[2023-03-18 01:03:22,770] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:03:22,770] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:03:22,770] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bc160e3-0f4f-4cf8-a88e-0106b7d05612/dqc_reference
[2023-03-18 01:03:23,891] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:03:23,892] [INFO] Task started: Prodigal
[2023-03-18 01:03:23,892] [INFO] Running command: cat /var/lib/cwl/stg4fcc9368-12c2-45a7-aaae-34a837ec6499/OceanDNA-b46704.fa | prodigal -d OceanDNA-b46704/cds.fna -a OceanDNA-b46704/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:03:55,771] [INFO] Task succeeded: Prodigal
[2023-03-18 01:03:55,771] [INFO] Task started: HMMsearch
[2023-03-18 01:03:55,771] [INFO] Running command: hmmsearch --tblout OceanDNA-b46704/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bc160e3-0f4f-4cf8-a88e-0106b7d05612/dqc_reference/reference_markers.hmm OceanDNA-b46704/protein.faa > /dev/null
[2023-03-18 01:03:55,997] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:03:55,998] [INFO] Found 6/6 markers.
[2023-03-18 01:03:56,021] [INFO] Query marker FASTA was written to OceanDNA-b46704/markers.fasta
[2023-03-18 01:03:56,022] [INFO] Task started: Blastn
[2023-03-18 01:03:56,022] [INFO] Running command: blastn -query OceanDNA-b46704/markers.fasta -db /var/lib/cwl/stg6bc160e3-0f4f-4cf8-a88e-0106b7d05612/dqc_reference/reference_markers.fasta -out OceanDNA-b46704/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:03:56,536] [INFO] Task succeeded: Blastn
[2023-03-18 01:03:56,537] [INFO] Selected 15 target genomes.
[2023-03-18 01:03:56,537] [INFO] Target genome list was writen to OceanDNA-b46704/target_genomes.txt
[2023-03-18 01:03:56,546] [INFO] Task started: fastANI
[2023-03-18 01:03:56,546] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fcc9368-12c2-45a7-aaae-34a837ec6499/OceanDNA-b46704.fa --refList OceanDNA-b46704/target_genomes.txt --output OceanDNA-b46704/fastani_result.tsv --threads 1
[2023-03-18 01:04:07,636] [INFO] Task succeeded: fastANI
[2023-03-18 01:04:07,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bc160e3-0f4f-4cf8-a88e-0106b7d05612/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:04:07,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bc160e3-0f4f-4cf8-a88e-0106b7d05612/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:04:07,637] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:04:07,637] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:04:07,637] [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 01:04:07,637] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46704/tc_result.tsv
[2023-03-18 01:04:07,637] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:04:07,637] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:04:07,638] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bc160e3-0f4f-4cf8-a88e-0106b7d05612/dqc_reference/checkm_data
[2023-03-18 01:04:07,640] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:04:07,646] [INFO] Task started: CheckM
[2023-03-18 01:04:07,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46704/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46704/checkm_input OceanDNA-b46704/checkm_result
[2023-03-18 01:05:27,224] [INFO] Task succeeded: CheckM
[2023-03-18 01:05:27,224] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:05:27,267] [INFO] ===== Completeness check finished =====
[2023-03-18 01:05:27,267] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:05:27,267] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46704/markers.fasta)
[2023-03-18 01:05:27,268] [INFO] Task started: Blastn
[2023-03-18 01:05:27,269] [INFO] Running command: blastn -query OceanDNA-b46704/markers.fasta -db /var/lib/cwl/stg6bc160e3-0f4f-4cf8-a88e-0106b7d05612/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46704/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:05:27,979] [INFO] Task succeeded: Blastn
[2023-03-18 01:05:27,983] [INFO] Selected 7 target genomes.
[2023-03-18 01:05:27,983] [INFO] Target genome list was writen to OceanDNA-b46704/target_genomes_gtdb.txt
[2023-03-18 01:05:27,990] [INFO] Task started: fastANI
[2023-03-18 01:05:27,990] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fcc9368-12c2-45a7-aaae-34a837ec6499/OceanDNA-b46704.fa --refList OceanDNA-b46704/target_genomes_gtdb.txt --output OceanDNA-b46704/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:05:33,917] [INFO] Task succeeded: fastANI
[2023-03-18 01:05:33,922] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:05:33,922] [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_002420305.1	s__Roseibacillus_B sp002420305	99.72	1094	1233	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	97.44	96.53	0.87	0.86	5	conclusive
GCA_002380675.1	s__Roseibacillus_B sp002380675	94.2768	859	1233	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.08	99.08	0.81	0.81	2	-
GCA_002686085.1	s__Roseibacillus_B sp002686085	93.604	1102	1233	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.30	99.30	0.96	0.96	3	-
GCA_002709915.1	s__Roseibacillus_B sp002709915	85.6878	904	1233	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.45	99.45	0.86	0.86	2	-
GCA_002729275.1	s__Roseibacillus_B sp002729275	84.8924	886	1233	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	98.94	98.88	0.91	0.89	3	-
GCA_002715825.1	s__Roseibacillus_B sp002715825	84.6043	933	1233	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_002723015.1	s__Roseibacillus_B sp002723015	79.5398	612	1233	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.32	99.32	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-18 01:05:33,923] [INFO] GTDB search result was written to OceanDNA-b46704/result_gtdb.tsv
[2023-03-18 01:05:33,923] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:05:33,924] [INFO] DFAST_QC result json was written to OceanDNA-b46704/dqc_result.json
[2023-03-18 01:05:33,924] [INFO] DFAST_QC completed!
[2023-03-18 01:05:33,924] [INFO] Total running time: 0h2m11s