF_011045155.1_ASM1104515v1_genomic.fna/checkm_result
[2024-01-24 14:16:12,346] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:12,347] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:12,367] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:12,368] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:12,368] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011045155.1_ASM1104515v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:12,368] [INFO] Task started: Blastn
[2024-01-24 14:16:12,368] [INFO] Running command: blastn -query GCF_011045155.1_ASM1104515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ec58ed7-25ea-4559-9288-392e57fdcac2/dqc_reference/reference_markers_gtdb.fasta -out GCF_011045155.1_ASM1104515v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:14,302] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:14,306] [INFO] Selected 11 target genomes.
[2024-01-24 14:16:14,306] [INFO] Target genome list was writen to GCF_011045155.1_ASM1104515v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:14,333] [INFO] Task started: fastANI
[2024-01-24 14:16:14,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg0abdc140-e82e-44e5-8758-df39a888a492/GCF_011045155.1_ASM1104515v1_genomic.fna.gz --refList GCF_011045155.1_ASM1104515v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011045155.1_ASM1104515v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:27,053] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:27,071] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:27,072] [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_014280875.1	s__Allorhizobium daejeonense	99.9999	1689	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_002600635.1	s__Allorhizobium sp002600635	92.1923	1416	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248775.1	s__Allorhizobium sp003248775	91.9518	1281	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900473245.1	s__Allorhizobium sp900473245	87.0681	1220	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	98.81	98.34	0.95	0.93	20	-
GCF_000518785.1	s__Allorhizobium selenitireducens	81.6447	974	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927355.1	s__Allorhizobium sp012927355	81.5491	955	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337715.1	s__Allorhizobium lividum	80.371	710	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002855515.1	s__Allorhizobium sp002855515	79.9977	726	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004135.1	s__Rhizobium_A straminoryzae	79.6026	644	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	98.62	98.62	0.94	0.94	2	-
GCF_014196535.1	s__Rhizobium_B borbori	79.379	560	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_B	95.0	98.16	98.16	0.88	0.88	2	-
GCF_004343585.1	s__Neorhizobium sp004343585	79.1192	563	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:27,074] [INFO] GTDB search result was written to GCF_011045155.1_ASM1104515v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:27,074] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:27,078] [INFO] DFAST_QC result json was written to GCF_011045155.1_ASM1104515v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:27,079] [INFO] DFAST_QC completed!
[2024-01-24 14:16:27,079] [INFO] Total running time: 0h1m40s