[2023-06-07 23:15:24,574] [INFO] DFAST_QC pipeline started.
[2023-06-07 23:15:24,576] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 23:15:24,577] [INFO] DQC Reference Directory: /var/lib/cwl/stg009f5bef-0834-46cf-8b98-78ce29ab2da8/dqc_reference
[2023-06-07 23:15:25,957] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 23:15:25,959] [INFO] Task started: Prodigal
[2023-06-07 23:15:25,959] [INFO] Running command: gunzip -c /var/lib/cwl/stg1cd16b75-a67b-4d75-b77f-251cbd89b993/GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 23:15:37,159] [INFO] Task succeeded: Prodigal
[2023-06-07 23:15:37,159] [INFO] Task started: HMMsearch
[2023-06-07 23:15:37,159] [INFO] Running command: hmmsearch --tblout GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg009f5bef-0834-46cf-8b98-78ce29ab2da8/dqc_reference/reference_markers.hmm GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 23:15:37,416] [INFO] Task succeeded: HMMsearch
[2023-06-07 23:15:37,417] [INFO] Found 6/6 markers.
[2023-06-07 23:15:37,443] [INFO] Query marker FASTA was written to GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 23:15:37,443] [INFO] Task started: Blastn
[2023-06-07 23:15:37,443] [INFO] Running command: blastn -query GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg009f5bef-0834-46cf-8b98-78ce29ab2da8/dqc_reference/reference_markers.fasta -out GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:15:38,020] [INFO] Task succeeded: Blastn
[2023-06-07 23:15:38,027] [INFO] Selected 26 target genomes.
[2023-06-07 23:15:38,028] [INFO] Target genome list was writen to GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 23:15:38,030] [INFO] Task started: fastANI
[2023-06-07 23:15:38,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cd16b75-a67b-4d75-b77f-251cbd89b993/GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 23:15:54,663] [INFO] Task succeeded: fastANI
[2023-06-07 23:15:54,664] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg009f5bef-0834-46cf-8b98-78ce29ab2da8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 23:15:54,664] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg009f5bef-0834-46cf-8b98-78ce29ab2da8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 23:15:54,666] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 23:15:54,666] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 23:15:54,666] [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
--------------------------------------------------------------------------------
[2023-06-07 23:15:54,668] [INFO] DFAST Taxonomy check result was written to GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 23:15:54,669] [INFO] ===== Taxonomy check completed =====
[2023-06-07 23:15:54,669] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 23:15:54,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg009f5bef-0834-46cf-8b98-78ce29ab2da8/dqc_reference/checkm_data
[2023-06-07 23:15:54,673] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 23:15:54,700] [INFO] Task started: CheckM
[2023-06-07 23:15:54,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 23:16:30,902] [INFO] Task succeeded: CheckM
[2023-06-07 23:16:30,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 23:16:30,922] [INFO] ===== Completeness check finished =====
[2023-06-07 23:16:30,923] [INFO] ===== Start GTDB Search =====
[2023-06-07 23:16:30,923] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 23:16:30,923] [INFO] Task started: Blastn
[2023-06-07 23:16:30,924] [INFO] Running command: blastn -query GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg009f5bef-0834-46cf-8b98-78ce29ab2da8/dqc_reference/reference_markers_gtdb.fasta -out GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:16:31,708] [INFO] Task succeeded: Blastn
[2023-06-07 23:16:31,713] [INFO] Selected 30 target genomes.
[2023-06-07 23:16:31,713] [INFO] Target genome list was writen to GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 23:16:31,761] [INFO] Task started: fastANI
[2023-06-07 23:16:31,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cd16b75-a67b-4d75-b77f-251cbd89b993/GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 23:16:42,844] [INFO] Task succeeded: fastANI
[2023-06-07 23:16:42,848] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 23:16:42,849] [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_900769885.1	s__Coprenecus sp900769885	77.7008	75	710	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Coprenecus	95.0	97.24	96.76	0.86	0.81	8	-
--------------------------------------------------------------------------------
[2023-06-07 23:16:42,851] [INFO] GTDB search result was written to GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 23:16:42,852] [INFO] ===== GTDB Search completed =====
[2023-06-07 23:16:42,854] [INFO] DFAST_QC result json was written to GCA_945977705.1_SRR12203188_bin.2_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 23:16:42,855] [INFO] DFAST_QC completed!
[2023-06-07 23:16:42,855] [INFO] Total running time: 0h1m18s