[2023-06-18 12:48:48,244] [INFO] DFAST_QC pipeline started.
[2023-06-18 12:48:48,247] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 12:48:48,248] [INFO] DQC Reference Directory: /var/lib/cwl/stg11e660c7-06b7-44a2-a1f3-ef6b620b926b/dqc_reference
[2023-06-18 12:48:49,787] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 12:48:49,788] [INFO] Task started: Prodigal
[2023-06-18 12:48:49,788] [INFO] Running command: gunzip -c /var/lib/cwl/stg97d67c9d-1a3a-498a-95ee-8a614bfd4f17/GCA_018895545.1_ASM1889554v1_genomic.fna.gz | prodigal -d GCA_018895545.1_ASM1889554v1_genomic.fna/cds.fna -a GCA_018895545.1_ASM1889554v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 12:48:57,786] [INFO] Task succeeded: Prodigal
[2023-06-18 12:48:57,786] [INFO] Task started: HMMsearch
[2023-06-18 12:48:57,786] [INFO] Running command: hmmsearch --tblout GCA_018895545.1_ASM1889554v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11e660c7-06b7-44a2-a1f3-ef6b620b926b/dqc_reference/reference_markers.hmm GCA_018895545.1_ASM1889554v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 12:48:58,012] [INFO] Task succeeded: HMMsearch
[2023-06-18 12:48:58,013] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg97d67c9d-1a3a-498a-95ee-8a614bfd4f17/GCA_018895545.1_ASM1889554v1_genomic.fna.gz]
[2023-06-18 12:48:58,048] [INFO] Query marker FASTA was written to GCA_018895545.1_ASM1889554v1_genomic.fna/markers.fasta
[2023-06-18 12:48:58,048] [INFO] Task started: Blastn
[2023-06-18 12:48:58,048] [INFO] Running command: blastn -query GCA_018895545.1_ASM1889554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11e660c7-06b7-44a2-a1f3-ef6b620b926b/dqc_reference/reference_markers.fasta -out GCA_018895545.1_ASM1889554v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:48:58,680] [INFO] Task succeeded: Blastn
[2023-06-18 12:48:58,687] [INFO] Selected 14 target genomes.
[2023-06-18 12:48:58,688] [INFO] Target genome list was writen to GCA_018895545.1_ASM1889554v1_genomic.fna/target_genomes.txt
[2023-06-18 12:48:58,689] [INFO] Task started: fastANI
[2023-06-18 12:48:58,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg97d67c9d-1a3a-498a-95ee-8a614bfd4f17/GCA_018895545.1_ASM1889554v1_genomic.fna.gz --refList GCA_018895545.1_ASM1889554v1_genomic.fna/target_genomes.txt --output GCA_018895545.1_ASM1889554v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 12:49:08,032] [INFO] Task succeeded: fastANI
[2023-06-18 12:49:08,033] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11e660c7-06b7-44a2-a1f3-ef6b620b926b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 12:49:08,033] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11e660c7-06b7-44a2-a1f3-ef6b620b926b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 12:49:08,035] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 12:49:08,035] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 12:49:08,035] [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
--------------------------------------------------------------------------------
[2023-06-18 12:49:08,037] [INFO] DFAST Taxonomy check result was written to GCA_018895545.1_ASM1889554v1_genomic.fna/tc_result.tsv
[2023-06-18 12:49:08,038] [INFO] ===== Taxonomy check completed =====
[2023-06-18 12:49:08,038] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 12:49:08,038] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11e660c7-06b7-44a2-a1f3-ef6b620b926b/dqc_reference/checkm_data
[2023-06-18 12:49:08,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 12:49:08,077] [INFO] Task started: CheckM
[2023-06-18 12:49:08,077] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018895545.1_ASM1889554v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018895545.1_ASM1889554v1_genomic.fna/checkm_input GCA_018895545.1_ASM1889554v1_genomic.fna/checkm_result
[2023-06-18 12:49:36,681] [INFO] Task succeeded: CheckM
[2023-06-18 12:49:36,682] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 12:49:36,707] [INFO] ===== Completeness check finished =====
[2023-06-18 12:49:36,708] [INFO] ===== Start GTDB Search =====
[2023-06-18 12:49:36,708] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018895545.1_ASM1889554v1_genomic.fna/markers.fasta)
[2023-06-18 12:49:36,708] [INFO] Task started: Blastn
[2023-06-18 12:49:36,709] [INFO] Running command: blastn -query GCA_018895545.1_ASM1889554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11e660c7-06b7-44a2-a1f3-ef6b620b926b/dqc_reference/reference_markers_gtdb.fasta -out GCA_018895545.1_ASM1889554v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:49:37,484] [INFO] Task succeeded: Blastn
[2023-06-18 12:49:37,491] [INFO] Selected 14 target genomes.
[2023-06-18 12:49:37,491] [INFO] Target genome list was writen to GCA_018895545.1_ASM1889554v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 12:49:37,492] [INFO] Task started: fastANI
[2023-06-18 12:49:37,492] [INFO] Running command: fastANI --query /var/lib/cwl/stg97d67c9d-1a3a-498a-95ee-8a614bfd4f17/GCA_018895545.1_ASM1889554v1_genomic.fna.gz --refList GCA_018895545.1_ASM1889554v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018895545.1_ASM1889554v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 12:49:47,717] [INFO] Task succeeded: fastANI
[2023-06-18 12:49:47,725] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 12:49:47,726] [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_018896525.1	s__JAHIPE01 sp018896525	99.9554	866	909	d__Bacteria;p__Actinobacteriota;c__Geothermincolia;o__Fen-727;f__Anoxymicrobiaceae;g__JAHIPE01	95.0	99.92	99.86	0.95	0.93	6	conclusive
GCA_018894655.1	s__JAHIPE01 sp018894655	85.1191	386	909	d__Bacteria;p__Actinobacteriota;c__Geothermincolia;o__Fen-727;f__Anoxymicrobiaceae;g__JAHIPE01	95.0	99.01	98.98	0.81	0.81	3	-
--------------------------------------------------------------------------------
[2023-06-18 12:49:47,728] [INFO] GTDB search result was written to GCA_018895545.1_ASM1889554v1_genomic.fna/result_gtdb.tsv
[2023-06-18 12:49:47,729] [INFO] ===== GTDB Search completed =====
[2023-06-18 12:49:47,732] [INFO] DFAST_QC result json was written to GCA_018895545.1_ASM1889554v1_genomic.fna/dqc_result.json
[2023-06-18 12:49:47,732] [INFO] DFAST_QC completed!
[2023-06-18 12:49:47,733] [INFO] Total running time: 0h0m59s