[2024-01-25 20:12:05,831] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:05,833] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:05,833] [INFO] DQC Reference Directory: /var/lib/cwl/stg00227a0b-12ee-487f-9229-1b54eaf930ba/dqc_reference
[2024-01-25 20:12:07,026] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:07,027] [INFO] Task started: Prodigal
[2024-01-25 20:12:07,027] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c7ca515-f914-49e1-b899-6ad5f9e8118c/GCF_000960975.1_ASM96097v1_genomic.fna.gz | prodigal -d GCF_000960975.1_ASM96097v1_genomic.fna/cds.fna -a GCF_000960975.1_ASM96097v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:19,690] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:19,691] [INFO] Task started: HMMsearch
[2024-01-25 20:12:19,691] [INFO] Running command: hmmsearch --tblout GCF_000960975.1_ASM96097v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00227a0b-12ee-487f-9229-1b54eaf930ba/dqc_reference/reference_markers.hmm GCF_000960975.1_ASM96097v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:19,943] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:19,944] [INFO] Found 6/6 markers.
[2024-01-25 20:12:19,982] [INFO] Query marker FASTA was written to GCF_000960975.1_ASM96097v1_genomic.fna/markers.fasta
[2024-01-25 20:12:19,983] [INFO] Task started: Blastn
[2024-01-25 20:12:19,983] [INFO] Running command: blastn -query GCF_000960975.1_ASM96097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00227a0b-12ee-487f-9229-1b54eaf930ba/dqc_reference/reference_markers.fasta -out GCF_000960975.1_ASM96097v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:20,981] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:20,985] [INFO] Selected 12 target genomes.
[2024-01-25 20:12:20,985] [INFO] Target genome list was writen to GCF_000960975.1_ASM96097v1_genomic.fna/target_genomes.txt
[2024-01-25 20:12:21,019] [INFO] Task started: fastANI
[2024-01-25 20:12:21,019] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c7ca515-f914-49e1-b899-6ad5f9e8118c/GCF_000960975.1_ASM96097v1_genomic.fna.gz --refList GCF_000960975.1_ASM96097v1_genomic.fna/target_genomes.txt --output GCF_000960975.1_ASM96097v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:34,206] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:34,206] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00227a0b-12ee-487f-9229-1b54eaf930ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:34,207] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00227a0b-12ee-487f-9229-1b54eaf930ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:34,215] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:12:34,216] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:12:34,216] [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 endophytica	strain=YC6887	GCA_000960975.1	1486262	1486262	type	True	100.0	1603	1605	95	conclusive
Martelella radicis	strain=DSM 28101	GCA_014196625.1	1397476	1397476	type	True	83.2098	929	1605	95	below_threshold
Martelella mediterranea	strain=MACL11	GCA_002043005.1	293089	293089	type	True	83.2077	932	1605	95	below_threshold
Martelella mediterranea	strain=DSM 17316	GCA_000376125.1	293089	293089	type	True	83.1255	922	1605	95	below_threshold
Martelella lutilitoris	strain=GH2-6	GCA_005924265.1	2583532	2583532	type	True	82.9003	910	1605	95	below_threshold
Martelella limonii	strain=NBRC 109441	GCA_013344475.1	1647649	1647649	type	True	82.176	794	1605	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	78.9438	472	1605	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.873	490	1605	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	78.8414	532	1605	95	below_threshold
Rhizobium vallis	strain=CCBAU 65647	GCA_003985155.1	634290	634290	type	True	78.5324	473	1605	95	below_threshold
Rhizobium petrolearium	strain=DSM 26482	GCA_017873175.1	515361	515361	type	True	78.4951	434	1605	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	78.4722	432	1605	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:34,217] [INFO] DFAST Taxonomy check result was written to GCF_000960975.1_ASM96097v1_genomic.fna/tc_result.tsv
[2024-01-25 20:12:34,217] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:34,217] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:34,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00227a0b-12ee-487f-9229-1b54eaf930ba/dqc_reference/checkm_data
[2024-01-25 20:12:34,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:34,276] [INFO] Task started: CheckM
[2024-01-25 20:12:34,276] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000960975.1_ASM96097v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000960975.1_ASM96097v1_genomic.fna/checkm_input GCF_000960975.1_ASM96097v1_genomic.fna/checkm_result
[2024-01-25 20:13:15,791] [INFO] Task succeeded: CheckM
[2024-01-25 20:13:15,792] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:13:15,810] [INFO] ===== Completeness check finished =====
[2024-01-25 20:13:15,810] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:13:15,810] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000960975.1_ASM96097v1_genomic.fna/markers.fasta)
[2024-01-25 20:13:15,811] [INFO] Task started: Blastn
[2024-01-25 20:13:15,811] [INFO] Running command: blastn -query GCF_000960975.1_ASM96097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00227a0b-12ee-487f-9229-1b54eaf930ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_000960975.1_ASM96097v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:17,814] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:17,818] [INFO] Selected 9 target genomes.
[2024-01-25 20:13:17,818] [INFO] Target genome list was writen to GCF_000960975.1_ASM96097v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:13:17,829] [INFO] Task started: fastANI
[2024-01-25 20:13:17,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c7ca515-f914-49e1-b899-6ad5f9e8118c/GCF_000960975.1_ASM96097v1_genomic.fna.gz --refList GCF_000960975.1_ASM96097v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000960975.1_ASM96097v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:13:28,388] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:28,395] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:13:28,395] [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_000960975.1	s__Martelella endophytica	100.0	1605	1605	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_002043005.1	s__Martelella mediterranea	83.2183	930	1605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	97.32	95.96	0.90	0.83	4	-
GCF_014196625.1	s__Martelella radicis	83.1918	931	1605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005924265.1	s__Martelella lutilitoris	82.8838	913	1605	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	82.8039	917	1605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	97.55	95.11	0.93	0.87	3	-
GCF_013459645.1	s__Martelella sp013459645	82.5133	889	1605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003001975.1	s__Martelella mediterranea_A	82.4235	856	1605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013344475.1	s__Martelella limonii	82.1696	792	1605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013184775.1	s__Martelella sp013184775	80.0016	737	1605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:13:28,396] [INFO] GTDB search result was written to GCF_000960975.1_ASM96097v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:13:28,397] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:13:28,399] [INFO] DFAST_QC result json was written to GCF_000960975.1_ASM96097v1_genomic.fna/dqc_result.json
[2024-01-25 20:13:28,399] [INFO] DFAST_QC completed!
[2024-01-25 20:13:28,399] [INFO] Total running time: 0h1m23s