[2023-03-15 12:44:24,476] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:44:24,476] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:44:24,476] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e8dec71-b956-4938-8ac7-53b8c911bcb5/dqc_reference
[2023-03-15 12:44:26,207] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:44:26,207] [INFO] Task started: Prodigal
[2023-03-15 12:44:26,207] [INFO] Running command: cat /var/lib/cwl/stg32bbd862-31c2-4e14-8416-7094cc793bd8/OceanDNA-b3032.fa | prodigal -d OceanDNA-b3032/cds.fna -a OceanDNA-b3032/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:44:28,968] [INFO] Task succeeded: Prodigal
[2023-03-15 12:44:28,968] [INFO] Task started: HMMsearch
[2023-03-15 12:44:28,968] [INFO] Running command: hmmsearch --tblout OceanDNA-b3032/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e8dec71-b956-4938-8ac7-53b8c911bcb5/dqc_reference/reference_markers.hmm OceanDNA-b3032/protein.faa > /dev/null
[2023-03-15 12:44:29,126] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:44:29,126] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg32bbd862-31c2-4e14-8416-7094cc793bd8/OceanDNA-b3032.fa]
[2023-03-15 12:44:29,134] [INFO] Query marker FASTA was written to OceanDNA-b3032/markers.fasta
[2023-03-15 12:44:29,134] [INFO] Task started: Blastn
[2023-03-15 12:44:29,134] [INFO] Running command: blastn -query OceanDNA-b3032/markers.fasta -db /var/lib/cwl/stg3e8dec71-b956-4938-8ac7-53b8c911bcb5/dqc_reference/reference_markers.fasta -out OceanDNA-b3032/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:44:30,656] [INFO] Task succeeded: Blastn
[2023-03-15 12:44:30,657] [INFO] Selected 11 target genomes.
[2023-03-15 12:44:30,658] [INFO] Target genome list was writen to OceanDNA-b3032/target_genomes.txt
[2023-03-15 12:44:30,664] [INFO] Task started: fastANI
[2023-03-15 12:44:30,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg32bbd862-31c2-4e14-8416-7094cc793bd8/OceanDNA-b3032.fa --refList OceanDNA-b3032/target_genomes.txt --output OceanDNA-b3032/fastani_result.tsv --threads 1
[2023-03-15 12:44:35,965] [INFO] Task succeeded: fastANI
[2023-03-15 12:44:35,965] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e8dec71-b956-4938-8ac7-53b8c911bcb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:44:35,965] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e8dec71-b956-4938-8ac7-53b8c911bcb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:44:35,965] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:44:35,966] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 12:44:35,966] [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
--------------------------------------------------------------------------------
[2023-03-15 12:44:35,966] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3032/tc_result.tsv
[2023-03-15 12:44:35,966] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:44:35,966] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:44:35,966] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e8dec71-b956-4938-8ac7-53b8c911bcb5/dqc_reference/checkm_data
[2023-03-15 12:44:35,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:44:35,971] [INFO] Task started: CheckM
[2023-03-15 12:44:35,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3032/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3032/checkm_input OceanDNA-b3032/checkm_result
[2023-03-15 12:44:50,002] [INFO] Task succeeded: CheckM
[2023-03-15 12:44:50,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.29%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:44:50,004] [INFO] ===== Completeness check finished =====
[2023-03-15 12:44:50,004] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:44:50,004] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3032/markers.fasta)
[2023-03-15 12:44:50,005] [INFO] Task started: Blastn
[2023-03-15 12:44:50,005] [INFO] Running command: blastn -query OceanDNA-b3032/markers.fasta -db /var/lib/cwl/stg3e8dec71-b956-4938-8ac7-53b8c911bcb5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3032/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:44:50,697] [INFO] Task succeeded: Blastn
[2023-03-15 12:44:50,698] [INFO] Selected 15 target genomes.
[2023-03-15 12:44:50,698] [INFO] Target genome list was writen to OceanDNA-b3032/target_genomes_gtdb.txt
[2023-03-15 12:44:50,838] [INFO] Task started: fastANI
[2023-03-15 12:44:50,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg32bbd862-31c2-4e14-8416-7094cc793bd8/OceanDNA-b3032.fa --refList OceanDNA-b3032/target_genomes_gtdb.txt --output OceanDNA-b3032/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:44:54,039] [INFO] Task succeeded: fastANI
[2023-03-15 12:44:54,045] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 12:44:54,045] [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_010030895.1	s__Nanopelagicus sp010030895	99.2045	120	132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	98.34	97.93	0.89	0.87	8	conclusive
GCA_903897475.1	s__Nanopelagicus sp903897475	82.0276	83	132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	98.94	98.64	0.81	0.80	6	-
GCA_009700155.1	s__Nanopelagicus sp009700155	81.3056	71	132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	98.43	98.37	0.82	0.81	3	-
GCA_001437855.1	s__Nanopelagicus sp001437855	80.6887	62	132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	96.40	95.11	0.72	0.67	12	-
GCF_002287885.2	s__Nanopelagicus limnes	79.6251	66	132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003569185.1	s__Nanopelagicus sp003569185	79.5411	59	132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000378865.1	s__Nanopelagicus sp000378865	78.9845	50	132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000294575.1	s__Nanopelagicus sp000294575	78.4681	65	132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	98.86	98.86	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-15 12:44:54,046] [INFO] GTDB search result was written to OceanDNA-b3032/result_gtdb.tsv
[2023-03-15 12:44:54,046] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:44:54,047] [INFO] DFAST_QC result json was written to OceanDNA-b3032/dqc_result.json
[2023-03-15 12:44:54,047] [INFO] DFAST_QC completed!
[2023-03-15 12:44:54,047] [INFO] Total running time: 0h0m30s