[2024-01-24 13:22:02,152] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:02,154] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:02,154] [INFO] DQC Reference Directory: /var/lib/cwl/stg1481f41a-98a1-4a30-add8-6e7dcd8ea77d/dqc_reference
[2024-01-24 13:22:03,501] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:03,502] [INFO] Task started: Prodigal
[2024-01-24 13:22:03,502] [INFO] Running command: gunzip -c /var/lib/cwl/stg90597bee-6960-4b35-81a0-35b2b13f9cd5/GCF_003368535.1_ASM336853v1_genomic.fna.gz | prodigal -d GCF_003368535.1_ASM336853v1_genomic.fna/cds.fna -a GCF_003368535.1_ASM336853v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:08,887] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:08,888] [INFO] Task started: HMMsearch
[2024-01-24 13:22:08,888] [INFO] Running command: hmmsearch --tblout GCF_003368535.1_ASM336853v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1481f41a-98a1-4a30-add8-6e7dcd8ea77d/dqc_reference/reference_markers.hmm GCF_003368535.1_ASM336853v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:09,199] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:09,201] [INFO] Found 6/6 markers.
[2024-01-24 13:22:09,226] [INFO] Query marker FASTA was written to GCF_003368535.1_ASM336853v1_genomic.fna/markers.fasta
[2024-01-24 13:22:09,226] [INFO] Task started: Blastn
[2024-01-24 13:22:09,226] [INFO] Running command: blastn -query GCF_003368535.1_ASM336853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1481f41a-98a1-4a30-add8-6e7dcd8ea77d/dqc_reference/reference_markers.fasta -out GCF_003368535.1_ASM336853v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:09,889] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:09,893] [INFO] Selected 18 target genomes.
[2024-01-24 13:22:09,893] [INFO] Target genome list was writen to GCF_003368535.1_ASM336853v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:09,955] [INFO] Task started: fastANI
[2024-01-24 13:22:09,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg90597bee-6960-4b35-81a0-35b2b13f9cd5/GCF_003368535.1_ASM336853v1_genomic.fna.gz --refList GCF_003368535.1_ASM336853v1_genomic.fna/target_genomes.txt --output GCF_003368535.1_ASM336853v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:19,716] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:19,717] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1481f41a-98a1-4a30-add8-6e7dcd8ea77d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:19,717] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1481f41a-98a1-4a30-add8-6e7dcd8ea77d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:19,723] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:19,723] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:19,724] [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
Ammonifex thiophilus	strain=SR	GCA_003368535.1	444093	444093	type	True	100.0	670	674	95	conclusive
Ammonifex degensii	strain=KC4	GCA_000024605.1	42838	42838	type	True	88.5222	538	674	95	below_threshold
Desulfovirgula thermocuniculi	strain=DSM 16036	GCA_000429345.1	348842	348842	type	True	76.636	72	674	95	below_threshold
Thermodesulfitimonas autotrophica	strain=DSM 102936	GCA_003815015.1	1894989	1894989	type	True	76.5674	51	674	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:19,726] [INFO] DFAST Taxonomy check result was written to GCF_003368535.1_ASM336853v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:19,726] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:19,726] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:19,727] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1481f41a-98a1-4a30-add8-6e7dcd8ea77d/dqc_reference/checkm_data
[2024-01-24 13:22:19,728] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:19,758] [INFO] Task started: CheckM
[2024-01-24 13:22:19,758] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003368535.1_ASM336853v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003368535.1_ASM336853v1_genomic.fna/checkm_input GCF_003368535.1_ASM336853v1_genomic.fna/checkm_result
[2024-01-24 13:22:43,213] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:43,214] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:43,230] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:43,230] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:43,231] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003368535.1_ASM336853v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:43,231] [INFO] Task started: Blastn
[2024-01-24 13:22:43,232] [INFO] Running command: blastn -query GCF_003368535.1_ASM336853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1481f41a-98a1-4a30-add8-6e7dcd8ea77d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003368535.1_ASM336853v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:44,205] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:44,209] [INFO] Selected 19 target genomes.
[2024-01-24 13:22:44,209] [INFO] Target genome list was writen to GCF_003368535.1_ASM336853v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:44,246] [INFO] Task started: fastANI
[2024-01-24 13:22:44,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg90597bee-6960-4b35-81a0-35b2b13f9cd5/GCF_003368535.1_ASM336853v1_genomic.fna.gz --refList GCF_003368535.1_ASM336853v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003368535.1_ASM336853v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:53,411] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:53,416] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:53,416] [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_003368535.1	s__Ammonifex thiophilus	100.0	670	674	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Ammonifexales;f__Ammonificaceae;g__Ammonifex	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000024605.1	s__Ammonifex degensii	88.4984	538	674	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Ammonifexales;f__Ammonificaceae;g__Ammonifex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429345.1	s__Desulfovirgula thermocuniculi	76.5899	71	674	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfovirgula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815015.1	s__Thermodesulfitimonas autotrophica	76.5674	51	674	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Ammonifexales;f__Ammonificaceae;g__Thermodesulfitimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:53,418] [INFO] GTDB search result was written to GCF_003368535.1_ASM336853v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:53,418] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:53,421] [INFO] DFAST_QC result json was written to GCF_003368535.1_ASM336853v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:53,421] [INFO] DFAST_QC completed!
[2024-01-24 13:22:53,421] [INFO] Total running time: 0h0m51s