[2023-03-15 14:38:33,827] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:38:33,828] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:38:33,828] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ade83dc-ef55-4c25-8e34-fe882d9925b4/dqc_reference
[2023-03-15 14:38:34,918] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:38:34,919] [INFO] Task started: Prodigal
[2023-03-15 14:38:34,919] [INFO] Running command: cat /var/lib/cwl/stg7123ff19-1b6e-40b1-af8c-99b573743c3a/OceanDNA-b7651.fa | prodigal -d OceanDNA-b7651/cds.fna -a OceanDNA-b7651/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:38:41,263] [INFO] Task succeeded: Prodigal
[2023-03-15 14:38:41,263] [INFO] Task started: HMMsearch
[2023-03-15 14:38:41,263] [INFO] Running command: hmmsearch --tblout OceanDNA-b7651/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ade83dc-ef55-4c25-8e34-fe882d9925b4/dqc_reference/reference_markers.hmm OceanDNA-b7651/protein.faa > /dev/null
[2023-03-15 14:38:41,448] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:38:41,449] [INFO] Found 6/6 markers.
[2023-03-15 14:38:41,459] [INFO] Query marker FASTA was written to OceanDNA-b7651/markers.fasta
[2023-03-15 14:38:41,460] [INFO] Task started: Blastn
[2023-03-15 14:38:41,460] [INFO] Running command: blastn -query OceanDNA-b7651/markers.fasta -db /var/lib/cwl/stg8ade83dc-ef55-4c25-8e34-fe882d9925b4/dqc_reference/reference_markers.fasta -out OceanDNA-b7651/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:38:42,054] [INFO] Task succeeded: Blastn
[2023-03-15 14:38:42,054] [INFO] Selected 27 target genomes.
[2023-03-15 14:38:42,055] [INFO] Target genome list was writen to OceanDNA-b7651/target_genomes.txt
[2023-03-15 14:38:42,071] [INFO] Task started: fastANI
[2023-03-15 14:38:42,071] [INFO] Running command: fastANI --query /var/lib/cwl/stg7123ff19-1b6e-40b1-af8c-99b573743c3a/OceanDNA-b7651.fa --refList OceanDNA-b7651/target_genomes.txt --output OceanDNA-b7651/fastani_result.tsv --threads 1
[2023-03-15 14:38:55,648] [INFO] Task succeeded: fastANI
[2023-03-15 14:38:55,648] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ade83dc-ef55-4c25-8e34-fe882d9925b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:38:55,648] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ade83dc-ef55-4c25-8e34-fe882d9925b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:38:55,648] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:38:55,648] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 14:38:55,648] [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
--------------------------------------------------------------------------------
[2023-03-15 14:38:55,649] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7651/tc_result.tsv
[2023-03-15 14:38:55,649] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:38:55,649] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:38:55,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ade83dc-ef55-4c25-8e34-fe882d9925b4/dqc_reference/checkm_data
[2023-03-15 14:38:55,652] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:38:55,655] [INFO] Task started: CheckM
[2023-03-15 14:38:55,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7651/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7651/checkm_input OceanDNA-b7651/checkm_result
[2023-03-15 14:39:15,537] [INFO] Task succeeded: CheckM
[2023-03-15 14:39:15,538] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:39:15,540] [INFO] ===== Completeness check finished =====
[2023-03-15 14:39:15,540] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:39:15,540] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7651/markers.fasta)
[2023-03-15 14:39:15,541] [INFO] Task started: Blastn
[2023-03-15 14:39:15,541] [INFO] Running command: blastn -query OceanDNA-b7651/markers.fasta -db /var/lib/cwl/stg8ade83dc-ef55-4c25-8e34-fe882d9925b4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7651/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:39:16,507] [INFO] Task succeeded: Blastn
[2023-03-15 14:39:16,508] [INFO] Selected 12 target genomes.
[2023-03-15 14:39:16,508] [INFO] Target genome list was writen to OceanDNA-b7651/target_genomes_gtdb.txt
[2023-03-15 14:39:16,515] [INFO] Task started: fastANI
[2023-03-15 14:39:16,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg7123ff19-1b6e-40b1-af8c-99b573743c3a/OceanDNA-b7651.fa --refList OceanDNA-b7651/target_genomes_gtdb.txt --output OceanDNA-b7651/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:39:19,682] [INFO] Task succeeded: fastANI
[2023-03-15 14:39:19,689] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 14:39:19,690] [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_018662905.1	s__MAG-121220-bin8 sp018662905	99.2042	199	277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.06	99.06	0.75	0.75	2	conclusive
GCA_905182765.1	s__MAG-121220-bin8 sp905182765	87.5712	242	277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479415.1	s__MAG-121220-bin8 sp905479415	85.1953	234	277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	98.94	98.70	0.82	0.77	8	-
GCA_902510655.1	s__MAG-121220-bin8 sp902510655	84.9688	157	277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700465.1	s__MAG-121220-bin8 sp002700465	83.9343	190	277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.15	98.67	0.80	0.80	3	-
GCA_902559035.1	s__MAG-121220-bin8 sp902559035	79.1471	160	277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.40	96.04	0.82	0.79	6	-
GCA_004214185.1	s__MAG-121220-bin8 sp004214185	78.0618	142	277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.26	95.81	0.84	0.82	5	-
GCA_902635895.1	s__MAG-121220-bin8 sp902635895	78.0602	126	277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.57	96.57	0.70	0.70	2	-
GCA_905181625.1	s__MAG-121220-bin8 sp905181625	77.9937	147	277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331265.1	s__MAG-121220-bin8 sp003331265	77.9012	118	277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959395.1	s__MAG-121220-bin8 sp012959395	77.8871	135	277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	97.96	97.81	0.81	0.77	13	-
GCA_002702895.1	s__MAG-121220-bin8 sp002702895	77.0463	123	277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 14:39:19,690] [INFO] GTDB search result was written to OceanDNA-b7651/result_gtdb.tsv
[2023-03-15 14:39:19,690] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:39:19,691] [INFO] DFAST_QC result json was written to OceanDNA-b7651/dqc_result.json
[2023-03-15 14:39:19,691] [INFO] DFAST_QC completed!
[2023-03-15 14:39:19,691] [INFO] Total running time: 0h0m46s