[2023-06-29 19:44:47,202] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:44:47,204] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:44:47,204] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f21e2f6-dd0b-4f3d-a466-81cd51fdbab9/dqc_reference
[2023-06-29 19:44:48,471] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:44:48,472] [INFO] Task started: Prodigal
[2023-06-29 19:44:48,472] [INFO] Running command: gunzip -c /var/lib/cwl/stg0dc1c1fa-9ac5-46a6-b1c7-5d491d7d7ea7/GCA_011772425.1_ASM1177242v1_genomic.fna.gz | prodigal -d GCA_011772425.1_ASM1177242v1_genomic.fna/cds.fna -a GCA_011772425.1_ASM1177242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:45:15,068] [INFO] Task succeeded: Prodigal
[2023-06-29 19:45:15,068] [INFO] Task started: HMMsearch
[2023-06-29 19:45:15,068] [INFO] Running command: hmmsearch --tblout GCA_011772425.1_ASM1177242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f21e2f6-dd0b-4f3d-a466-81cd51fdbab9/dqc_reference/reference_markers.hmm GCA_011772425.1_ASM1177242v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:45:15,591] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:45:15,593] [INFO] Found 6/6 markers.
[2023-06-29 19:45:15,668] [INFO] Query marker FASTA was written to GCA_011772425.1_ASM1177242v1_genomic.fna/markers.fasta
[2023-06-29 19:45:15,669] [INFO] Task started: Blastn
[2023-06-29 19:45:15,669] [INFO] Running command: blastn -query GCA_011772425.1_ASM1177242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f21e2f6-dd0b-4f3d-a466-81cd51fdbab9/dqc_reference/reference_markers.fasta -out GCA_011772425.1_ASM1177242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:45:16,310] [INFO] Task succeeded: Blastn
[2023-06-29 19:45:16,314] [INFO] Selected 16 target genomes.
[2023-06-29 19:45:16,315] [INFO] Target genome list was writen to GCA_011772425.1_ASM1177242v1_genomic.fna/target_genomes.txt
[2023-06-29 19:45:16,316] [INFO] Task started: fastANI
[2023-06-29 19:45:16,316] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dc1c1fa-9ac5-46a6-b1c7-5d491d7d7ea7/GCA_011772425.1_ASM1177242v1_genomic.fna.gz --refList GCA_011772425.1_ASM1177242v1_genomic.fna/target_genomes.txt --output GCA_011772425.1_ASM1177242v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:45:26,516] [INFO] Task succeeded: fastANI
[2023-06-29 19:45:26,517] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f21e2f6-dd0b-4f3d-a466-81cd51fdbab9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:45:26,517] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f21e2f6-dd0b-4f3d-a466-81cd51fdbab9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:45:26,519] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:45:26,519] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 19:45:26,519] [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
--------------------------------------------------------------------------------
[2023-06-29 19:45:26,521] [INFO] DFAST Taxonomy check result was written to GCA_011772425.1_ASM1177242v1_genomic.fna/tc_result.tsv
[2023-06-29 19:45:26,522] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:45:26,522] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:45:26,522] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f21e2f6-dd0b-4f3d-a466-81cd51fdbab9/dqc_reference/checkm_data
[2023-06-29 19:45:26,525] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:45:26,624] [INFO] Task started: CheckM
[2023-06-29 19:45:26,624] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011772425.1_ASM1177242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011772425.1_ASM1177242v1_genomic.fna/checkm_input GCA_011772425.1_ASM1177242v1_genomic.fna/checkm_result
[2023-06-29 19:46:45,801] [INFO] Task succeeded: CheckM
[2023-06-29 19:46:45,803] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 12.50%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:46:45,834] [INFO] ===== Completeness check finished =====
[2023-06-29 19:46:45,834] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:46:45,835] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011772425.1_ASM1177242v1_genomic.fna/markers.fasta)
[2023-06-29 19:46:45,835] [INFO] Task started: Blastn
[2023-06-29 19:46:45,835] [INFO] Running command: blastn -query GCA_011772425.1_ASM1177242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f21e2f6-dd0b-4f3d-a466-81cd51fdbab9/dqc_reference/reference_markers_gtdb.fasta -out GCA_011772425.1_ASM1177242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:46:46,563] [INFO] Task succeeded: Blastn
[2023-06-29 19:46:46,569] [INFO] Selected 27 target genomes.
[2023-06-29 19:46:46,569] [INFO] Target genome list was writen to GCA_011772425.1_ASM1177242v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:46:46,570] [INFO] Task started: fastANI
[2023-06-29 19:46:46,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dc1c1fa-9ac5-46a6-b1c7-5d491d7d7ea7/GCA_011772425.1_ASM1177242v1_genomic.fna.gz --refList GCA_011772425.1_ASM1177242v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011772425.1_ASM1177242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:46:59,925] [INFO] Task succeeded: fastANI
[2023-06-29 19:46:59,928] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 19:46:59,928] [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
--------------------------------------------------------------------------------
[2023-06-29 19:46:59,931] [INFO] GTDB search result was written to GCA_011772425.1_ASM1177242v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:46:59,931] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:46:59,934] [INFO] DFAST_QC result json was written to GCA_011772425.1_ASM1177242v1_genomic.fna/dqc_result.json
[2023-06-29 19:46:59,934] [INFO] DFAST_QC completed!
[2023-06-29 19:46:59,934] [INFO] Total running time: 0h2m13s