[2023-03-18 23:44:06,356] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:44:06,357] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:44:06,357] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2025479-e850-4ba2-b268-68964ea151dd/dqc_reference
[2023-03-18 23:44:07,496] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:44:07,496] [INFO] Task started: Prodigal
[2023-03-18 23:44:07,496] [INFO] Running command: cat /var/lib/cwl/stgf80a3ddd-b6c8-45d6-8e30-5ee750d9eebe/OceanDNA-b46689.fa | prodigal -d OceanDNA-b46689/cds.fna -a OceanDNA-b46689/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:44:37,309] [INFO] Task succeeded: Prodigal
[2023-03-18 23:44:37,309] [INFO] Task started: HMMsearch
[2023-03-18 23:44:37,309] [INFO] Running command: hmmsearch --tblout OceanDNA-b46689/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2025479-e850-4ba2-b268-68964ea151dd/dqc_reference/reference_markers.hmm OceanDNA-b46689/protein.faa > /dev/null
[2023-03-18 23:44:37,514] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:44:37,515] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf80a3ddd-b6c8-45d6-8e30-5ee750d9eebe/OceanDNA-b46689.fa]
[2023-03-18 23:44:37,540] [INFO] Query marker FASTA was written to OceanDNA-b46689/markers.fasta
[2023-03-18 23:44:37,541] [INFO] Task started: Blastn
[2023-03-18 23:44:37,541] [INFO] Running command: blastn -query OceanDNA-b46689/markers.fasta -db /var/lib/cwl/stgc2025479-e850-4ba2-b268-68964ea151dd/dqc_reference/reference_markers.fasta -out OceanDNA-b46689/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:44:38,055] [INFO] Task succeeded: Blastn
[2023-03-18 23:44:38,056] [INFO] Selected 18 target genomes.
[2023-03-18 23:44:38,056] [INFO] Target genome list was writen to OceanDNA-b46689/target_genomes.txt
[2023-03-18 23:44:38,068] [INFO] Task started: fastANI
[2023-03-18 23:44:38,068] [INFO] Running command: fastANI --query /var/lib/cwl/stgf80a3ddd-b6c8-45d6-8e30-5ee750d9eebe/OceanDNA-b46689.fa --refList OceanDNA-b46689/target_genomes.txt --output OceanDNA-b46689/fastani_result.tsv --threads 1
[2023-03-18 23:44:49,888] [INFO] Task succeeded: fastANI
[2023-03-18 23:44:49,888] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2025479-e850-4ba2-b268-68964ea151dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:44:49,889] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2025479-e850-4ba2-b268-68964ea151dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:44:49,889] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:44:49,889] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:44:49,889] [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
--------------------------------------------------------------------------------
[2023-03-18 23:44:49,890] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46689/tc_result.tsv
[2023-03-18 23:44:49,891] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:44:49,891] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:44:49,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2025479-e850-4ba2-b268-68964ea151dd/dqc_reference/checkm_data
[2023-03-18 23:44:49,894] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:44:49,916] [INFO] Task started: CheckM
[2023-03-18 23:44:49,916] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46689/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46689/checkm_input OceanDNA-b46689/checkm_result
[2023-03-18 23:46:04,427] [INFO] Task succeeded: CheckM
[2023-03-18 23:46:04,427] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.71%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:46:04,430] [INFO] ===== Completeness check finished =====
[2023-03-18 23:46:04,430] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:46:04,430] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46689/markers.fasta)
[2023-03-18 23:46:04,431] [INFO] Task started: Blastn
[2023-03-18 23:46:04,431] [INFO] Running command: blastn -query OceanDNA-b46689/markers.fasta -db /var/lib/cwl/stgc2025479-e850-4ba2-b268-68964ea151dd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46689/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:46:05,143] [INFO] Task succeeded: Blastn
[2023-03-18 23:46:05,144] [INFO] Selected 18 target genomes.
[2023-03-18 23:46:05,144] [INFO] Target genome list was writen to OceanDNA-b46689/target_genomes_gtdb.txt
[2023-03-18 23:46:05,160] [INFO] Task started: fastANI
[2023-03-18 23:46:05,160] [INFO] Running command: fastANI --query /var/lib/cwl/stgf80a3ddd-b6c8-45d6-8e30-5ee750d9eebe/OceanDNA-b46689.fa --refList OceanDNA-b46689/target_genomes_gtdb.txt --output OceanDNA-b46689/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:46:17,327] [INFO] Task succeeded: fastANI
[2023-03-18 23:46:17,332] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:46:17,332] [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_002721695.1	s__Roseibacillus_B sp002721695	82.6362	712	1045	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709395.1	s__Roseibacillus_B sp002709395	77.823	244	1045	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	97.31	97.31	0.76	0.76	2	-
GCA_002501065.1	s__Roseibacillus_B sp002501065	77.5133	357	1045	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.61	99.55	0.90	0.89	3	-
GCA_014240355.1	s__Roseibacillus_B sp014240355	77.4726	231	1045	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003483645.1	s__Roseibacillus_B sp003483645	77.0027	231	1045	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715825.1	s__Roseibacillus_B sp002715825	76.4494	91	1045	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.08	98.76	0.87	0.85	4	-
GCA_013001695.1	s__Roseibacillus_B sp013001695	76.4433	116	1045	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002420305.1	s__Roseibacillus_B sp002420305	76.3585	115	1045	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	97.44	96.53	0.87	0.86	5	-
--------------------------------------------------------------------------------
[2023-03-18 23:46:17,332] [INFO] GTDB search result was written to OceanDNA-b46689/result_gtdb.tsv
[2023-03-18 23:46:17,333] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:46:17,333] [INFO] DFAST_QC result json was written to OceanDNA-b46689/dqc_result.json
[2023-03-18 23:46:17,333] [INFO] DFAST_QC completed!
[2023-03-18 23:46:17,333] [INFO] Total running time: 0h2m11s