[2024-01-24 13:12:34,724] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:34,727] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:34,727] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc5ff706-68e1-474f-875f-db19e6e7e156/dqc_reference
[2024-01-24 13:12:35,993] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:35,994] [INFO] Task started: Prodigal
[2024-01-24 13:12:35,994] [INFO] Running command: gunzip -c /var/lib/cwl/stg759d74cb-cf56-4adc-bc3a-0754eff124b6/GCF_014196625.1_ASM1419662v1_genomic.fna.gz | prodigal -d GCF_014196625.1_ASM1419662v1_genomic.fna/cds.fna -a GCF_014196625.1_ASM1419662v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:50,738] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:50,738] [INFO] Task started: HMMsearch
[2024-01-24 13:12:50,738] [INFO] Running command: hmmsearch --tblout GCF_014196625.1_ASM1419662v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc5ff706-68e1-474f-875f-db19e6e7e156/dqc_reference/reference_markers.hmm GCF_014196625.1_ASM1419662v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:51,100] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:51,101] [INFO] Found 6/6 markers.
[2024-01-24 13:12:51,145] [INFO] Query marker FASTA was written to GCF_014196625.1_ASM1419662v1_genomic.fna/markers.fasta
[2024-01-24 13:12:51,146] [INFO] Task started: Blastn
[2024-01-24 13:12:51,146] [INFO] Running command: blastn -query GCF_014196625.1_ASM1419662v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc5ff706-68e1-474f-875f-db19e6e7e156/dqc_reference/reference_markers.fasta -out GCF_014196625.1_ASM1419662v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:52,238] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:52,241] [INFO] Selected 11 target genomes.
[2024-01-24 13:12:52,241] [INFO] Target genome list was writen to GCF_014196625.1_ASM1419662v1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:52,246] [INFO] Task started: fastANI
[2024-01-24 13:12:52,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg759d74cb-cf56-4adc-bc3a-0754eff124b6/GCF_014196625.1_ASM1419662v1_genomic.fna.gz --refList GCF_014196625.1_ASM1419662v1_genomic.fna/target_genomes.txt --output GCF_014196625.1_ASM1419662v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:04,443] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:04,444] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc5ff706-68e1-474f-875f-db19e6e7e156/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:04,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc5ff706-68e1-474f-875f-db19e6e7e156/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:04,460] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:04,460] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:04,460] [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
Martelella radicis	strain=DSM 28101	GCA_014196625.1	1397476	1397476	type	True	100.0	1641	1643	95	conclusive
Martelella lutilitoris	strain=GH2-6	GCA_005924265.1	2583532	2583532	type	True	90.8684	1200	1643	95	below_threshold
Martelella mediterranea	strain=MACL11	GCA_002043005.1	293089	293089	type	True	83.4479	949	1643	95	below_threshold
Martelella mediterranea	strain=DSM 17316	GCA_000376125.1	293089	293089	type	True	83.4439	942	1643	95	below_threshold
Martelella endophytica	strain=YC6887	GCA_000960975.1	1486262	1486262	type	True	83.1238	940	1643	95	below_threshold
Martelella limonii	strain=NBRC 109441	GCA_013344475.1	1647649	1647649	type	True	81.9079	850	1643	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	78.5941	434	1643	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	78.5248	411	1643	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	78.4655	432	1643	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	77.3912	256	1643	95	below_threshold
Rhizobium skierniewicense	strain=DSM 26438	GCA_014196515.1	984260	984260	type	True	77.3129	255	1643	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:04,462] [INFO] DFAST Taxonomy check result was written to GCF_014196625.1_ASM1419662v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:04,463] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:04,463] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:04,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc5ff706-68e1-474f-875f-db19e6e7e156/dqc_reference/checkm_data
[2024-01-24 13:13:04,464] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:04,518] [INFO] Task started: CheckM
[2024-01-24 13:13:04,518] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196625.1_ASM1419662v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196625.1_ASM1419662v1_genomic.fna/checkm_input GCF_014196625.1_ASM1419662v1_genomic.fna/checkm_result
[2024-01-24 13:13:49,741] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:49,742] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:49,764] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:49,764] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:49,765] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196625.1_ASM1419662v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:49,765] [INFO] Task started: Blastn
[2024-01-24 13:13:49,765] [INFO] Running command: blastn -query GCF_014196625.1_ASM1419662v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc5ff706-68e1-474f-875f-db19e6e7e156/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196625.1_ASM1419662v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:51,840] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:51,843] [INFO] Selected 7 target genomes.
[2024-01-24 13:13:51,843] [INFO] Target genome list was writen to GCF_014196625.1_ASM1419662v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:51,850] [INFO] Task started: fastANI
[2024-01-24 13:13:51,850] [INFO] Running command: fastANI --query /var/lib/cwl/stg759d74cb-cf56-4adc-bc3a-0754eff124b6/GCF_014196625.1_ASM1419662v1_genomic.fna.gz --refList GCF_014196625.1_ASM1419662v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196625.1_ASM1419662v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:00,765] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:00,779] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:00,779] [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_014196625.1	s__Martelella radicis	100.0	1641	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005924265.1	s__Martelella lutilitoris	90.872	1200	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001578105.1	s__Martelella sp001578105	88.9874	1217	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	97.55	95.11	0.93	0.87	3	-
GCA_003001975.1	s__Martelella mediterranea_A	85.1192	1019	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002043005.1	s__Martelella mediterranea	83.439	950	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	97.32	95.96	0.90	0.83	4	-
GCF_000960975.1	s__Martelella endophytica	83.099	943	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013459645.1	s__Martelella sp013459645	82.8531	981	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:00,788] [INFO] GTDB search result was written to GCF_014196625.1_ASM1419662v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:00,788] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:00,796] [INFO] DFAST_QC result json was written to GCF_014196625.1_ASM1419662v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:00,796] [INFO] DFAST_QC completed!
[2024-01-24 13:14:00,796] [INFO] Total running time: 0h1m26s