[2023-06-04 23:11:55,118] [INFO] DFAST_QC pipeline started.
[2023-06-04 23:11:55,120] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 23:11:55,120] [INFO] DQC Reference Directory: /var/lib/cwl/stg67f71d71-ec94-4ed8-8390-bec255f9f741/dqc_reference
[2023-06-04 23:11:57,948] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 23:11:57,949] [INFO] Task started: Prodigal
[2023-06-04 23:11:57,949] [INFO] Running command: gunzip -c /var/lib/cwl/stg68e55786-1745-4fa3-a959-6f403846c616/GCA_902628535.1_AH-324-B11_genomic.fna.gz | prodigal -d GCA_902628535.1_AH-324-B11_genomic.fna/cds.fna -a GCA_902628535.1_AH-324-B11_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 23:11:59,488] [INFO] Task succeeded: Prodigal
[2023-06-04 23:11:59,489] [INFO] Task started: HMMsearch
[2023-06-04 23:11:59,489] [INFO] Running command: hmmsearch --tblout GCA_902628535.1_AH-324-B11_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67f71d71-ec94-4ed8-8390-bec255f9f741/dqc_reference/reference_markers.hmm GCA_902628535.1_AH-324-B11_genomic.fna/protein.faa > /dev/null
[2023-06-04 23:11:59,651] [INFO] Task succeeded: HMMsearch
[2023-06-04 23:11:59,653] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg68e55786-1745-4fa3-a959-6f403846c616/GCA_902628535.1_AH-324-B11_genomic.fna.gz]
[2023-06-04 23:11:59,666] [INFO] Query marker FASTA was written to GCA_902628535.1_AH-324-B11_genomic.fna/markers.fasta
[2023-06-04 23:11:59,666] [INFO] Task started: Blastn
[2023-06-04 23:11:59,667] [INFO] Running command: blastn -query GCA_902628535.1_AH-324-B11_genomic.fna/markers.fasta -db /var/lib/cwl/stg67f71d71-ec94-4ed8-8390-bec255f9f741/dqc_reference/reference_markers.fasta -out GCA_902628535.1_AH-324-B11_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:12:01,511] [INFO] Task succeeded: Blastn
[2023-06-04 23:12:01,516] [INFO] Selected 5 target genomes.
[2023-06-04 23:12:01,516] [INFO] Target genome list was writen to GCA_902628535.1_AH-324-B11_genomic.fna/target_genomes.txt
[2023-06-04 23:12:01,522] [INFO] Task started: fastANI
[2023-06-04 23:12:01,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg68e55786-1745-4fa3-a959-6f403846c616/GCA_902628535.1_AH-324-B11_genomic.fna.gz --refList GCA_902628535.1_AH-324-B11_genomic.fna/target_genomes.txt --output GCA_902628535.1_AH-324-B11_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 23:12:03,300] [INFO] Task succeeded: fastANI
[2023-06-04 23:12:03,301] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67f71d71-ec94-4ed8-8390-bec255f9f741/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 23:12:03,301] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67f71d71-ec94-4ed8-8390-bec255f9f741/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 23:12:03,303] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 23:12:03,303] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 23:12:03,304] [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
--------------------------------------------------------------------------------
[2023-06-04 23:12:03,306] [INFO] DFAST Taxonomy check result was written to GCA_902628535.1_AH-324-B11_genomic.fna/tc_result.tsv
[2023-06-04 23:12:03,307] [INFO] ===== Taxonomy check completed =====
[2023-06-04 23:12:03,307] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 23:12:03,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67f71d71-ec94-4ed8-8390-bec255f9f741/dqc_reference/checkm_data
[2023-06-04 23:12:03,312] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 23:12:03,328] [INFO] Task started: CheckM
[2023-06-04 23:12:03,328] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902628535.1_AH-324-B11_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902628535.1_AH-324-B11_genomic.fna/checkm_input GCA_902628535.1_AH-324-B11_genomic.fna/checkm_result
[2023-06-04 23:12:15,709] [INFO] Task succeeded: CheckM
[2023-06-04 23:12:15,711] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 23:12:15,728] [INFO] ===== Completeness check finished =====
[2023-06-04 23:12:15,729] [INFO] ===== Start GTDB Search =====
[2023-06-04 23:12:15,729] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902628535.1_AH-324-B11_genomic.fna/markers.fasta)
[2023-06-04 23:12:15,729] [INFO] Task started: Blastn
[2023-06-04 23:12:15,730] [INFO] Running command: blastn -query GCA_902628535.1_AH-324-B11_genomic.fna/markers.fasta -db /var/lib/cwl/stg67f71d71-ec94-4ed8-8390-bec255f9f741/dqc_reference/reference_markers_gtdb.fasta -out GCA_902628535.1_AH-324-B11_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:12:16,195] [INFO] Task succeeded: Blastn
[2023-06-04 23:12:16,199] [INFO] Selected 5 target genomes.
[2023-06-04 23:12:16,199] [INFO] Target genome list was writen to GCA_902628535.1_AH-324-B11_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 23:12:16,204] [INFO] Task started: fastANI
[2023-06-04 23:12:16,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg68e55786-1745-4fa3-a959-6f403846c616/GCA_902628535.1_AH-324-B11_genomic.fna.gz --refList GCA_902628535.1_AH-324-B11_genomic.fna/target_genomes_gtdb.txt --output GCA_902628535.1_AH-324-B11_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 23:12:17,067] [INFO] Task succeeded: fastANI
[2023-06-04 23:12:17,076] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-04 23:12:17,077] [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_902561075.1	s__Pelagibacter sp902561075	92.2537	113	171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902529105.1	s__Pelagibacter sp902529105	83.2134	97	171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902524235.1	s__Pelagibacter sp902524235	82.2084	93	171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902603925.1	s__Pelagibacter sp902603925	80.5742	75	171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 23:12:17,079] [INFO] GTDB search result was written to GCA_902628535.1_AH-324-B11_genomic.fna/result_gtdb.tsv
[2023-06-04 23:12:17,079] [INFO] ===== GTDB Search completed =====
[2023-06-04 23:12:17,082] [INFO] DFAST_QC result json was written to GCA_902628535.1_AH-324-B11_genomic.fna/dqc_result.json
[2023-06-04 23:12:17,082] [INFO] DFAST_QC completed!
[2023-06-04 23:12:17,082] [INFO] Total running time: 0h0m22s