[2023-06-29 10:29:50,946] [INFO] DFAST_QC pipeline started.
[2023-06-29 10:29:50,949] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 10:29:50,949] [INFO] DQC Reference Directory: /var/lib/cwl/stg321b4a3d-5a33-4ea1-8be9-9b8d38428f83/dqc_reference
[2023-06-29 10:29:52,337] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 10:29:52,338] [INFO] Task started: Prodigal
[2023-06-29 10:29:52,339] [INFO] Running command: gunzip -c /var/lib/cwl/stg741c5255-2e71-4f4d-b3ea-79af8d23b66e/GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 10:29:56,148] [INFO] Task succeeded: Prodigal
[2023-06-29 10:29:56,149] [INFO] Task started: HMMsearch
[2023-06-29 10:29:56,149] [INFO] Running command: hmmsearch --tblout GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg321b4a3d-5a33-4ea1-8be9-9b8d38428f83/dqc_reference/reference_markers.hmm GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 10:29:56,371] [INFO] Task succeeded: HMMsearch
[2023-06-29 10:29:56,372] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg741c5255-2e71-4f4d-b3ea-79af8d23b66e/GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-29 10:29:56,391] [INFO] Query marker FASTA was written to GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-29 10:29:56,391] [INFO] Task started: Blastn
[2023-06-29 10:29:56,391] [INFO] Running command: blastn -query GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg321b4a3d-5a33-4ea1-8be9-9b8d38428f83/dqc_reference/reference_markers.fasta -out GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 10:29:56,964] [INFO] Task succeeded: Blastn
[2023-06-29 10:29:56,968] [INFO] Selected 15 target genomes.
[2023-06-29 10:29:56,968] [INFO] Target genome list was writen to GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-29 10:29:56,969] [INFO] Task started: fastANI
[2023-06-29 10:29:56,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg741c5255-2e71-4f4d-b3ea-79af8d23b66e/GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 10:30:05,991] [INFO] Task succeeded: fastANI
[2023-06-29 10:30:05,992] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg321b4a3d-5a33-4ea1-8be9-9b8d38428f83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 10:30:05,992] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg321b4a3d-5a33-4ea1-8be9-9b8d38428f83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 10:30:05,994] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 10:30:05,994] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 10:30:05,994] [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 10:30:05,996] [INFO] DFAST Taxonomy check result was written to GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-29 10:30:05,997] [INFO] ===== Taxonomy check completed =====
[2023-06-29 10:30:05,997] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 10:30:05,997] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg321b4a3d-5a33-4ea1-8be9-9b8d38428f83/dqc_reference/checkm_data
[2023-06-29 10:30:06,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 10:30:06,021] [INFO] Task started: CheckM
[2023-06-29 10:30:06,021] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-29 10:30:25,071] [INFO] Task succeeded: CheckM
[2023-06-29 10:30:25,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 10:30:25,090] [INFO] ===== Completeness check finished =====
[2023-06-29 10:30:25,091] [INFO] ===== Start GTDB Search =====
[2023-06-29 10:30:25,091] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-29 10:30:25,092] [INFO] Task started: Blastn
[2023-06-29 10:30:25,092] [INFO] Running command: blastn -query GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg321b4a3d-5a33-4ea1-8be9-9b8d38428f83/dqc_reference/reference_markers_gtdb.fasta -out GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 10:30:25,769] [INFO] Task succeeded: Blastn
[2023-06-29 10:30:25,772] [INFO] Selected 13 target genomes.
[2023-06-29 10:30:25,772] [INFO] Target genome list was writen to GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 10:30:25,779] [INFO] Task started: fastANI
[2023-06-29 10:30:25,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg741c5255-2e71-4f4d-b3ea-79af8d23b66e/GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 10:30:32,956] [INFO] Task succeeded: fastANI
[2023-06-29 10:30:32,960] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 10:30:32,961] [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_910586125.1	s__RGIG7193 sp910586125	99.8148	367	408	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG7193	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-29 10:30:32,963] [INFO] GTDB search result was written to GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 10:30:32,963] [INFO] ===== GTDB Search completed =====
[2023-06-29 10:30:32,966] [INFO] DFAST_QC result json was written to GCA_948468085.1_SRR15604626_bin.11_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-29 10:30:32,966] [INFO] DFAST_QC completed!
[2023-06-29 10:30:32,966] [INFO] Total running time: 0h0m42s