[2023-06-14 00:41:34,282] [INFO] DFAST_QC pipeline started.
[2023-06-14 00:41:34,285] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 00:41:34,286] [INFO] DQC Reference Directory: /var/lib/cwl/stg370c7b08-9471-4588-a13b-498861d3ac96/dqc_reference
[2023-06-14 00:41:35,802] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 00:41:35,803] [INFO] Task started: Prodigal
[2023-06-14 00:41:35,803] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ea4c7c5-0573-42a4-b980-d5a984df3d51/GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 00:41:37,375] [INFO] Task succeeded: Prodigal
[2023-06-14 00:41:37,376] [INFO] Task started: HMMsearch
[2023-06-14 00:41:37,376] [INFO] Running command: hmmsearch --tblout GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg370c7b08-9471-4588-a13b-498861d3ac96/dqc_reference/reference_markers.hmm GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-14 00:41:37,667] [INFO] Task succeeded: HMMsearch
[2023-06-14 00:41:37,669] [INFO] Found 6/6 markers.
[2023-06-14 00:41:37,691] [INFO] Query marker FASTA was written to GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-14 00:41:37,692] [INFO] Task started: Blastn
[2023-06-14 00:41:37,692] [INFO] Running command: blastn -query GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg370c7b08-9471-4588-a13b-498861d3ac96/dqc_reference/reference_markers.fasta -out GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 00:41:40,573] [INFO] Task succeeded: Blastn
[2023-06-14 00:41:40,577] [INFO] Selected 15 target genomes.
[2023-06-14 00:41:40,578] [INFO] Target genome list was writen to GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-14 00:41:40,583] [INFO] Task started: fastANI
[2023-06-14 00:41:40,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ea4c7c5-0573-42a4-b980-d5a984df3d51/GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 00:41:49,696] [INFO] Task succeeded: fastANI
[2023-06-14 00:41:49,697] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg370c7b08-9471-4588-a13b-498861d3ac96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 00:41:49,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg370c7b08-9471-4588-a13b-498861d3ac96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 00:41:49,699] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 00:41:49,699] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-14 00:41:49,699] [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
--------------------------------------------------------------------------------
[2023-06-14 00:41:49,701] [INFO] DFAST Taxonomy check result was written to GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-14 00:41:49,702] [INFO] ===== Taxonomy check completed =====
[2023-06-14 00:41:49,702] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 00:41:49,702] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg370c7b08-9471-4588-a13b-498861d3ac96/dqc_reference/checkm_data
[2023-06-14 00:41:49,705] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 00:41:49,730] [INFO] Task started: CheckM
[2023-06-14 00:41:49,730] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-14 00:42:03,214] [INFO] Task succeeded: CheckM
[2023-06-14 00:42:03,215] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.87%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 00:42:03,242] [INFO] ===== Completeness check finished =====
[2023-06-14 00:42:03,243] [INFO] ===== Start GTDB Search =====
[2023-06-14 00:42:03,243] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-14 00:42:03,244] [INFO] Task started: Blastn
[2023-06-14 00:42:03,244] [INFO] Running command: blastn -query GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg370c7b08-9471-4588-a13b-498861d3ac96/dqc_reference/reference_markers_gtdb.fasta -out GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 00:42:04,041] [INFO] Task succeeded: Blastn
[2023-06-14 00:42:04,049] [INFO] Selected 6 target genomes.
[2023-06-14 00:42:04,049] [INFO] Target genome list was writen to GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 00:42:04,053] [INFO] Task started: fastANI
[2023-06-14 00:42:04,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ea4c7c5-0573-42a4-b980-d5a984df3d51/GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 00:42:05,248] [INFO] Task succeeded: fastANI
[2023-06-14 00:42:05,259] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-14 00:42:05,260] [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_905373385.1	s__Nanoperiomorbus sp905373385	93.3791	185	207	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanoperiomorbaceae;g__Nanoperiomorbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905372225.1	s__Nanoperiomorbus sp905372225	93.278	184	207	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanoperiomorbaceae;g__Nanoperiomorbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905373275.1	s__Nanoperiomorbus sp905373275	93.0793	142	207	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanoperiomorbaceae;g__Nanoperiomorbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013333515.2	s__Nanoperiomorbus sp013333515	93.0342	180	207	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanoperiomorbaceae;g__Nanoperiomorbus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138455.1	s__Nanoperiomorbus periodonticus	92.9464	170	207	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanoperiomorbaceae;g__Nanoperiomorbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905365345.1	s__Nanoperiomorbus sp905365345	92.7924	163	207	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanoperiomorbaceae;g__Nanoperiomorbus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-14 00:42:05,261] [INFO] GTDB search result was written to GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-14 00:42:05,262] [INFO] ===== GTDB Search completed =====
[2023-06-14 00:42:05,265] [INFO] DFAST_QC result json was written to GCA_938044095.1_ERR589693_bin.13_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-14 00:42:05,265] [INFO] DFAST_QC completed!
[2023-06-14 00:42:05,265] [INFO] Total running time: 0h0m31s