[2023-06-19 08:27:35,527] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:27:35,530] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:27:35,530] [INFO] DQC Reference Directory: /var/lib/cwl/stge12b380a-2ce1-4ae6-967c-40006fb65d77/dqc_reference
[2023-06-19 08:27:36,740] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:27:36,740] [INFO] Task started: Prodigal
[2023-06-19 08:27:36,740] [INFO] Running command: gunzip -c /var/lib/cwl/stg81c0eb2c-a4d1-4c3e-9fda-cef4bc3ad124/GCA_018401135.1_ASM1840113v1_genomic.fna.gz | prodigal -d GCA_018401135.1_ASM1840113v1_genomic.fna/cds.fna -a GCA_018401135.1_ASM1840113v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:27:40,039] [INFO] Task succeeded: Prodigal
[2023-06-19 08:27:40,040] [INFO] Task started: HMMsearch
[2023-06-19 08:27:40,040] [INFO] Running command: hmmsearch --tblout GCA_018401135.1_ASM1840113v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge12b380a-2ce1-4ae6-967c-40006fb65d77/dqc_reference/reference_markers.hmm GCA_018401135.1_ASM1840113v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:27:40,167] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:27:40,168] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg81c0eb2c-a4d1-4c3e-9fda-cef4bc3ad124/GCA_018401135.1_ASM1840113v1_genomic.fna.gz]
[2023-06-19 08:27:40,180] [INFO] Query marker FASTA was written to GCA_018401135.1_ASM1840113v1_genomic.fna/markers.fasta
[2023-06-19 08:27:40,180] [INFO] Task started: Blastn
[2023-06-19 08:27:40,180] [INFO] Running command: blastn -query GCA_018401135.1_ASM1840113v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge12b380a-2ce1-4ae6-967c-40006fb65d77/dqc_reference/reference_markers.fasta -out GCA_018401135.1_ASM1840113v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:27:40,776] [INFO] Task succeeded: Blastn
[2023-06-19 08:27:40,780] [INFO] Selected 10 target genomes.
[2023-06-19 08:27:40,780] [INFO] Target genome list was writen to GCA_018401135.1_ASM1840113v1_genomic.fna/target_genomes.txt
[2023-06-19 08:27:40,786] [INFO] Task started: fastANI
[2023-06-19 08:27:40,787] [INFO] Running command: fastANI --query /var/lib/cwl/stg81c0eb2c-a4d1-4c3e-9fda-cef4bc3ad124/GCA_018401135.1_ASM1840113v1_genomic.fna.gz --refList GCA_018401135.1_ASM1840113v1_genomic.fna/target_genomes.txt --output GCA_018401135.1_ASM1840113v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:27:45,074] [INFO] Task succeeded: fastANI
[2023-06-19 08:27:45,075] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge12b380a-2ce1-4ae6-967c-40006fb65d77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:27:45,075] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge12b380a-2ce1-4ae6-967c-40006fb65d77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:27:45,076] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:27:45,077] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 08:27:45,077] [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
--------------------------------------------------------------------------------
[2023-06-19 08:27:45,079] [INFO] DFAST Taxonomy check result was written to GCA_018401135.1_ASM1840113v1_genomic.fna/tc_result.tsv
[2023-06-19 08:27:45,079] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:27:45,079] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:27:45,080] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge12b380a-2ce1-4ae6-967c-40006fb65d77/dqc_reference/checkm_data
[2023-06-19 08:27:45,082] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:27:45,094] [INFO] Task started: CheckM
[2023-06-19 08:27:45,094] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018401135.1_ASM1840113v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018401135.1_ASM1840113v1_genomic.fna/checkm_input GCA_018401135.1_ASM1840113v1_genomic.fna/checkm_result
[2023-06-19 08:28:01,705] [INFO] Task succeeded: CheckM
[2023-06-19 08:28:01,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.70%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:28:01,719] [INFO] ===== Completeness check finished =====
[2023-06-19 08:28:01,719] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:28:01,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018401135.1_ASM1840113v1_genomic.fna/markers.fasta)
[2023-06-19 08:28:01,720] [INFO] Task started: Blastn
[2023-06-19 08:28:01,720] [INFO] Running command: blastn -query GCA_018401135.1_ASM1840113v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge12b380a-2ce1-4ae6-967c-40006fb65d77/dqc_reference/reference_markers_gtdb.fasta -out GCA_018401135.1_ASM1840113v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:28:02,155] [INFO] Task succeeded: Blastn
[2023-06-19 08:28:02,167] [INFO] Selected 12 target genomes.
[2023-06-19 08:28:02,167] [INFO] Target genome list was writen to GCA_018401135.1_ASM1840113v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:28:02,172] [INFO] Task started: fastANI
[2023-06-19 08:28:02,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg81c0eb2c-a4d1-4c3e-9fda-cef4bc3ad124/GCA_018401135.1_ASM1840113v1_genomic.fna.gz --refList GCA_018401135.1_ASM1840113v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018401135.1_ASM1840113v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:28:06,047] [INFO] Task succeeded: fastANI
[2023-06-19 08:28:06,050] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:28:06,051] [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_018401135.1	s__M50B92 sp018401135	100.0	242	243	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Moranbacterales;f__GCA-2747515;g__M50B92	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-19 08:28:06,052] [INFO] GTDB search result was written to GCA_018401135.1_ASM1840113v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:28:06,053] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:28:06,055] [INFO] DFAST_QC result json was written to GCA_018401135.1_ASM1840113v1_genomic.fna/dqc_result.json
[2023-06-19 08:28:06,056] [INFO] DFAST_QC completed!
[2023-06-19 08:28:06,056] [INFO] Total running time: 0h0m31s