[2023-06-08 20:36:33,288] [INFO] DFAST_QC pipeline started.
[2023-06-08 20:36:33,293] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 20:36:33,293] [INFO] DQC Reference Directory: /var/lib/cwl/stg42069067-8970-4bce-8ba4-88bcb2fb982c/dqc_reference
[2023-06-08 20:36:34,722] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 20:36:34,723] [INFO] Task started: Prodigal
[2023-06-08 20:36:34,723] [INFO] Running command: gunzip -c /var/lib/cwl/stg97f07332-27ce-4c87-b716-7dc80e7ceedb/GCA_945860435.1_GE-07nov19-273_genomic.fna.gz | prodigal -d GCA_945860435.1_GE-07nov19-273_genomic.fna/cds.fna -a GCA_945860435.1_GE-07nov19-273_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 20:36:39,231] [INFO] Task succeeded: Prodigal
[2023-06-08 20:36:39,231] [INFO] Task started: HMMsearch
[2023-06-08 20:36:39,231] [INFO] Running command: hmmsearch --tblout GCA_945860435.1_GE-07nov19-273_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42069067-8970-4bce-8ba4-88bcb2fb982c/dqc_reference/reference_markers.hmm GCA_945860435.1_GE-07nov19-273_genomic.fna/protein.faa > /dev/null
[2023-06-08 20:36:39,520] [INFO] Task succeeded: HMMsearch
[2023-06-08 20:36:39,521] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg97f07332-27ce-4c87-b716-7dc80e7ceedb/GCA_945860435.1_GE-07nov19-273_genomic.fna.gz]
[2023-06-08 20:36:39,545] [INFO] Query marker FASTA was written to GCA_945860435.1_GE-07nov19-273_genomic.fna/markers.fasta
[2023-06-08 20:36:39,545] [INFO] Task started: Blastn
[2023-06-08 20:36:39,545] [INFO] Running command: blastn -query GCA_945860435.1_GE-07nov19-273_genomic.fna/markers.fasta -db /var/lib/cwl/stg42069067-8970-4bce-8ba4-88bcb2fb982c/dqc_reference/reference_markers.fasta -out GCA_945860435.1_GE-07nov19-273_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:36:40,263] [INFO] Task succeeded: Blastn
[2023-06-08 20:36:40,269] [INFO] Selected 30 target genomes.
[2023-06-08 20:36:40,269] [INFO] Target genome list was writen to GCA_945860435.1_GE-07nov19-273_genomic.fna/target_genomes.txt
[2023-06-08 20:36:40,275] [INFO] Task started: fastANI
[2023-06-08 20:36:40,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg97f07332-27ce-4c87-b716-7dc80e7ceedb/GCA_945860435.1_GE-07nov19-273_genomic.fna.gz --refList GCA_945860435.1_GE-07nov19-273_genomic.fna/target_genomes.txt --output GCA_945860435.1_GE-07nov19-273_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 20:36:56,561] [INFO] Task succeeded: fastANI
[2023-06-08 20:36:56,562] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42069067-8970-4bce-8ba4-88bcb2fb982c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 20:36:56,562] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42069067-8970-4bce-8ba4-88bcb2fb982c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 20:36:56,564] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 20:36:56,564] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 20:36:56,565] [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
--------------------------------------------------------------------------------
[2023-06-08 20:36:56,566] [INFO] DFAST Taxonomy check result was written to GCA_945860435.1_GE-07nov19-273_genomic.fna/tc_result.tsv
[2023-06-08 20:36:56,567] [INFO] ===== Taxonomy check completed =====
[2023-06-08 20:36:56,567] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 20:36:56,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42069067-8970-4bce-8ba4-88bcb2fb982c/dqc_reference/checkm_data
[2023-06-08 20:36:56,572] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 20:36:56,599] [INFO] Task started: CheckM
[2023-06-08 20:36:56,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945860435.1_GE-07nov19-273_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945860435.1_GE-07nov19-273_genomic.fna/checkm_input GCA_945860435.1_GE-07nov19-273_genomic.fna/checkm_result
[2023-06-08 20:37:17,875] [INFO] Task succeeded: CheckM
[2023-06-08 20:37:17,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 20:37:17,900] [INFO] ===== Completeness check finished =====
[2023-06-08 20:37:17,900] [INFO] ===== Start GTDB Search =====
[2023-06-08 20:37:17,900] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945860435.1_GE-07nov19-273_genomic.fna/markers.fasta)
[2023-06-08 20:37:17,901] [INFO] Task started: Blastn
[2023-06-08 20:37:17,901] [INFO] Running command: blastn -query GCA_945860435.1_GE-07nov19-273_genomic.fna/markers.fasta -db /var/lib/cwl/stg42069067-8970-4bce-8ba4-88bcb2fb982c/dqc_reference/reference_markers_gtdb.fasta -out GCA_945860435.1_GE-07nov19-273_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:37:18,903] [INFO] Task succeeded: Blastn
[2023-06-08 20:37:18,908] [INFO] Selected 12 target genomes.
[2023-06-08 20:37:18,908] [INFO] Target genome list was writen to GCA_945860435.1_GE-07nov19-273_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 20:37:18,913] [INFO] Task started: fastANI
[2023-06-08 20:37:18,913] [INFO] Running command: fastANI --query /var/lib/cwl/stg97f07332-27ce-4c87-b716-7dc80e7ceedb/GCA_945860435.1_GE-07nov19-273_genomic.fna.gz --refList GCA_945860435.1_GE-07nov19-273_genomic.fna/target_genomes_gtdb.txt --output GCA_945860435.1_GE-07nov19-273_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 20:37:24,690] [INFO] Task succeeded: fastANI
[2023-06-08 20:37:24,703] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 20:37:24,703] [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_903953455.1	s__UBA10906 sp903953455	98.9756	478	632	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	98.68	98.30	0.76	0.67	7	conclusive
GCA_903848905.1	s__UBA10906 sp903848905	94.7662	510	632	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	99.42	99.33	0.87	0.85	4	-
GCA_900299045.1	s__UBA10906 sp900299045	83.6909	424	632	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003542275.1	s__UBA10906 sp003542275	79.4966	209	632	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903834465.1	s__UBA10906 sp903834465	78.2605	209	632	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	99.94	99.94	0.97	0.97	2	-
GCA_903867225.1	s__UBA10906 sp903867225	77.7893	182	632	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	99.97	99.94	0.99	0.99	4	-
GCA_903870545.1	s__UBA10906 sp903870545	77.6487	181	632	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	99.93	99.78	0.98	0.96	8	-
GCA_903848935.1	s__UBA10906 sp903848935	77.6048	178	632	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	99.97	99.93	0.98	0.96	8	-
GCA_903877065.1	s__UBA10906 sp903877065	77.5751	164	632	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903876445.1	s__UBA10906 sp903876445	77.4545	185	632	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	99.87	99.87	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-08 20:37:24,705] [INFO] GTDB search result was written to GCA_945860435.1_GE-07nov19-273_genomic.fna/result_gtdb.tsv
[2023-06-08 20:37:24,705] [INFO] ===== GTDB Search completed =====
[2023-06-08 20:37:24,708] [INFO] DFAST_QC result json was written to GCA_945860435.1_GE-07nov19-273_genomic.fna/dqc_result.json
[2023-06-08 20:37:24,708] [INFO] DFAST_QC completed!
[2023-06-08 20:37:24,708] [INFO] Total running time: 0h0m51s