[2023-06-18 20:30:36,741] [INFO] DFAST_QC pipeline started.
[2023-06-18 20:30:36,743] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 20:30:36,743] [INFO] DQC Reference Directory: /var/lib/cwl/stgf84b9cce-48f1-43ea-8395-8d3cc85ba428/dqc_reference
[2023-06-18 20:30:38,216] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 20:30:38,217] [INFO] Task started: Prodigal
[2023-06-18 20:30:38,217] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb515be3-5368-40c3-9d8c-aff2ca543668/GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 20:30:43,686] [INFO] Task succeeded: Prodigal
[2023-06-18 20:30:43,686] [INFO] Task started: HMMsearch
[2023-06-18 20:30:43,686] [INFO] Running command: hmmsearch --tblout GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf84b9cce-48f1-43ea-8395-8d3cc85ba428/dqc_reference/reference_markers.hmm GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-18 20:30:43,864] [INFO] Task succeeded: HMMsearch
[2023-06-18 20:30:43,865] [INFO] Found 6/6 markers.
[2023-06-18 20:30:43,886] [INFO] Query marker FASTA was written to GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-18 20:30:43,886] [INFO] Task started: Blastn
[2023-06-18 20:30:43,887] [INFO] Running command: blastn -query GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf84b9cce-48f1-43ea-8395-8d3cc85ba428/dqc_reference/reference_markers.fasta -out GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:30:44,454] [INFO] Task succeeded: Blastn
[2023-06-18 20:30:44,459] [INFO] Selected 14 target genomes.
[2023-06-18 20:30:44,459] [INFO] Target genome list was writen to GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-18 20:30:44,461] [INFO] Task started: fastANI
[2023-06-18 20:30:44,461] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb515be3-5368-40c3-9d8c-aff2ca543668/GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 20:30:51,708] [INFO] Task succeeded: fastANI
[2023-06-18 20:30:51,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf84b9cce-48f1-43ea-8395-8d3cc85ba428/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 20:30:51,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf84b9cce-48f1-43ea-8395-8d3cc85ba428/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 20:30:51,711] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 20:30:51,711] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 20:30:51,711] [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
--------------------------------------------------------------------------------
[2023-06-18 20:30:51,713] [INFO] DFAST Taxonomy check result was written to GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-18 20:30:51,713] [INFO] ===== Taxonomy check completed =====
[2023-06-18 20:30:51,713] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 20:30:51,714] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf84b9cce-48f1-43ea-8395-8d3cc85ba428/dqc_reference/checkm_data
[2023-06-18 20:30:51,717] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 20:30:51,749] [INFO] Task started: CheckM
[2023-06-18 20:30:51,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-18 20:31:13,425] [INFO] Task succeeded: CheckM
[2023-06-18 20:31:13,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 20:31:13,443] [INFO] ===== Completeness check finished =====
[2023-06-18 20:31:13,443] [INFO] ===== Start GTDB Search =====
[2023-06-18 20:31:13,443] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-18 20:31:13,443] [INFO] Task started: Blastn
[2023-06-18 20:31:13,443] [INFO] Running command: blastn -query GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf84b9cce-48f1-43ea-8395-8d3cc85ba428/dqc_reference/reference_markers_gtdb.fasta -out GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:31:14,271] [INFO] Task succeeded: Blastn
[2023-06-18 20:31:14,275] [INFO] Selected 14 target genomes.
[2023-06-18 20:31:14,275] [INFO] Target genome list was writen to GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 20:31:14,300] [INFO] Task started: fastANI
[2023-06-18 20:31:14,300] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb515be3-5368-40c3-9d8c-aff2ca543668/GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 20:31:20,714] [INFO] Task succeeded: fastANI
[2023-06-18 20:31:20,722] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 20:31:20,723] [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_905372875.1	s__CAJPQU01 sp905372875	97.8353	485	662	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__CAJPQU01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905373705.1	s__CAJPQU01 sp905373705	81.5086	166	662	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__CAJPQU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016280345.1	s__RGIG3544 sp016280345	77.1497	106	662	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__RGIG3544	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017444395.1	s__RGIG3544 sp017444395	76.8177	91	662	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__RGIG3544	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900321035.1	s__RUG12372 sp900321035	76.7402	78	662	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__RUG12372	95.0	97.54	95.68	0.88	0.79	6	-
GCA_902777615.1	s__RUG12372 sp902777615	76.6799	63	662	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__RUG12372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016286075.1	s__RUG12372 sp016286075	76.4322	71	662	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__RUG12372	95.0	98.08	97.93	0.83	0.79	3	-
--------------------------------------------------------------------------------
[2023-06-18 20:31:20,725] [INFO] GTDB search result was written to GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-18 20:31:20,726] [INFO] ===== GTDB Search completed =====
[2023-06-18 20:31:20,729] [INFO] DFAST_QC result json was written to GCA_937925065.1_ERR589367_bin.31_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-18 20:31:20,729] [INFO] DFAST_QC completed!
[2023-06-18 20:31:20,729] [INFO] Total running time: 0h0m44s