[2024-01-24 11:12:38,513] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:38,516] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:38,516] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd465cc4-0e8e-4182-9d3b-f30e02228013/dqc_reference
[2024-01-24 11:12:39,866] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:39,867] [INFO] Task started: Prodigal
[2024-01-24 11:12:39,867] [INFO] Running command: gunzip -c /var/lib/cwl/stgba051881-dec4-412d-b444-42bc86f4d905/GCF_005924265.1_ASM592426v1_genomic.fna.gz | prodigal -d GCF_005924265.1_ASM592426v1_genomic.fna/cds.fna -a GCF_005924265.1_ASM592426v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:52,835] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:52,836] [INFO] Task started: HMMsearch
[2024-01-24 11:12:52,836] [INFO] Running command: hmmsearch --tblout GCF_005924265.1_ASM592426v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd465cc4-0e8e-4182-9d3b-f30e02228013/dqc_reference/reference_markers.hmm GCF_005924265.1_ASM592426v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:53,126] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:53,127] [INFO] Found 6/6 markers.
[2024-01-24 11:12:53,166] [INFO] Query marker FASTA was written to GCF_005924265.1_ASM592426v1_genomic.fna/markers.fasta
[2024-01-24 11:12:53,167] [INFO] Task started: Blastn
[2024-01-24 11:12:53,167] [INFO] Running command: blastn -query GCF_005924265.1_ASM592426v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd465cc4-0e8e-4182-9d3b-f30e02228013/dqc_reference/reference_markers.fasta -out GCF_005924265.1_ASM592426v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:54,215] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:54,218] [INFO] Selected 11 target genomes.
[2024-01-24 11:12:54,219] [INFO] Target genome list was writen to GCF_005924265.1_ASM592426v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:54,225] [INFO] Task started: fastANI
[2024-01-24 11:12:54,226] [INFO] Running command: fastANI --query /var/lib/cwl/stgba051881-dec4-412d-b444-42bc86f4d905/GCF_005924265.1_ASM592426v1_genomic.fna.gz --refList GCF_005924265.1_ASM592426v1_genomic.fna/target_genomes.txt --output GCF_005924265.1_ASM592426v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:06,219] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:06,220] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd465cc4-0e8e-4182-9d3b-f30e02228013/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:06,221] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd465cc4-0e8e-4182-9d3b-f30e02228013/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:06,239] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:06,239] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:06,239] [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 lutilitoris	strain=GH2-6	GCA_005924265.1	2583532	2583532	type	True	100.0	1473	1474	95	conclusive
Martelella radicis	strain=DSM 28101	GCA_014196625.1	1397476	1397476	type	True	91.0472	1183	1474	95	below_threshold
Martelella mediterranea	strain=MACL11	GCA_002043005.1	293089	293089	type	True	83.4201	925	1474	95	below_threshold
Martelella mediterranea	strain=DSM 17316	GCA_000376125.1	293089	293089	type	True	83.404	905	1474	95	below_threshold
Martelella endophytica	strain=YC6887	GCA_000960975.1	1486262	1486262	type	True	82.8765	902	1474	95	below_threshold
Martelella limonii	strain=NBRC 109441	GCA_013344475.1	1647649	1647649	type	True	82.069	814	1474	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.8885	481	1474	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	78.6785	460	1474	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	78.6368	431	1474	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	78.4483	391	1474	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	78.387	424	1474	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:06,241] [INFO] DFAST Taxonomy check result was written to GCF_005924265.1_ASM592426v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:06,242] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:06,242] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:06,242] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd465cc4-0e8e-4182-9d3b-f30e02228013/dqc_reference/checkm_data
[2024-01-24 11:13:06,243] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:06,286] [INFO] Task started: CheckM
[2024-01-24 11:13:06,286] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005924265.1_ASM592426v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005924265.1_ASM592426v1_genomic.fna/checkm_input GCF_005924265.1_ASM592426v1_genomic.fna/checkm_result
[2024-01-24 11:13:48,282] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:48,285] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:48,308] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:48,308] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:48,309] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005924265.1_ASM592426v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:48,309] [INFO] Task started: Blastn
[2024-01-24 11:13:48,309] [INFO] Running command: blastn -query GCF_005924265.1_ASM592426v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd465cc4-0e8e-4182-9d3b-f30e02228013/dqc_reference/reference_markers_gtdb.fasta -out GCF_005924265.1_ASM592426v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:50,421] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:50,425] [INFO] Selected 8 target genomes.
[2024-01-24 11:13:50,425] [INFO] Target genome list was writen to GCF_005924265.1_ASM592426v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:50,434] [INFO] Task started: fastANI
[2024-01-24 11:13:50,434] [INFO] Running command: fastANI --query /var/lib/cwl/stgba051881-dec4-412d-b444-42bc86f4d905/GCF_005924265.1_ASM592426v1_genomic.fna.gz --refList GCF_005924265.1_ASM592426v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005924265.1_ASM592426v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:00,236] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:00,249] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:00,249] [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_005924265.1	s__Martelella lutilitoris	100.0	1473	1474	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_014196625.1	s__Martelella radicis	91.0474	1183	1474	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	90.3905	1211	1474	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	84.8146	962	1474	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	83.4144	926	1474	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	82.8628	904	1474	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	82.5388	937	1474	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013344475.1	s__Martelella limonii	82.0231	820	1474	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:00,251] [INFO] GTDB search result was written to GCF_005924265.1_ASM592426v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:00,252] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:00,254] [INFO] DFAST_QC result json was written to GCF_005924265.1_ASM592426v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:00,254] [INFO] DFAST_QC completed!
[2024-01-24 11:14:00,255] [INFO] Total running time: 0h1m22s