[2023-03-18 22:09:38,387] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:09:38,388] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:09:38,388] [INFO] DQC Reference Directory: /var/lib/cwl/stg224e8e89-46c6-4c73-9974-f71ff5d4b2fc/dqc_reference
[2023-03-18 22:09:40,573] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:09:40,574] [INFO] Task started: Prodigal
[2023-03-18 22:09:40,574] [INFO] Running command: cat /var/lib/cwl/stg0b98981b-601f-46f6-8490-6dd0c7be601a/OceanDNA-b3129.fa | prodigal -d OceanDNA-b3129/cds.fna -a OceanDNA-b3129/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:09:47,761] [INFO] Task succeeded: Prodigal
[2023-03-18 22:09:47,762] [INFO] Task started: HMMsearch
[2023-03-18 22:09:47,762] [INFO] Running command: hmmsearch --tblout OceanDNA-b3129/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg224e8e89-46c6-4c73-9974-f71ff5d4b2fc/dqc_reference/reference_markers.hmm OceanDNA-b3129/protein.faa > /dev/null
[2023-03-18 22:09:47,926] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:09:47,926] [INFO] Found 6/6 markers.
[2023-03-18 22:09:47,936] [INFO] Query marker FASTA was written to OceanDNA-b3129/markers.fasta
[2023-03-18 22:09:47,937] [INFO] Task started: Blastn
[2023-03-18 22:09:47,937] [INFO] Running command: blastn -query OceanDNA-b3129/markers.fasta -db /var/lib/cwl/stg224e8e89-46c6-4c73-9974-f71ff5d4b2fc/dqc_reference/reference_markers.fasta -out OceanDNA-b3129/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:09:48,493] [INFO] Task succeeded: Blastn
[2023-03-18 22:09:48,494] [INFO] Selected 30 target genomes.
[2023-03-18 22:09:48,494] [INFO] Target genome list was writen to OceanDNA-b3129/target_genomes.txt
[2023-03-18 22:09:48,509] [INFO] Task started: fastANI
[2023-03-18 22:09:48,509] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b98981b-601f-46f6-8490-6dd0c7be601a/OceanDNA-b3129.fa --refList OceanDNA-b3129/target_genomes.txt --output OceanDNA-b3129/fastani_result.tsv --threads 1
[2023-03-18 22:10:00,294] [INFO] Task succeeded: fastANI
[2023-03-18 22:10:00,294] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg224e8e89-46c6-4c73-9974-f71ff5d4b2fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:10:00,294] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg224e8e89-46c6-4c73-9974-f71ff5d4b2fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:10:00,295] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:10:00,295] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:10:00,295] [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 22:10:00,295] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3129/tc_result.tsv
[2023-03-18 22:10:00,295] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:10:00,295] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:10:00,295] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg224e8e89-46c6-4c73-9974-f71ff5d4b2fc/dqc_reference/checkm_data
[2023-03-18 22:10:00,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:10:00,301] [INFO] Task started: CheckM
[2023-03-18 22:10:00,301] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3129/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3129/checkm_input OceanDNA-b3129/checkm_result
[2023-03-18 22:10:23,682] [INFO] Task succeeded: CheckM
[2023-03-18 22:10:23,683] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:10:23,692] [INFO] ===== Completeness check finished =====
[2023-03-18 22:10:23,692] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:10:23,693] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3129/markers.fasta)
[2023-03-18 22:10:23,693] [INFO] Task started: Blastn
[2023-03-18 22:10:23,694] [INFO] Running command: blastn -query OceanDNA-b3129/markers.fasta -db /var/lib/cwl/stg224e8e89-46c6-4c73-9974-f71ff5d4b2fc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3129/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:10:24,593] [INFO] Task succeeded: Blastn
[2023-03-18 22:10:24,597] [INFO] Selected 10 target genomes.
[2023-03-18 22:10:24,597] [INFO] Target genome list was writen to OceanDNA-b3129/target_genomes_gtdb.txt
[2023-03-18 22:10:24,607] [INFO] Task started: fastANI
[2023-03-18 22:10:24,607] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b98981b-601f-46f6-8490-6dd0c7be601a/OceanDNA-b3129.fa --refList OceanDNA-b3129/target_genomes_gtdb.txt --output OceanDNA-b3129/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:10:26,933] [INFO] Task succeeded: fastANI
[2023-03-18 22:10:26,940] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:10:26,940] [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_002430075.1	s__Planktophila sp002430075	99.3868	316	415	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002284855.1	s__Planktophila sp002284855	80.1989	222	415	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002288225.1	s__Planktophila dulcis	80.089	231	415	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	97.64	97.42	0.94	0.93	3	-
GCA_903845465.1	s__Planktophila sp903845465	80.0134	166	415	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.37	98.68	0.87	0.84	5	-
GCA_000372185.1	s__Planktophila sp000372185	79.9236	178	415	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002288065.1	s__Planktophila sulfonica	79.9181	229	415	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694515.1	s__Planktophila sp009694515	79.2106	118	415	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	100.00	100.00	0.88	0.88	2	-
GCA_009701945.1	s__Planktophila sp009701945	79.1196	119	415	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	79.049	158	415	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	78.399	132	415	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.64	98.64	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-03-18 22:10:26,941] [INFO] GTDB search result was written to OceanDNA-b3129/result_gtdb.tsv
[2023-03-18 22:10:26,941] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:10:26,943] [INFO] DFAST_QC result json was written to OceanDNA-b3129/dqc_result.json
[2023-03-18 22:10:26,943] [INFO] DFAST_QC completed!
[2023-03-18 22:10:26,943] [INFO] Total running time: 0h0m49s