[2024-01-24 14:28:15,688] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:15,691] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:15,691] [INFO] DQC Reference Directory: /var/lib/cwl/stg6285d3cd-2e54-4c25-b75e-3b4311a055ca/dqc_reference
[2024-01-24 14:28:17,091] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:17,092] [INFO] Task started: Prodigal
[2024-01-24 14:28:17,092] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2944e9e-10ad-4c3f-8963-cee4be48d223/GCF_003313465.1_ASM331346v1_genomic.fna.gz | prodigal -d GCF_003313465.1_ASM331346v1_genomic.fna/cds.fna -a GCF_003313465.1_ASM331346v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:25,419] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:25,420] [INFO] Task started: HMMsearch
[2024-01-24 14:28:25,420] [INFO] Running command: hmmsearch --tblout GCF_003313465.1_ASM331346v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6285d3cd-2e54-4c25-b75e-3b4311a055ca/dqc_reference/reference_markers.hmm GCF_003313465.1_ASM331346v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:25,746] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:25,748] [INFO] Found 6/6 markers.
[2024-01-24 14:28:25,803] [INFO] Query marker FASTA was written to GCF_003313465.1_ASM331346v1_genomic.fna/markers.fasta
[2024-01-24 14:28:25,804] [INFO] Task started: Blastn
[2024-01-24 14:28:25,804] [INFO] Running command: blastn -query GCF_003313465.1_ASM331346v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6285d3cd-2e54-4c25-b75e-3b4311a055ca/dqc_reference/reference_markers.fasta -out GCF_003313465.1_ASM331346v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:26,553] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:26,556] [INFO] Selected 18 target genomes.
[2024-01-24 14:28:26,557] [INFO] Target genome list was writen to GCF_003313465.1_ASM331346v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:26,591] [INFO] Task started: fastANI
[2024-01-24 14:28:26,591] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2944e9e-10ad-4c3f-8963-cee4be48d223/GCF_003313465.1_ASM331346v1_genomic.fna.gz --refList GCF_003313465.1_ASM331346v1_genomic.fna/target_genomes.txt --output GCF_003313465.1_ASM331346v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:38,185] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:38,185] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6285d3cd-2e54-4c25-b75e-3b4311a055ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:38,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6285d3cd-2e54-4c25-b75e-3b4311a055ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:38,190] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:38,190] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:38,191] [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
Thermoflavimicrobium daqui	strain=FBKL4.011	GCA_003313465.1	2137476	2137476	type	True	100.0	1268	1269	95	conclusive
Thermoflavimicrobium dichotomicum	strain=DSM 44778	GCA_900114055.1	46223	46223	type	True	77.7559	276	1269	95	below_threshold
Laceyella sediminis	strain=RHA1	GCA_003003125.1	573074	573074	type	True	77.2079	53	1269	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:38,192] [INFO] DFAST Taxonomy check result was written to GCF_003313465.1_ASM331346v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:38,193] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:38,193] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:38,193] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6285d3cd-2e54-4c25-b75e-3b4311a055ca/dqc_reference/checkm_data
[2024-01-24 14:28:38,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:38,232] [INFO] Task started: CheckM
[2024-01-24 14:28:38,232] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003313465.1_ASM331346v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003313465.1_ASM331346v1_genomic.fna/checkm_input GCF_003313465.1_ASM331346v1_genomic.fna/checkm_result
[2024-01-24 14:29:08,470] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:08,471] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:08,493] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:08,493] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:08,494] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003313465.1_ASM331346v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:08,494] [INFO] Task started: Blastn
[2024-01-24 14:29:08,495] [INFO] Running command: blastn -query GCF_003313465.1_ASM331346v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6285d3cd-2e54-4c25-b75e-3b4311a055ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_003313465.1_ASM331346v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:09,295] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:09,299] [INFO] Selected 21 target genomes.
[2024-01-24 14:29:09,299] [INFO] Target genome list was writen to GCF_003313465.1_ASM331346v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:09,338] [INFO] Task started: fastANI
[2024-01-24 14:29:09,338] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2944e9e-10ad-4c3f-8963-cee4be48d223/GCF_003313465.1_ASM331346v1_genomic.fna.gz --refList GCF_003313465.1_ASM331346v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003313465.1_ASM331346v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:22,537] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:22,547] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:22,548] [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_003313465.1	s__Thermoflavimicrobium sp003313465	100.0	1268	1269	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Thermoflavimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900114055.1	s__Thermoflavimicrobium dichotomicum	77.7688	276	1269	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Thermoflavimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003125.1	s__Laceyella sediminis	77.2456	54	1269	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Laceyella	95.237	97.79	97.73	0.93	0.93	3	-
GCF_014773435.2	s__IB182353 sp014773435	77.1013	55	1269	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__IB182353	95.0	99.11	99.11	0.95	0.95	2	-
GCF_016055185.1	s__Paenactinomyces guangxiensis	76.5067	71	1269	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Paenactinomyces	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:22,549] [INFO] GTDB search result was written to GCF_003313465.1_ASM331346v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:22,550] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:22,552] [INFO] DFAST_QC result json was written to GCF_003313465.1_ASM331346v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:22,552] [INFO] DFAST_QC completed!
[2024-01-24 14:29:22,552] [INFO] Total running time: 0h1m7s