[2023-06-19 10:43:00,564] [INFO] DFAST_QC pipeline started.
[2023-06-19 10:43:00,566] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 10:43:00,567] [INFO] DQC Reference Directory: /var/lib/cwl/stg41bc577c-bb0d-408e-8853-8c70b5765cd4/dqc_reference
[2023-06-19 10:43:02,569] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 10:43:02,570] [INFO] Task started: Prodigal
[2023-06-19 10:43:02,571] [INFO] Running command: gunzip -c /var/lib/cwl/stg07b7631a-d9d7-473f-8584-5421a8e2c6c9/GCA_013287465.1_ASM1328746v1_genomic.fna.gz | prodigal -d GCA_013287465.1_ASM1328746v1_genomic.fna/cds.fna -a GCA_013287465.1_ASM1328746v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 10:43:06,860] [INFO] Task succeeded: Prodigal
[2023-06-19 10:43:06,861] [INFO] Task started: HMMsearch
[2023-06-19 10:43:06,861] [INFO] Running command: hmmsearch --tblout GCA_013287465.1_ASM1328746v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41bc577c-bb0d-408e-8853-8c70b5765cd4/dqc_reference/reference_markers.hmm GCA_013287465.1_ASM1328746v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 10:43:07,120] [INFO] Task succeeded: HMMsearch
[2023-06-19 10:43:07,121] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg07b7631a-d9d7-473f-8584-5421a8e2c6c9/GCA_013287465.1_ASM1328746v1_genomic.fna.gz]
[2023-06-19 10:43:07,145] [INFO] Query marker FASTA was written to GCA_013287465.1_ASM1328746v1_genomic.fna/markers.fasta
[2023-06-19 10:43:07,145] [INFO] Task started: Blastn
[2023-06-19 10:43:07,145] [INFO] Running command: blastn -query GCA_013287465.1_ASM1328746v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41bc577c-bb0d-408e-8853-8c70b5765cd4/dqc_reference/reference_markers.fasta -out GCA_013287465.1_ASM1328746v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:43:08,294] [INFO] Task succeeded: Blastn
[2023-06-19 10:43:08,298] [INFO] Selected 14 target genomes.
[2023-06-19 10:43:08,299] [INFO] Target genome list was writen to GCA_013287465.1_ASM1328746v1_genomic.fna/target_genomes.txt
[2023-06-19 10:43:08,303] [INFO] Task started: fastANI
[2023-06-19 10:43:08,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg07b7631a-d9d7-473f-8584-5421a8e2c6c9/GCA_013287465.1_ASM1328746v1_genomic.fna.gz --refList GCA_013287465.1_ASM1328746v1_genomic.fna/target_genomes.txt --output GCA_013287465.1_ASM1328746v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 10:43:14,913] [INFO] Task succeeded: fastANI
[2023-06-19 10:43:14,914] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41bc577c-bb0d-408e-8853-8c70b5765cd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 10:43:14,914] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41bc577c-bb0d-408e-8853-8c70b5765cd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 10:43:14,917] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 10:43:14,917] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 10:43:14,917] [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 10:43:14,919] [INFO] DFAST Taxonomy check result was written to GCA_013287465.1_ASM1328746v1_genomic.fna/tc_result.tsv
[2023-06-19 10:43:14,920] [INFO] ===== Taxonomy check completed =====
[2023-06-19 10:43:14,920] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 10:43:14,920] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41bc577c-bb0d-408e-8853-8c70b5765cd4/dqc_reference/checkm_data
[2023-06-19 10:43:14,924] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 10:43:14,955] [INFO] Task started: CheckM
[2023-06-19 10:43:14,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013287465.1_ASM1328746v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013287465.1_ASM1328746v1_genomic.fna/checkm_input GCA_013287465.1_ASM1328746v1_genomic.fna/checkm_result
[2023-06-19 10:43:35,275] [INFO] Task succeeded: CheckM
[2023-06-19 10:43:35,281] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 10:43:35,303] [INFO] ===== Completeness check finished =====
[2023-06-19 10:43:35,304] [INFO] ===== Start GTDB Search =====
[2023-06-19 10:43:35,304] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013287465.1_ASM1328746v1_genomic.fna/markers.fasta)
[2023-06-19 10:43:35,305] [INFO] Task started: Blastn
[2023-06-19 10:43:35,305] [INFO] Running command: blastn -query GCA_013287465.1_ASM1328746v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41bc577c-bb0d-408e-8853-8c70b5765cd4/dqc_reference/reference_markers_gtdb.fasta -out GCA_013287465.1_ASM1328746v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:43:36,118] [INFO] Task succeeded: Blastn
[2023-06-19 10:43:36,124] [INFO] Selected 19 target genomes.
[2023-06-19 10:43:36,124] [INFO] Target genome list was writen to GCA_013287465.1_ASM1328746v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 10:43:36,145] [INFO] Task started: fastANI
[2023-06-19 10:43:36,145] [INFO] Running command: fastANI --query /var/lib/cwl/stg07b7631a-d9d7-473f-8584-5421a8e2c6c9/GCA_013287465.1_ASM1328746v1_genomic.fna.gz --refList GCA_013287465.1_ASM1328746v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013287465.1_ASM1328746v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 10:43:43,710] [INFO] Task succeeded: fastANI
[2023-06-19 10:43:43,716] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 10:43:43,716] [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_013287465.1	s__JABDDS01 sp013287465	100.0	648	652	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Parachlamydiaceae;g__JABDDS01	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-19 10:43:43,718] [INFO] GTDB search result was written to GCA_013287465.1_ASM1328746v1_genomic.fna/result_gtdb.tsv
[2023-06-19 10:43:43,719] [INFO] ===== GTDB Search completed =====
[2023-06-19 10:43:43,721] [INFO] DFAST_QC result json was written to GCA_013287465.1_ASM1328746v1_genomic.fna/dqc_result.json
[2023-06-19 10:43:43,721] [INFO] DFAST_QC completed!
[2023-06-19 10:43:43,721] [INFO] Total running time: 0h0m43s