[2023-03-16 03:23:48,507] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:23:48,507] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:23:48,507] [INFO] DQC Reference Directory: /var/lib/cwl/stg479193fc-9b31-49fd-a73b-055b33d48bb1/dqc_reference
[2023-03-16 03:23:50,648] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:23:50,648] [INFO] Task started: Prodigal
[2023-03-16 03:23:50,649] [INFO] Running command: cat /var/lib/cwl/stg92af561d-e006-4f7b-ba33-0da0bf13e3e6/OceanDNA-b3111.fa | prodigal -d OceanDNA-b3111/cds.fna -a OceanDNA-b3111/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:23:57,353] [INFO] Task succeeded: Prodigal
[2023-03-16 03:23:57,353] [INFO] Task started: HMMsearch
[2023-03-16 03:23:57,353] [INFO] Running command: hmmsearch --tblout OceanDNA-b3111/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg479193fc-9b31-49fd-a73b-055b33d48bb1/dqc_reference/reference_markers.hmm OceanDNA-b3111/protein.faa > /dev/null
[2023-03-16 03:23:57,546] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:23:57,546] [INFO] Found 6/6 markers.
[2023-03-16 03:23:57,556] [INFO] Query marker FASTA was written to OceanDNA-b3111/markers.fasta
[2023-03-16 03:23:57,556] [INFO] Task started: Blastn
[2023-03-16 03:23:57,556] [INFO] Running command: blastn -query OceanDNA-b3111/markers.fasta -db /var/lib/cwl/stg479193fc-9b31-49fd-a73b-055b33d48bb1/dqc_reference/reference_markers.fasta -out OceanDNA-b3111/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:23:58,133] [INFO] Task succeeded: Blastn
[2023-03-16 03:23:58,134] [INFO] Selected 27 target genomes.
[2023-03-16 03:23:58,134] [INFO] Target genome list was writen to OceanDNA-b3111/target_genomes.txt
[2023-03-16 03:23:58,155] [INFO] Task started: fastANI
[2023-03-16 03:23:58,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg92af561d-e006-4f7b-ba33-0da0bf13e3e6/OceanDNA-b3111.fa --refList OceanDNA-b3111/target_genomes.txt --output OceanDNA-b3111/fastani_result.tsv --threads 1
[2023-03-16 03:24:13,926] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:13,927] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg479193fc-9b31-49fd-a73b-055b33d48bb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:24:13,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg479193fc-9b31-49fd-a73b-055b33d48bb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:24:13,927] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:24:13,927] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 03:24:13,927] [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
--------------------------------------------------------------------------------
[2023-03-16 03:24:13,927] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3111/tc_result.tsv
[2023-03-16 03:24:13,927] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:24:13,927] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:24:13,928] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg479193fc-9b31-49fd-a73b-055b33d48bb1/dqc_reference/checkm_data
[2023-03-16 03:24:13,930] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:24:13,932] [INFO] Task started: CheckM
[2023-03-16 03:24:13,933] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3111/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3111/checkm_input OceanDNA-b3111/checkm_result
[2023-03-16 03:24:36,510] [INFO] Task succeeded: CheckM
[2023-03-16 03:24:36,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:24:36,512] [INFO] ===== Completeness check finished =====
[2023-03-16 03:24:36,513] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:24:36,513] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3111/markers.fasta)
[2023-03-16 03:24:36,513] [INFO] Task started: Blastn
[2023-03-16 03:24:36,513] [INFO] Running command: blastn -query OceanDNA-b3111/markers.fasta -db /var/lib/cwl/stg479193fc-9b31-49fd-a73b-055b33d48bb1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3111/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:37,404] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:37,405] [INFO] Selected 17 target genomes.
[2023-03-16 03:24:37,405] [INFO] Target genome list was writen to OceanDNA-b3111/target_genomes_gtdb.txt
[2023-03-16 03:24:37,838] [INFO] Task started: fastANI
[2023-03-16 03:24:37,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg92af561d-e006-4f7b-ba33-0da0bf13e3e6/OceanDNA-b3111.fa --refList OceanDNA-b3111/target_genomes_gtdb.txt --output OceanDNA-b3111/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:24:41,886] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:41,896] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 03:24:41,896] [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_001438925.1	s__Planktophila sp001438925	99.2422	266	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.36	99.31	0.82	0.80	5	conclusive
GCA_018970885.1	s__Planktophila sp018970885	83.201	240	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903922745.1	s__Planktophila sp903922745	80.2889	148	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002284895.1	s__Planktophila sp002284895	79.3967	163	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000378885.1	s__Planktophila sp000378885	79.0662	140	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	96.66	96.52	0.78	0.69	3	-
GCA_903820565.1	s__Planktophila sp903820565	79.0427	156	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009705235.1	s__Planktophila sp009705235	79.008	145	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903832395.1	s__Planktophila sp903832395	78.7663	80	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.52	97.23	0.83	0.79	6	-
GCA_903921405.1	s__Planktophila sp903921405	78.0711	89	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.46	97.48	0.83	0.78	9	-
GCA_903825015.1	s__Planktophila sp903825015	77.898	92	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.76	99.71	0.87	0.84	4	-
GCA_009704505.1	s__Planktophila sp009704505	77.8929	105	377	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	77.8438	96	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.61	99.61	0.91	0.91	2	-
GCA_903874255.1	s__Planktophila sp903874255	77.791	115	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.56	99.42	0.86	0.85	4	-
GCA_009702925.1	s__Planktophila sp009702925	77.626	97	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.82	99.81	0.90	0.89	3	-
GCA_009704445.1	s__Planktophila sp009704445	77.1987	74	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699645.1	s__Planktophila sp009699645	77.1158	69	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009702835.1	s__Planktophila sp009702835	76.9675	87	377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.51	97.96	0.78	0.76	3	-
--------------------------------------------------------------------------------
[2023-03-16 03:24:41,896] [INFO] GTDB search result was written to OceanDNA-b3111/result_gtdb.tsv
[2023-03-16 03:24:41,896] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:24:41,898] [INFO] DFAST_QC result json was written to OceanDNA-b3111/dqc_result.json
[2023-03-16 03:24:41,898] [INFO] DFAST_QC completed!
[2023-03-16 03:24:41,898] [INFO] Total running time: 0h0m53s