[2023-06-29 16:30:20,774] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:30:20,777] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:30:20,777] [INFO] DQC Reference Directory: /var/lib/cwl/stgfaec6a5f-d01d-464d-8c8c-bef6e71e1cbd/dqc_reference
[2023-06-29 16:30:22,189] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:30:22,190] [INFO] Task started: Prodigal
[2023-06-29 16:30:22,190] [INFO] Running command: gunzip -c /var/lib/cwl/stge7dc0d3a-55b7-4b59-bfdb-46980a6b5fcc/GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:30:25,391] [INFO] Task succeeded: Prodigal
[2023-06-29 16:30:25,391] [INFO] Task started: HMMsearch
[2023-06-29 16:30:25,391] [INFO] Running command: hmmsearch --tblout GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfaec6a5f-d01d-464d-8c8c-bef6e71e1cbd/dqc_reference/reference_markers.hmm GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:30:25,586] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:30:25,587] [INFO] Found 6/6 markers.
[2023-06-29 16:30:25,602] [INFO] Query marker FASTA was written to GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 16:30:25,603] [INFO] Task started: Blastn
[2023-06-29 16:30:25,603] [INFO] Running command: blastn -query GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgfaec6a5f-d01d-464d-8c8c-bef6e71e1cbd/dqc_reference/reference_markers.fasta -out GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:30:26,214] [INFO] Task succeeded: Blastn
[2023-06-29 16:30:26,221] [INFO] Selected 15 target genomes.
[2023-06-29 16:30:26,221] [INFO] Target genome list was writen to GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 16:30:26,250] [INFO] Task started: fastANI
[2023-06-29 16:30:26,250] [INFO] Running command: fastANI --query /var/lib/cwl/stge7dc0d3a-55b7-4b59-bfdb-46980a6b5fcc/GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:30:36,609] [INFO] Task succeeded: fastANI
[2023-06-29 16:30:36,610] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfaec6a5f-d01d-464d-8c8c-bef6e71e1cbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:30:36,610] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfaec6a5f-d01d-464d-8c8c-bef6e71e1cbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:30:36,612] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:30:36,612] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 16:30:36,612] [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 16:30:36,614] [INFO] DFAST Taxonomy check result was written to GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 16:30:36,615] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:30:36,615] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:30:36,615] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfaec6a5f-d01d-464d-8c8c-bef6e71e1cbd/dqc_reference/checkm_data
[2023-06-29 16:30:36,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:30:36,646] [INFO] Task started: CheckM
[2023-06-29 16:30:36,647] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 16:30:55,057] [INFO] Task succeeded: CheckM
[2023-06-29 16:30:55,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:30:55,084] [INFO] ===== Completeness check finished =====
[2023-06-29 16:30:55,085] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:30:55,085] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 16:30:55,086] [INFO] Task started: Blastn
[2023-06-29 16:30:55,086] [INFO] Running command: blastn -query GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgfaec6a5f-d01d-464d-8c8c-bef6e71e1cbd/dqc_reference/reference_markers_gtdb.fasta -out GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:30:55,995] [INFO] Task succeeded: Blastn
[2023-06-29 16:30:55,998] [INFO] Selected 13 target genomes.
[2023-06-29 16:30:55,998] [INFO] Target genome list was writen to GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:30:56,004] [INFO] Task started: fastANI
[2023-06-29 16:30:56,005] [INFO] Running command: fastANI --query /var/lib/cwl/stge7dc0d3a-55b7-4b59-bfdb-46980a6b5fcc/GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:30:58,623] [INFO] Task succeeded: fastANI
[2023-06-29 16:30:58,633] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 16:30:58,633] [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_015257665.1	s__Saccharimonas sp015257665	95.0611	307	358	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Saccharimonadaceae;g__Saccharimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013333645.2	s__Saccharimonas sp013333645	92.5988	289	358	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Saccharimonadaceae;g__Saccharimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905373835.1	s__Saccharimonas sp905373835	92.1599	292	358	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Saccharimonadaceae;g__Saccharimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013333595.2	s__SDRW01 sp013333595	79.4913	54	358	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__UBA10027;g__SDRW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:30:58,636] [INFO] GTDB search result was written to GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 16:30:58,636] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:30:58,639] [INFO] DFAST_QC result json was written to GCA_937981355.1_ERR589354_bin.5_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 16:30:58,640] [INFO] DFAST_QC completed!
[2023-06-29 16:30:58,640] [INFO] Total running time: 0h0m38s