[2023-03-18 09:41:07,186] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:41:07,186] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:41:07,186] [INFO] DQC Reference Directory: /var/lib/cwl/stge3f4d921-6ade-46c8-8bb2-b533724a71bd/dqc_reference
[2023-03-18 09:41:08,335] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:41:08,335] [INFO] Task started: Prodigal
[2023-03-18 09:41:08,336] [INFO] Running command: cat /var/lib/cwl/stg84568f69-59c3-481a-bdeb-30f39e2a874b/OceanDNA-b3077.fa | prodigal -d OceanDNA-b3077/cds.fna -a OceanDNA-b3077/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:41:15,167] [INFO] Task succeeded: Prodigal
[2023-03-18 09:41:15,167] [INFO] Task started: HMMsearch
[2023-03-18 09:41:15,167] [INFO] Running command: hmmsearch --tblout OceanDNA-b3077/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3f4d921-6ade-46c8-8bb2-b533724a71bd/dqc_reference/reference_markers.hmm OceanDNA-b3077/protein.faa > /dev/null
[2023-03-18 09:41:15,337] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:41:15,338] [INFO] Found 6/6 markers.
[2023-03-18 09:41:15,347] [INFO] Query marker FASTA was written to OceanDNA-b3077/markers.fasta
[2023-03-18 09:41:15,348] [INFO] Task started: Blastn
[2023-03-18 09:41:15,348] [INFO] Running command: blastn -query OceanDNA-b3077/markers.fasta -db /var/lib/cwl/stge3f4d921-6ade-46c8-8bb2-b533724a71bd/dqc_reference/reference_markers.fasta -out OceanDNA-b3077/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:15,874] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:15,876] [INFO] Selected 27 target genomes.
[2023-03-18 09:41:15,876] [INFO] Target genome list was writen to OceanDNA-b3077/target_genomes.txt
[2023-03-18 09:41:15,907] [INFO] Task started: fastANI
[2023-03-18 09:41:15,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg84568f69-59c3-481a-bdeb-30f39e2a874b/OceanDNA-b3077.fa --refList OceanDNA-b3077/target_genomes.txt --output OceanDNA-b3077/fastani_result.tsv --threads 1
[2023-03-18 09:41:28,818] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:28,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3f4d921-6ade-46c8-8bb2-b533724a71bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:41:28,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3f4d921-6ade-46c8-8bb2-b533724a71bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:41:28,819] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:41:28,819] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:41:28,819] [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 09:41:28,819] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3077/tc_result.tsv
[2023-03-18 09:41:28,819] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:41:28,819] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:41:28,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3f4d921-6ade-46c8-8bb2-b533724a71bd/dqc_reference/checkm_data
[2023-03-18 09:41:28,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:41:28,824] [INFO] Task started: CheckM
[2023-03-18 09:41:28,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3077/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3077/checkm_input OceanDNA-b3077/checkm_result
[2023-03-18 09:41:51,710] [INFO] Task succeeded: CheckM
[2023-03-18 09:41:51,710] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.73%
Contamintation: 12.50%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-18 09:41:51,712] [INFO] ===== Completeness check finished =====
[2023-03-18 09:41:51,713] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:41:51,713] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3077/markers.fasta)
[2023-03-18 09:41:51,713] [INFO] Task started: Blastn
[2023-03-18 09:41:51,713] [INFO] Running command: blastn -query OceanDNA-b3077/markers.fasta -db /var/lib/cwl/stge3f4d921-6ade-46c8-8bb2-b533724a71bd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3077/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:52,470] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:52,471] [INFO] Selected 12 target genomes.
[2023-03-18 09:41:52,471] [INFO] Target genome list was writen to OceanDNA-b3077/target_genomes_gtdb.txt
[2023-03-18 09:41:52,482] [INFO] Task started: fastANI
[2023-03-18 09:41:52,482] [INFO] Running command: fastANI --query /var/lib/cwl/stg84568f69-59c3-481a-bdeb-30f39e2a874b/OceanDNA-b3077.fa --refList OceanDNA-b3077/target_genomes_gtdb.txt --output OceanDNA-b3077/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:41:55,303] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:55,311] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:41:55,312] [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
GCF_002288065.1	s__Planktophila sulfonica	81.2663	246	388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002288225.1	s__Planktophila dulcis	81.2308	248	388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	97.64	97.42	0.94	0.93	3	-
GCA_002284855.1	s__Planktophila sp002284855	80.8008	261	388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000372185.1	s__Planktophila sp000372185	80.5562	173	388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009701085.1	s__Planktophila sp009701085	80.246	123	388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.29	98.29	0.74	0.74	2	-
GCA_903845465.1	s__Planktophila sp903845465	80.238	162	388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.37	98.68	0.87	0.84	5	-
GCA_903865885.1	s__Planktophila sp903865885	79.9656	149	388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009701945.1	s__Planktophila sp009701945	79.4601	138	388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.37	98.37	0.73	0.73	2	-
GCA_009923805.1	s__Planktophila sp009923805	79.1845	149	388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009700365.1	s__Planktophila sp009700365	78.8387	137	388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.64	98.64	0.85	0.85	2	-
GCA_009705185.1	s__Planktophila sp009705185	78.4089	117	388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903904665.1	s__Planktophila sp903904665	76.7562	57	388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.61	99.61	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-18 09:41:55,312] [INFO] GTDB search result was written to OceanDNA-b3077/result_gtdb.tsv
[2023-03-18 09:41:55,312] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:41:55,313] [INFO] DFAST_QC result json was written to OceanDNA-b3077/dqc_result.json
[2023-03-18 09:41:55,313] [INFO] DFAST_QC completed!
[2023-03-18 09:41:55,313] [INFO] Total running time: 0h0m48s