[2023-06-29 19:25:30,395] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:25:30,397] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:25:30,397] [INFO] DQC Reference Directory: /var/lib/cwl/stg55c84443-8302-4269-a75f-2b7451646761/dqc_reference
[2023-06-29 19:25:31,560] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:25:31,561] [INFO] Task started: Prodigal
[2023-06-29 19:25:31,561] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d0810b7-0df5-4d4d-b5f7-b85b38c8338e/GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:25:38,756] [INFO] Task succeeded: Prodigal
[2023-06-29 19:25:38,757] [INFO] Task started: HMMsearch
[2023-06-29 19:25:38,757] [INFO] Running command: hmmsearch --tblout GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55c84443-8302-4269-a75f-2b7451646761/dqc_reference/reference_markers.hmm GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:25:38,955] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:25:38,956] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg7d0810b7-0df5-4d4d-b5f7-b85b38c8338e/GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-29 19:25:38,983] [INFO] Query marker FASTA was written to GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 19:25:38,983] [INFO] Task started: Blastn
[2023-06-29 19:25:38,983] [INFO] Running command: blastn -query GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg55c84443-8302-4269-a75f-2b7451646761/dqc_reference/reference_markers.fasta -out GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:25:39,471] [INFO] Task succeeded: Blastn
[2023-06-29 19:25:39,476] [INFO] Selected 1 target genomes.
[2023-06-29 19:25:39,477] [INFO] Target genome list was writen to GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 19:25:39,479] [INFO] Task started: fastANI
[2023-06-29 19:25:39,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d0810b7-0df5-4d4d-b5f7-b85b38c8338e/GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:25:39,952] [INFO] Task succeeded: fastANI
[2023-06-29 19:25:39,952] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55c84443-8302-4269-a75f-2b7451646761/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:25:39,953] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55c84443-8302-4269-a75f-2b7451646761/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:25:39,955] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:25:39,955] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 19:25:39,955] [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 19:25:39,958] [INFO] DFAST Taxonomy check result was written to GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 19:25:39,958] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:25:39,959] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:25:39,959] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55c84443-8302-4269-a75f-2b7451646761/dqc_reference/checkm_data
[2023-06-29 19:25:39,963] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:25:39,987] [INFO] Task started: CheckM
[2023-06-29 19:25:39,987] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 19:26:06,353] [INFO] Task succeeded: CheckM
[2023-06-29 19:26:06,355] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:26:06,376] [INFO] ===== Completeness check finished =====
[2023-06-29 19:26:06,377] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:26:06,377] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 19:26:06,378] [INFO] Task started: Blastn
[2023-06-29 19:26:06,378] [INFO] Running command: blastn -query GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg55c84443-8302-4269-a75f-2b7451646761/dqc_reference/reference_markers_gtdb.fasta -out GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:26:06,848] [INFO] Task succeeded: Blastn
[2023-06-29 19:26:06,855] [INFO] Selected 5 target genomes.
[2023-06-29 19:26:06,855] [INFO] Target genome list was writen to GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:26:06,859] [INFO] Task started: fastANI
[2023-06-29 19:26:06,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d0810b7-0df5-4d4d-b5f7-b85b38c8338e/GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:26:08,286] [INFO] Task succeeded: fastANI
[2023-06-29 19:26:08,290] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 19:26:08,291] [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_003662205.1	s__B46-G15 sp003662205	76.1252	58	481	d__Archaea;p__Thermoproteota;c__Bathyarchaeia;o__TCS64;f__TCS64;g__B46-G15	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 19:26:08,293] [INFO] GTDB search result was written to GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 19:26:08,293] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:26:08,296] [INFO] DFAST_QC result json was written to GCA_937898665.1_SRR6823441_bin.104_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 19:26:08,296] [INFO] DFAST_QC completed!
[2023-06-29 19:26:08,296] [INFO] Total running time: 0h0m38s