[2024-01-24 11:42:20,308] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:42:20,311] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:42:20,311] [INFO] DQC Reference Directory: /var/lib/cwl/stg53da1245-170e-43bc-8d85-878469fde455/dqc_reference
[2024-01-24 11:42:24,523] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:42:24,524] [INFO] Task started: Prodigal
[2024-01-24 11:42:24,524] [INFO] Running command: gunzip -c /var/lib/cwl/stg017a1880-f786-453b-9f30-2a23e8ce71db/GCF_002995805.1_ASM299580v1_genomic.fna.gz | prodigal -d GCF_002995805.1_ASM299580v1_genomic.fna/cds.fna -a GCF_002995805.1_ASM299580v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:42:32,094] [INFO] Task succeeded: Prodigal
[2024-01-24 11:42:32,095] [INFO] Task started: HMMsearch
[2024-01-24 11:42:32,095] [INFO] Running command: hmmsearch --tblout GCF_002995805.1_ASM299580v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53da1245-170e-43bc-8d85-878469fde455/dqc_reference/reference_markers.hmm GCF_002995805.1_ASM299580v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:42:32,334] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:42:32,335] [INFO] Found 6/6 markers.
[2024-01-24 11:42:32,366] [INFO] Query marker FASTA was written to GCF_002995805.1_ASM299580v1_genomic.fna/markers.fasta
[2024-01-24 11:42:32,367] [INFO] Task started: Blastn
[2024-01-24 11:42:32,367] [INFO] Running command: blastn -query GCF_002995805.1_ASM299580v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53da1245-170e-43bc-8d85-878469fde455/dqc_reference/reference_markers.fasta -out GCF_002995805.1_ASM299580v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:42:32,941] [INFO] Task succeeded: Blastn
[2024-01-24 11:42:32,945] [INFO] Selected 12 target genomes.
[2024-01-24 11:42:32,946] [INFO] Target genome list was writen to GCF_002995805.1_ASM299580v1_genomic.fna/target_genomes.txt
[2024-01-24 11:42:32,998] [INFO] Task started: fastANI
[2024-01-24 11:42:32,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg017a1880-f786-453b-9f30-2a23e8ce71db/GCF_002995805.1_ASM299580v1_genomic.fna.gz --refList GCF_002995805.1_ASM299580v1_genomic.fna/target_genomes.txt --output GCF_002995805.1_ASM299580v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:42:39,278] [INFO] Task succeeded: fastANI
[2024-01-24 11:42:39,278] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53da1245-170e-43bc-8d85-878469fde455/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:42:39,279] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53da1245-170e-43bc-8d85-878469fde455/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:42:39,285] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:42:39,286] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:42:39,286] [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
Moorella stamsii	strain=DSM 26217	GCA_002995805.1	1266720	1266720	type	True	100.0	1066	1070	95	inconclusive
Moorella mulderi	strain=DSM 14980	GCA_001594015.1	202604	202604	type	True	95.1528	729	1070	95	inconclusive
Moorella glycerini	strain=DSM 11254	GCA_009735625.1	55779	55779	type	True	93.389	747	1070	95	below_threshold
Moorella humiferrea	strain=DSM 23265	GCA_002995755.1	676965	676965	type	True	82.1359	512	1070	95	below_threshold
Moorella thermoacetica	strain=DSM 2955	GCA_001267435.1	1525	1525	type	True	81.0658	490	1070	95	below_threshold
Moorella thermoacetica	strain=ATCC 35608	GCA_008121885.1	1525	1525	type	True	80.9955	490	1070	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:42:39,287] [INFO] DFAST Taxonomy check result was written to GCF_002995805.1_ASM299580v1_genomic.fna/tc_result.tsv
[2024-01-24 11:42:39,288] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:42:39,288] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:42:39,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53da1245-170e-43bc-8d85-878469fde455/dqc_reference/checkm_data
[2024-01-24 11:42:39,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:42:39,321] [INFO] Task started: CheckM
[2024-01-24 11:42:39,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002995805.1_ASM299580v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002995805.1_ASM299580v1_genomic.fna/checkm_input GCF_002995805.1_ASM299580v1_genomic.fna/checkm_result
[2024-01-24 11:43:06,593] [INFO] Task succeeded: CheckM
[2024-01-24 11:43:06,594] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:43:06,615] [INFO] ===== Completeness check finished =====
[2024-01-24 11:43:06,616] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:43:06,616] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002995805.1_ASM299580v1_genomic.fna/markers.fasta)
[2024-01-24 11:43:06,617] [INFO] Task started: Blastn
[2024-01-24 11:43:06,617] [INFO] Running command: blastn -query GCF_002995805.1_ASM299580v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53da1245-170e-43bc-8d85-878469fde455/dqc_reference/reference_markers_gtdb.fasta -out GCF_002995805.1_ASM299580v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:07,390] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:07,394] [INFO] Selected 9 target genomes.
[2024-01-24 11:43:07,394] [INFO] Target genome list was writen to GCF_002995805.1_ASM299580v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:43:07,403] [INFO] Task started: fastANI
[2024-01-24 11:43:07,403] [INFO] Running command: fastANI --query /var/lib/cwl/stg017a1880-f786-453b-9f30-2a23e8ce71db/GCF_002995805.1_ASM299580v1_genomic.fna.gz --refList GCF_002995805.1_ASM299580v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002995805.1_ASM299580v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:43:13,294] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:13,301] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:43:13,301] [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_002995805.1	s__Moorella stamsii	100.0	1066	1070	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.265	99.99	99.99	0.99	0.99	2	conclusive
GCF_001594015.1	s__Moorella mulderi	95.2085	727	1070	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.265	N/A	N/A	N/A	N/A	1	-
GCF_009735625.1	s__Moorella glycerini	93.3451	749	1070	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538365.1	s__Moorella sp006538365	90.5848	707	1070	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	99.18	99.18	0.87	0.87	2	-
GCF_002995755.1	s__Moorella humiferrea	82.1285	512	1070	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	97.49	97.49	0.85	0.85	2	-
GCF_003116935.1	s__Moorella sp003116935	80.2722	489	1070	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002383405.1	s__Moorella sp002383405	79.4889	319	1070	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:43:13,303] [INFO] GTDB search result was written to GCF_002995805.1_ASM299580v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:43:13,303] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:43:13,306] [INFO] DFAST_QC result json was written to GCF_002995805.1_ASM299580v1_genomic.fna/dqc_result.json
[2024-01-24 11:43:13,306] [INFO] DFAST_QC completed!
[2024-01-24 11:43:13,307] [INFO] Total running time: 0h0m53s