[2024-01-24 14:31:14,714] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:14,716] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:14,716] [INFO] DQC Reference Directory: /var/lib/cwl/stg1eb9f7f9-25ac-4ccb-87a4-9c476528bf47/dqc_reference
[2024-01-24 14:31:16,128] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:16,129] [INFO] Task started: Prodigal
[2024-01-24 14:31:16,129] [INFO] Running command: gunzip -c /var/lib/cwl/stgcac4704d-fa9f-4a2b-95a6-0a83a1b84639/GCF_002043005.1_ASM204300v1_genomic.fna.gz | prodigal -d GCF_002043005.1_ASM204300v1_genomic.fna/cds.fna -a GCF_002043005.1_ASM204300v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:34,407] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:34,408] [INFO] Task started: HMMsearch
[2024-01-24 14:31:34,408] [INFO] Running command: hmmsearch --tblout GCF_002043005.1_ASM204300v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1eb9f7f9-25ac-4ccb-87a4-9c476528bf47/dqc_reference/reference_markers.hmm GCF_002043005.1_ASM204300v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:34,725] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:34,726] [INFO] Found 6/6 markers.
[2024-01-24 14:31:34,777] [INFO] Query marker FASTA was written to GCF_002043005.1_ASM204300v1_genomic.fna/markers.fasta
[2024-01-24 14:31:34,777] [INFO] Task started: Blastn
[2024-01-24 14:31:34,777] [INFO] Running command: blastn -query GCF_002043005.1_ASM204300v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1eb9f7f9-25ac-4ccb-87a4-9c476528bf47/dqc_reference/reference_markers.fasta -out GCF_002043005.1_ASM204300v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:35,910] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:35,918] [INFO] Selected 11 target genomes.
[2024-01-24 14:31:35,919] [INFO] Target genome list was writen to GCF_002043005.1_ASM204300v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:35,923] [INFO] Task started: fastANI
[2024-01-24 14:31:35,924] [INFO] Running command: fastANI --query /var/lib/cwl/stgcac4704d-fa9f-4a2b-95a6-0a83a1b84639/GCF_002043005.1_ASM204300v1_genomic.fna.gz --refList GCF_002043005.1_ASM204300v1_genomic.fna/target_genomes.txt --output GCF_002043005.1_ASM204300v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:49,935] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:49,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1eb9f7f9-25ac-4ccb-87a4-9c476528bf47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:49,937] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1eb9f7f9-25ac-4ccb-87a4-9c476528bf47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:49,958] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:31:49,958] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:49,959] [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 mediterranea	strain=MACL11	GCA_002043005.1	293089	293089	type	True	100.0	1895	1896	95	conclusive
Martelella mediterranea	strain=DSM 17316	GCA_000376125.1	293089	293089	type	True	99.9594	1838	1896	95	conclusive
Martelella limonii	strain=NBRC 109441	GCA_013344475.1	1647649	1647649	type	True	85.1343	1060	1896	95	below_threshold
Martelella lutilitoris	strain=GH2-6	GCA_005924265.1	2583532	2583532	type	True	83.4279	919	1896	95	below_threshold
Martelella endophytica	strain=YC6887	GCA_000960975.1	1486262	1486262	type	True	83.294	910	1896	95	below_threshold
Martelella radicis	strain=DSM 28101	GCA_014196625.1	1397476	1397476	type	True	83.2399	960	1896	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	79.04	540	1896	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	78.8287	582	1896	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	78.8211	534	1896	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	78.5871	432	1896	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	78.578	492	1896	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:49,960] [INFO] DFAST Taxonomy check result was written to GCF_002043005.1_ASM204300v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:49,961] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:49,961] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:49,961] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1eb9f7f9-25ac-4ccb-87a4-9c476528bf47/dqc_reference/checkm_data
[2024-01-24 14:31:49,963] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:50,018] [INFO] Task started: CheckM
[2024-01-24 14:31:50,018] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002043005.1_ASM204300v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002043005.1_ASM204300v1_genomic.fna/checkm_input GCF_002043005.1_ASM204300v1_genomic.fna/checkm_result
[2024-01-24 14:32:42,548] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:42,550] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:42,573] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:42,573] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:42,574] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002043005.1_ASM204300v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:42,574] [INFO] Task started: Blastn
[2024-01-24 14:32:42,574] [INFO] Running command: blastn -query GCF_002043005.1_ASM204300v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1eb9f7f9-25ac-4ccb-87a4-9c476528bf47/dqc_reference/reference_markers_gtdb.fasta -out GCF_002043005.1_ASM204300v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:44,765] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:44,772] [INFO] Selected 8 target genomes.
[2024-01-24 14:32:44,772] [INFO] Target genome list was writen to GCF_002043005.1_ASM204300v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:44,778] [INFO] Task started: fastANI
[2024-01-24 14:32:44,779] [INFO] Running command: fastANI --query /var/lib/cwl/stgcac4704d-fa9f-4a2b-95a6-0a83a1b84639/GCF_002043005.1_ASM204300v1_genomic.fna.gz --refList GCF_002043005.1_ASM204300v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002043005.1_ASM204300v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:55,616] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:55,630] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:55,630] [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_002043005.1	s__Martelella mediterranea	100.0	1894	1896	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	97.32	95.96	0.90	0.83	4	conclusive
GCF_013459645.1	s__Martelella sp013459645	88.7178	1326	1896	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	85.1241	1061	1896	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	84.1961	1014	1896	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	97.55	95.11	0.93	0.87	3	-
GCF_005924265.1	s__Martelella lutilitoris	83.3753	924	1896	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196625.1	s__Martelella radicis	83.2559	957	1896	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000960975.1	s__Martelella endophytica	83.2458	913	1896	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003001975.1	s__Martelella mediterranea_A	82.642	865	1896	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 14:32:55,632] [INFO] GTDB search result was written to GCF_002043005.1_ASM204300v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:55,632] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:55,635] [INFO] DFAST_QC result json was written to GCF_002043005.1_ASM204300v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:55,636] [INFO] DFAST_QC completed!
[2024-01-24 14:32:55,636] [INFO] Total running time: 0h1m41s