[2023-06-08 10:32:33,314] [INFO] DFAST_QC pipeline started.
[2023-06-08 10:32:33,318] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 10:32:33,318] [INFO] DQC Reference Directory: /var/lib/cwl/stgd61efdd7-b409-4566-b715-90f1aa3a9154/dqc_reference
[2023-06-08 10:32:35,611] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 10:32:35,612] [INFO] Task started: Prodigal
[2023-06-08 10:32:35,613] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb28a1dd-b350-4579-8056-314ef852360e/GCA_945903435.1_ZH-03apr19-71_genomic.fna.gz | prodigal -d GCA_945903435.1_ZH-03apr19-71_genomic.fna/cds.fna -a GCA_945903435.1_ZH-03apr19-71_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 10:32:39,144] [INFO] Task succeeded: Prodigal
[2023-06-08 10:32:39,145] [INFO] Task started: HMMsearch
[2023-06-08 10:32:39,145] [INFO] Running command: hmmsearch --tblout GCA_945903435.1_ZH-03apr19-71_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd61efdd7-b409-4566-b715-90f1aa3a9154/dqc_reference/reference_markers.hmm GCA_945903435.1_ZH-03apr19-71_genomic.fna/protein.faa > /dev/null
[2023-06-08 10:32:39,369] [INFO] Task succeeded: HMMsearch
[2023-06-08 10:32:39,370] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfb28a1dd-b350-4579-8056-314ef852360e/GCA_945903435.1_ZH-03apr19-71_genomic.fna.gz]
[2023-06-08 10:32:39,391] [INFO] Query marker FASTA was written to GCA_945903435.1_ZH-03apr19-71_genomic.fna/markers.fasta
[2023-06-08 10:32:39,391] [INFO] Task started: Blastn
[2023-06-08 10:32:39,391] [INFO] Running command: blastn -query GCA_945903435.1_ZH-03apr19-71_genomic.fna/markers.fasta -db /var/lib/cwl/stgd61efdd7-b409-4566-b715-90f1aa3a9154/dqc_reference/reference_markers.fasta -out GCA_945903435.1_ZH-03apr19-71_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:32:40,187] [INFO] Task succeeded: Blastn
[2023-06-08 10:32:40,192] [INFO] Selected 24 target genomes.
[2023-06-08 10:32:40,192] [INFO] Target genome list was writen to GCA_945903435.1_ZH-03apr19-71_genomic.fna/target_genomes.txt
[2023-06-08 10:32:40,215] [INFO] Task started: fastANI
[2023-06-08 10:32:40,216] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb28a1dd-b350-4579-8056-314ef852360e/GCA_945903435.1_ZH-03apr19-71_genomic.fna.gz --refList GCA_945903435.1_ZH-03apr19-71_genomic.fna/target_genomes.txt --output GCA_945903435.1_ZH-03apr19-71_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 10:32:55,119] [INFO] Task succeeded: fastANI
[2023-06-08 10:32:55,120] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd61efdd7-b409-4566-b715-90f1aa3a9154/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 10:32:55,120] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd61efdd7-b409-4566-b715-90f1aa3a9154/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 10:32:55,122] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 10:32:55,122] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 10:32:55,122] [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 10:32:55,124] [INFO] DFAST Taxonomy check result was written to GCA_945903435.1_ZH-03apr19-71_genomic.fna/tc_result.tsv
[2023-06-08 10:32:55,125] [INFO] ===== Taxonomy check completed =====
[2023-06-08 10:32:55,125] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 10:32:55,125] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd61efdd7-b409-4566-b715-90f1aa3a9154/dqc_reference/checkm_data
[2023-06-08 10:32:55,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 10:32:55,158] [INFO] Task started: CheckM
[2023-06-08 10:32:55,158] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945903435.1_ZH-03apr19-71_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945903435.1_ZH-03apr19-71_genomic.fna/checkm_input GCA_945903435.1_ZH-03apr19-71_genomic.fna/checkm_result
[2023-06-08 10:33:13,518] [INFO] Task succeeded: CheckM
[2023-06-08 10:33:13,519] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 10:33:13,539] [INFO] ===== Completeness check finished =====
[2023-06-08 10:33:13,540] [INFO] ===== Start GTDB Search =====
[2023-06-08 10:33:13,540] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945903435.1_ZH-03apr19-71_genomic.fna/markers.fasta)
[2023-06-08 10:33:13,541] [INFO] Task started: Blastn
[2023-06-08 10:33:13,541] [INFO] Running command: blastn -query GCA_945903435.1_ZH-03apr19-71_genomic.fna/markers.fasta -db /var/lib/cwl/stgd61efdd7-b409-4566-b715-90f1aa3a9154/dqc_reference/reference_markers_gtdb.fasta -out GCA_945903435.1_ZH-03apr19-71_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:33:14,512] [INFO] Task succeeded: Blastn
[2023-06-08 10:33:14,517] [INFO] Selected 10 target genomes.
[2023-06-08 10:33:14,517] [INFO] Target genome list was writen to GCA_945903435.1_ZH-03apr19-71_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 10:33:14,523] [INFO] Task started: fastANI
[2023-06-08 10:33:14,523] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb28a1dd-b350-4579-8056-314ef852360e/GCA_945903435.1_ZH-03apr19-71_genomic.fna.gz --refList GCA_945903435.1_ZH-03apr19-71_genomic.fna/target_genomes_gtdb.txt --output GCA_945903435.1_ZH-03apr19-71_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 10:33:19,385] [INFO] Task succeeded: fastANI
[2023-06-08 10:33:19,401] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 10:33:19,401] [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_014191975.1	s__UBA10906 sp014191975	97.7177	422	492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903870545.1	s__UBA10906 sp903870545	81.6882	300	492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	99.93	99.78	0.98	0.96	8	-
GCA_903889445.1	s__UBA10906 sp903889445	81.3077	295	492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	99.91	99.91	0.94	0.94	2	-
GCA_903847275.1	s__UBA10906 sp903847275	81.1036	292	492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	99.84	99.83	0.91	0.90	4	-
GCA_903867225.1	s__UBA10906 sp903867225	81.1006	320	492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	99.97	99.94	0.99	0.99	4	-
GCA_903848935.1	s__UBA10906 sp903848935	80.4125	295	492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	99.97	99.93	0.98	0.96	8	-
GCA_903904275.1	s__UBA10906 sp903904275	79.8722	268	492	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	79.7564	258	492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	99.87	99.87	0.93	0.93	2	-
GCA_903877065.1	s__UBA10906 sp903877065	79.4404	239	492	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	79.2924	253	492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	99.94	99.94	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-08 10:33:19,403] [INFO] GTDB search result was written to GCA_945903435.1_ZH-03apr19-71_genomic.fna/result_gtdb.tsv
[2023-06-08 10:33:19,404] [INFO] ===== GTDB Search completed =====
[2023-06-08 10:33:19,406] [INFO] DFAST_QC result json was written to GCA_945903435.1_ZH-03apr19-71_genomic.fna/dqc_result.json
[2023-06-08 10:33:19,406] [INFO] DFAST_QC completed!
[2023-06-08 10:33:19,406] [INFO] Total running time: 0h0m46s