[2023-06-12 23:06:02,969] [INFO] DFAST_QC pipeline started.
[2023-06-12 23:06:02,973] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 23:06:02,974] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d599e84-5dfe-468b-ba30-3d5caf3ef98d/dqc_reference
[2023-06-12 23:06:04,263] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 23:06:04,265] [INFO] Task started: Prodigal
[2023-06-12 23:06:04,265] [INFO] Running command: gunzip -c /var/lib/cwl/stg1927a456-3e52-4d3a-b2e6-76f2ff6a3c02/GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 23:06:08,390] [INFO] Task succeeded: Prodigal
[2023-06-12 23:06:08,390] [INFO] Task started: HMMsearch
[2023-06-12 23:06:08,390] [INFO] Running command: hmmsearch --tblout GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d599e84-5dfe-468b-ba30-3d5caf3ef98d/dqc_reference/reference_markers.hmm GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-12 23:06:08,607] [INFO] Task succeeded: HMMsearch
[2023-06-12 23:06:08,608] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1927a456-3e52-4d3a-b2e6-76f2ff6a3c02/GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-12 23:06:08,630] [INFO] Query marker FASTA was written to GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-12 23:06:08,631] [INFO] Task started: Blastn
[2023-06-12 23:06:08,631] [INFO] Running command: blastn -query GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d599e84-5dfe-468b-ba30-3d5caf3ef98d/dqc_reference/reference_markers.fasta -out GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:06:09,119] [INFO] Task succeeded: Blastn
[2023-06-12 23:06:09,123] [INFO] Selected 5 target genomes.
[2023-06-12 23:06:09,123] [INFO] Target genome list was writen to GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-12 23:06:09,126] [INFO] Task started: fastANI
[2023-06-12 23:06:09,126] [INFO] Running command: fastANI --query /var/lib/cwl/stg1927a456-3e52-4d3a-b2e6-76f2ff6a3c02/GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 23:06:11,773] [INFO] Task succeeded: fastANI
[2023-06-12 23:06:11,774] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d599e84-5dfe-468b-ba30-3d5caf3ef98d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 23:06:11,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d599e84-5dfe-468b-ba30-3d5caf3ef98d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 23:06:11,776] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-12 23:06:11,777] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-12 23:06:11,777] [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
--------------------------------------------------------------------------------
[2023-06-12 23:06:11,779] [INFO] DFAST Taxonomy check result was written to GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-12 23:06:11,780] [INFO] ===== Taxonomy check completed =====
[2023-06-12 23:06:11,780] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 23:06:11,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d599e84-5dfe-468b-ba30-3d5caf3ef98d/dqc_reference/checkm_data
[2023-06-12 23:06:11,786] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 23:06:11,808] [INFO] Task started: CheckM
[2023-06-12 23:06:11,808] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-12 23:06:31,844] [INFO] Task succeeded: CheckM
[2023-06-12 23:06:31,845] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 23:06:31,865] [INFO] ===== Completeness check finished =====
[2023-06-12 23:06:31,866] [INFO] ===== Start GTDB Search =====
[2023-06-12 23:06:31,866] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-12 23:06:31,866] [INFO] Task started: Blastn
[2023-06-12 23:06:31,867] [INFO] Running command: blastn -query GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d599e84-5dfe-468b-ba30-3d5caf3ef98d/dqc_reference/reference_markers_gtdb.fasta -out GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:06:32,302] [INFO] Task succeeded: Blastn
[2023-06-12 23:06:32,305] [INFO] Selected 7 target genomes.
[2023-06-12 23:06:32,306] [INFO] Target genome list was writen to GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 23:06:32,310] [INFO] Task started: fastANI
[2023-06-12 23:06:32,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg1927a456-3e52-4d3a-b2e6-76f2ff6a3c02/GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 23:06:35,109] [INFO] Task succeeded: fastANI
[2023-06-12 23:06:35,115] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-12 23:06:35,115] [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_905203995.1	s__Methanomassiliicoccus_A sp905203995	100.0	510	582	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomassiliicoccaceae;g__Methanomassiliicoccus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-12 23:06:35,118] [INFO] GTDB search result was written to GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-12 23:06:35,118] [INFO] ===== GTDB Search completed =====
[2023-06-12 23:06:35,121] [INFO] DFAST_QC result json was written to GCA_938048195.1_ERR321597_bin.102_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-12 23:06:35,121] [INFO] DFAST_QC completed!
[2023-06-12 23:06:35,121] [INFO] Total running time: 0h0m32s