[2023-06-04 20:24:09,425] [INFO] DFAST_QC pipeline started.
[2023-06-04 20:24:09,428] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 20:24:09,429] [INFO] DQC Reference Directory: /var/lib/cwl/stg2dc3aa84-2e99-4b5c-81e1-0ee18f71c701/dqc_reference
[2023-06-04 20:24:11,041] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 20:24:11,043] [INFO] Task started: Prodigal
[2023-06-04 20:24:11,043] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b6e6505-b7c2-43c0-b8da-59fd6d5df93c/GCA_004367405.1_ASM436740v1_genomic.fna.gz | prodigal -d GCA_004367405.1_ASM436740v1_genomic.fna/cds.fna -a GCA_004367405.1_ASM436740v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 20:24:16,815] [INFO] Task succeeded: Prodigal
[2023-06-04 20:24:16,815] [INFO] Task started: HMMsearch
[2023-06-04 20:24:16,816] [INFO] Running command: hmmsearch --tblout GCA_004367405.1_ASM436740v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2dc3aa84-2e99-4b5c-81e1-0ee18f71c701/dqc_reference/reference_markers.hmm GCA_004367405.1_ASM436740v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 20:24:17,037] [INFO] Task succeeded: HMMsearch
[2023-06-04 20:24:17,038] [INFO] Found 6/6 markers.
[2023-06-04 20:24:17,062] [INFO] Query marker FASTA was written to GCA_004367405.1_ASM436740v1_genomic.fna/markers.fasta
[2023-06-04 20:24:17,063] [INFO] Task started: Blastn
[2023-06-04 20:24:17,063] [INFO] Running command: blastn -query GCA_004367405.1_ASM436740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dc3aa84-2e99-4b5c-81e1-0ee18f71c701/dqc_reference/reference_markers.fasta -out GCA_004367405.1_ASM436740v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:24:17,678] [INFO] Task succeeded: Blastn
[2023-06-04 20:24:17,682] [INFO] Selected 15 target genomes.
[2023-06-04 20:24:17,683] [INFO] Target genome list was writen to GCA_004367405.1_ASM436740v1_genomic.fna/target_genomes.txt
[2023-06-04 20:24:17,687] [INFO] Task started: fastANI
[2023-06-04 20:24:17,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b6e6505-b7c2-43c0-b8da-59fd6d5df93c/GCA_004367405.1_ASM436740v1_genomic.fna.gz --refList GCA_004367405.1_ASM436740v1_genomic.fna/target_genomes.txt --output GCA_004367405.1_ASM436740v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 20:24:26,315] [INFO] Task succeeded: fastANI
[2023-06-04 20:24:26,316] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2dc3aa84-2e99-4b5c-81e1-0ee18f71c701/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 20:24:26,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2dc3aa84-2e99-4b5c-81e1-0ee18f71c701/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 20:24:26,319] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 20:24:26,319] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 20:24:26,319] [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
--------------------------------------------------------------------------------
[2023-06-04 20:24:26,321] [INFO] DFAST Taxonomy check result was written to GCA_004367405.1_ASM436740v1_genomic.fna/tc_result.tsv
[2023-06-04 20:24:26,322] [INFO] ===== Taxonomy check completed =====
[2023-06-04 20:24:26,322] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 20:24:26,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2dc3aa84-2e99-4b5c-81e1-0ee18f71c701/dqc_reference/checkm_data
[2023-06-04 20:24:26,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 20:24:26,354] [INFO] Task started: CheckM
[2023-06-04 20:24:26,354] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004367405.1_ASM436740v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004367405.1_ASM436740v1_genomic.fna/checkm_input GCA_004367405.1_ASM436740v1_genomic.fna/checkm_result
[2023-06-04 20:24:49,012] [INFO] Task succeeded: CheckM
[2023-06-04 20:24:49,014] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 20:24:49,039] [INFO] ===== Completeness check finished =====
[2023-06-04 20:24:49,040] [INFO] ===== Start GTDB Search =====
[2023-06-04 20:24:49,040] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004367405.1_ASM436740v1_genomic.fna/markers.fasta)
[2023-06-04 20:24:49,040] [INFO] Task started: Blastn
[2023-06-04 20:24:49,041] [INFO] Running command: blastn -query GCA_004367405.1_ASM436740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dc3aa84-2e99-4b5c-81e1-0ee18f71c701/dqc_reference/reference_markers_gtdb.fasta -out GCA_004367405.1_ASM436740v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:24:49,894] [INFO] Task succeeded: Blastn
[2023-06-04 20:24:49,898] [INFO] Selected 22 target genomes.
[2023-06-04 20:24:49,898] [INFO] Target genome list was writen to GCA_004367405.1_ASM436740v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 20:24:50,154] [INFO] Task started: fastANI
[2023-06-04 20:24:50,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b6e6505-b7c2-43c0-b8da-59fd6d5df93c/GCA_004367405.1_ASM436740v1_genomic.fna.gz --refList GCA_004367405.1_ASM436740v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004367405.1_ASM436740v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 20:25:00,524] [INFO] Task succeeded: fastANI
[2023-06-04 20:25:00,536] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 20:25:00,536] [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
GCA_002375985.1	s__Desulfopertinax sp002375985	99.9134	630	650	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Ammonifexales;f__Desulforudaceae;g__Desulfopertinax	95.0	99.97	99.97	0.97	0.97	2	conclusive
GCA_001899445.1	s__Desulfopertinax cowenii	80.2207	331	650	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Ammonifexales;f__Desulforudaceae;g__Desulfopertinax	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014859075.1	s__Desulfopertinax sp014859075	77.9436	186	650	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Ammonifexales;f__Desulforudaceae;g__Desulfopertinax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018425.1	s__Desulforudis audaxviator	77.8496	198	650	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Ammonifexales;f__Desulforudaceae;g__Desulforudis	95.0	99.94	99.94	0.99	0.99	2	-
GCA_002294005.1	s__Desulforudis sp002294005	77.705	135	650	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Ammonifexales;f__Desulforudaceae;g__Desulforudis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009428905.1	s__Desulfofundulus_A thermobenzoicus	75.9951	53	650	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfofundulus_A	95.0	96.96	95.37	0.88	0.86	3	-
--------------------------------------------------------------------------------
[2023-06-04 20:25:00,538] [INFO] GTDB search result was written to GCA_004367405.1_ASM436740v1_genomic.fna/result_gtdb.tsv
[2023-06-04 20:25:00,539] [INFO] ===== GTDB Search completed =====
[2023-06-04 20:25:00,541] [INFO] DFAST_QC result json was written to GCA_004367405.1_ASM436740v1_genomic.fna/dqc_result.json
[2023-06-04 20:25:00,542] [INFO] DFAST_QC completed!
[2023-06-04 20:25:00,542] [INFO] Total running time: 0h0m51s