[2023-06-05 07:16:23,881] [INFO] DFAST_QC pipeline started.
[2023-06-05 07:16:23,890] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 07:16:23,890] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f8fc958-4d32-4dd5-bec3-58ca8aa27411/dqc_reference
[2023-06-05 07:16:27,030] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 07:16:27,031] [INFO] Task started: Prodigal
[2023-06-05 07:16:27,032] [INFO] Running command: gunzip -c /var/lib/cwl/stg211228e8-5e66-475a-813a-392767b190d4/GCA_934086355.1_ERR7738223_bin.124_genomic.fna.gz | prodigal -d GCA_934086355.1_ERR7738223_bin.124_genomic.fna/cds.fna -a GCA_934086355.1_ERR7738223_bin.124_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 07:16:28,036] [INFO] Task succeeded: Prodigal
[2023-06-05 07:16:28,037] [INFO] Task started: HMMsearch
[2023-06-05 07:16:28,037] [INFO] Running command: hmmsearch --tblout GCA_934086355.1_ERR7738223_bin.124_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f8fc958-4d32-4dd5-bec3-58ca8aa27411/dqc_reference/reference_markers.hmm GCA_934086355.1_ERR7738223_bin.124_genomic.fna/protein.faa > /dev/null
[2023-06-05 07:16:28,194] [INFO] Task succeeded: HMMsearch
[2023-06-05 07:16:28,196] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg211228e8-5e66-475a-813a-392767b190d4/GCA_934086355.1_ERR7738223_bin.124_genomic.fna.gz]
[2023-06-05 07:16:28,232] [INFO] Query marker FASTA was written to GCA_934086355.1_ERR7738223_bin.124_genomic.fna/markers.fasta
[2023-06-05 07:16:28,232] [INFO] Task started: Blastn
[2023-06-05 07:16:28,232] [INFO] Running command: blastn -query GCA_934086355.1_ERR7738223_bin.124_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f8fc958-4d32-4dd5-bec3-58ca8aa27411/dqc_reference/reference_markers.fasta -out GCA_934086355.1_ERR7738223_bin.124_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:16:29,748] [INFO] Task succeeded: Blastn
[2023-06-05 07:16:29,752] [INFO] Selected 10 target genomes.
[2023-06-05 07:16:29,753] [INFO] Target genome list was writen to GCA_934086355.1_ERR7738223_bin.124_genomic.fna/target_genomes.txt
[2023-06-05 07:16:29,756] [INFO] Task started: fastANI
[2023-06-05 07:16:29,756] [INFO] Running command: fastANI --query /var/lib/cwl/stg211228e8-5e66-475a-813a-392767b190d4/GCA_934086355.1_ERR7738223_bin.124_genomic.fna.gz --refList GCA_934086355.1_ERR7738223_bin.124_genomic.fna/target_genomes.txt --output GCA_934086355.1_ERR7738223_bin.124_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 07:16:32,566] [INFO] Task succeeded: fastANI
[2023-06-05 07:16:32,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f8fc958-4d32-4dd5-bec3-58ca8aa27411/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 07:16:32,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f8fc958-4d32-4dd5-bec3-58ca8aa27411/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 07:16:32,569] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 07:16:32,569] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 07:16:32,569] [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
--------------------------------------------------------------------------------
[2023-06-05 07:16:32,571] [INFO] DFAST Taxonomy check result was written to GCA_934086355.1_ERR7738223_bin.124_genomic.fna/tc_result.tsv
[2023-06-05 07:16:32,572] [INFO] ===== Taxonomy check completed =====
[2023-06-05 07:16:32,572] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 07:16:32,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f8fc958-4d32-4dd5-bec3-58ca8aa27411/dqc_reference/checkm_data
[2023-06-05 07:16:32,576] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 07:16:32,593] [INFO] Task started: CheckM
[2023-06-05 07:16:32,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934086355.1_ERR7738223_bin.124_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934086355.1_ERR7738223_bin.124_genomic.fna/checkm_input GCA_934086355.1_ERR7738223_bin.124_genomic.fna/checkm_result
[2023-06-05 07:16:44,922] [INFO] Task succeeded: CheckM
[2023-06-05 07:16:44,923] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 44.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 07:16:44,943] [INFO] ===== Completeness check finished =====
[2023-06-05 07:16:44,943] [INFO] ===== Start GTDB Search =====
[2023-06-05 07:16:44,943] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934086355.1_ERR7738223_bin.124_genomic.fna/markers.fasta)
[2023-06-05 07:16:44,944] [INFO] Task started: Blastn
[2023-06-05 07:16:44,944] [INFO] Running command: blastn -query GCA_934086355.1_ERR7738223_bin.124_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f8fc958-4d32-4dd5-bec3-58ca8aa27411/dqc_reference/reference_markers_gtdb.fasta -out GCA_934086355.1_ERR7738223_bin.124_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:16:45,566] [INFO] Task succeeded: Blastn
[2023-06-05 07:16:45,570] [INFO] Selected 8 target genomes.
[2023-06-05 07:16:45,571] [INFO] Target genome list was writen to GCA_934086355.1_ERR7738223_bin.124_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 07:16:45,575] [INFO] Task started: fastANI
[2023-06-05 07:16:45,575] [INFO] Running command: fastANI --query /var/lib/cwl/stg211228e8-5e66-475a-813a-392767b190d4/GCA_934086355.1_ERR7738223_bin.124_genomic.fna.gz --refList GCA_934086355.1_ERR7738223_bin.124_genomic.fna/target_genomes_gtdb.txt --output GCA_934086355.1_ERR7738223_bin.124_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 07:16:47,214] [INFO] Task succeeded: fastANI
[2023-06-05 07:16:47,218] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 07:16:47,218] [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_900548725.1	s__UMGS1124 sp900548725	94.5693	173	219	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1124	95.0	99.98	99.98	0.92	0.92	2	-
GCA_017411405.1	s__UMGS1124 sp017411405	78.5412	117	219	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1124	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 07:16:47,220] [INFO] GTDB search result was written to GCA_934086355.1_ERR7738223_bin.124_genomic.fna/result_gtdb.tsv
[2023-06-05 07:16:47,221] [INFO] ===== GTDB Search completed =====
[2023-06-05 07:16:47,223] [INFO] DFAST_QC result json was written to GCA_934086355.1_ERR7738223_bin.124_genomic.fna/dqc_result.json
[2023-06-05 07:16:47,224] [INFO] DFAST_QC completed!
[2023-06-05 07:16:47,224] [INFO] Total running time: 0h0m23s