[2024-01-24 13:50:10,738] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:50:10,740] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:50:10,740] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb70904c-6042-4d76-b144-38214fea4c07/dqc_reference
[2024-01-24 13:50:12,049] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:50:12,050] [INFO] Task started: Prodigal
[2024-01-24 13:50:12,051] [INFO] Running command: gunzip -c /var/lib/cwl/stg71914a77-b29d-49a8-85c5-562180f362f7/GCF_013409775.1_ASM1340977v1_genomic.fna.gz | prodigal -d GCF_013409775.1_ASM1340977v1_genomic.fna/cds.fna -a GCF_013409775.1_ASM1340977v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:17,237] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:17,238] [INFO] Task started: HMMsearch
[2024-01-24 13:50:17,238] [INFO] Running command: hmmsearch --tblout GCF_013409775.1_ASM1340977v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb70904c-6042-4d76-b144-38214fea4c07/dqc_reference/reference_markers.hmm GCF_013409775.1_ASM1340977v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:17,497] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:17,498] [INFO] Found 6/6 markers.
[2024-01-24 13:50:17,524] [INFO] Query marker FASTA was written to GCF_013409775.1_ASM1340977v1_genomic.fna/markers.fasta
[2024-01-24 13:50:17,524] [INFO] Task started: Blastn
[2024-01-24 13:50:17,524] [INFO] Running command: blastn -query GCF_013409775.1_ASM1340977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb70904c-6042-4d76-b144-38214fea4c07/dqc_reference/reference_markers.fasta -out GCF_013409775.1_ASM1340977v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:18,139] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:18,143] [INFO] Selected 10 target genomes.
[2024-01-24 13:50:18,143] [INFO] Target genome list was writen to GCF_013409775.1_ASM1340977v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:18,148] [INFO] Task started: fastANI
[2024-01-24 13:50:18,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg71914a77-b29d-49a8-85c5-562180f362f7/GCF_013409775.1_ASM1340977v1_genomic.fna.gz --refList GCF_013409775.1_ASM1340977v1_genomic.fna/target_genomes.txt --output GCF_013409775.1_ASM1340977v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:23,162] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:23,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb70904c-6042-4d76-b144-38214fea4c07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:23,163] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb70904c-6042-4d76-b144-38214fea4c07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:23,168] [INFO] Found 4 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:50:23,168] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:50:23,168] [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
Carboxydothermus ferrireducens	strain=DSM 11255	GCA_013409775.1	54265	54265	type	True	100.0	816	816	95	inconclusive
Carboxydothermus ferrireducens	strain=DSM 11255	GCA_000427565.1	54265	54265	type	True	99.9366	763	816	95	inconclusive
Carboxydothermus hydrogenoformans	strain=Z-2901	GCA_000012865.1	129958	129958	type	True	97.633	693	816	95	inconclusive
Carboxydothermus pertinax	strain=Ug1	GCA_001950255.1	870242	870242	type	True	84.816	538	816	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:23,170] [INFO] DFAST Taxonomy check result was written to GCF_013409775.1_ASM1340977v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:23,170] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:23,170] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:23,171] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb70904c-6042-4d76-b144-38214fea4c07/dqc_reference/checkm_data
[2024-01-24 13:50:23,172] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:23,197] [INFO] Task started: CheckM
[2024-01-24 13:50:23,197] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013409775.1_ASM1340977v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013409775.1_ASM1340977v1_genomic.fna/checkm_input GCF_013409775.1_ASM1340977v1_genomic.fna/checkm_result
[2024-01-24 13:50:44,998] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:44,999] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:45,016] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:45,017] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:45,017] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013409775.1_ASM1340977v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:45,017] [INFO] Task started: Blastn
[2024-01-24 13:50:45,018] [INFO] Running command: blastn -query GCF_013409775.1_ASM1340977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb70904c-6042-4d76-b144-38214fea4c07/dqc_reference/reference_markers_gtdb.fasta -out GCF_013409775.1_ASM1340977v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:45,825] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:45,829] [INFO] Selected 14 target genomes.
[2024-01-24 13:50:45,830] [INFO] Target genome list was writen to GCF_013409775.1_ASM1340977v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:45,841] [INFO] Task started: fastANI
[2024-01-24 13:50:45,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg71914a77-b29d-49a8-85c5-562180f362f7/GCF_013409775.1_ASM1340977v1_genomic.fna.gz --refList GCF_013409775.1_ASM1340977v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013409775.1_ASM1340977v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:52,922] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:52,929] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:52,929] [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_000012865.1	s__Carboxydothermus hydrogenoformans	97.6317	693	816	d__Bacteria;p__Firmicutes_B;c__Z-2901;o__Carboxydothermales;f__Carboxydothermaceae;g__Carboxydothermus	95.0	97.66	97.66	0.87	0.85	3	conclusive
GCF_001950325.1	s__Carboxydothermus islandicus	92.8538	633	816	d__Bacteria;p__Firmicutes_B;c__Z-2901;o__Carboxydothermales;f__Carboxydothermaceae;g__Carboxydothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001950255.1	s__Carboxydothermus pertinax	84.8168	537	816	d__Bacteria;p__Firmicutes_B;c__Z-2901;o__Carboxydothermales;f__Carboxydothermaceae;g__Carboxydothermus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:52,931] [INFO] GTDB search result was written to GCF_013409775.1_ASM1340977v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:52,932] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:52,935] [INFO] DFAST_QC result json was written to GCF_013409775.1_ASM1340977v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:52,935] [INFO] DFAST_QC completed!
[2024-01-24 13:50:52,935] [INFO] Total running time: 0h0m42s