[2023-03-14 12:25:41,425] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:25:41,425] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:25:41,425] [INFO] DQC Reference Directory: /var/lib/cwl/stg1768cba0-f43b-4a58-915d-0f9958f74361/dqc_reference
[2023-03-14 12:25:42,679] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:25:42,679] [INFO] Task started: Prodigal
[2023-03-14 12:25:42,680] [INFO] Running command: cat /var/lib/cwl/stgcf5cafd2-b243-451c-9613-6e71dc64cafe/OceanDNA-a3364.fa | prodigal -d OceanDNA-a3364/cds.fna -a OceanDNA-a3364/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:25:52,435] [INFO] Task succeeded: Prodigal
[2023-03-14 12:25:52,435] [INFO] Task started: HMMsearch
[2023-03-14 12:25:52,435] [INFO] Running command: hmmsearch --tblout OceanDNA-a3364/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1768cba0-f43b-4a58-915d-0f9958f74361/dqc_reference/reference_markers.hmm OceanDNA-a3364/protein.faa > /dev/null
[2023-03-14 12:25:52,610] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:25:52,610] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgcf5cafd2-b243-451c-9613-6e71dc64cafe/OceanDNA-a3364.fa]
[2023-03-14 12:25:52,622] [INFO] Query marker FASTA was written to OceanDNA-a3364/markers.fasta
[2023-03-14 12:25:52,624] [INFO] Task started: Blastn
[2023-03-14 12:25:52,624] [INFO] Running command: blastn -query OceanDNA-a3364/markers.fasta -db /var/lib/cwl/stg1768cba0-f43b-4a58-915d-0f9958f74361/dqc_reference/reference_markers.fasta -out OceanDNA-a3364/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:25:53,054] [INFO] Task succeeded: Blastn
[2023-03-14 12:25:53,055] [INFO] Selected 3 target genomes.
[2023-03-14 12:25:53,055] [INFO] Target genome list was writen to OceanDNA-a3364/target_genomes.txt
[2023-03-14 12:25:53,058] [INFO] Task started: fastANI
[2023-03-14 12:25:53,058] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf5cafd2-b243-451c-9613-6e71dc64cafe/OceanDNA-a3364.fa --refList OceanDNA-a3364/target_genomes.txt --output OceanDNA-a3364/fastani_result.tsv --threads 1
[2023-03-14 12:25:54,191] [INFO] Task succeeded: fastANI
[2023-03-14 12:25:54,192] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1768cba0-f43b-4a58-915d-0f9958f74361/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:25:54,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1768cba0-f43b-4a58-915d-0f9958f74361/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:25:54,192] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:25:54,192] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:25:54,192] [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
--------------------------------------------------------------------------------
[2023-03-14 12:25:54,192] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3364/tc_result.tsv
[2023-03-14 12:25:54,193] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:25:54,193] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:25:54,193] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1768cba0-f43b-4a58-915d-0f9958f74361/dqc_reference/checkm_data
[2023-03-14 12:25:54,195] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:25:54,203] [INFO] Task started: CheckM
[2023-03-14 12:25:54,203] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3364/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3364/checkm_input OceanDNA-a3364/checkm_result
[2023-03-14 12:26:23,853] [INFO] Task succeeded: CheckM
[2023-03-14 12:26:23,853] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:26:23,855] [INFO] ===== Completeness check finished =====
[2023-03-14 12:26:23,855] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:26:23,855] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3364/markers.fasta)
[2023-03-14 12:26:23,856] [INFO] Task started: Blastn
[2023-03-14 12:26:23,856] [INFO] Running command: blastn -query OceanDNA-a3364/markers.fasta -db /var/lib/cwl/stg1768cba0-f43b-4a58-915d-0f9958f74361/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3364/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:26:24,299] [INFO] Task succeeded: Blastn
[2023-03-14 12:26:24,300] [INFO] Selected 8 target genomes.
[2023-03-14 12:26:24,300] [INFO] Target genome list was writen to OceanDNA-a3364/target_genomes_gtdb.txt
[2023-03-14 12:26:24,313] [INFO] Task started: fastANI
[2023-03-14 12:26:24,314] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf5cafd2-b243-451c-9613-6e71dc64cafe/OceanDNA-a3364.fa --refList OceanDNA-a3364/target_genomes_gtdb.txt --output OceanDNA-a3364/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:26:26,662] [INFO] Task succeeded: fastANI
[2023-03-14 12:26:26,665] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:26:26,665] [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_002497905.1	s__MGIIb-N2 sp002497905	99.7635	461	542	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	99.55	99.55	0.87	0.87	3	conclusive
GCA_002506875.1	s__MGIIb-N2 sp002506875	93.3027	444	542	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	97.18	97.18	0.84	0.84	3	-
GCA_002713585.1	s__MGIIb-N2 sp002713585	88.1213	452	542	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	98.11	98.05	0.86	0.82	4	-
GCA_002708015.1	s__MGIIb-N2 sp002708015	77.2896	57	542	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:26:26,665] [INFO] GTDB search result was written to OceanDNA-a3364/result_gtdb.tsv
[2023-03-14 12:26:26,666] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:26:26,666] [INFO] DFAST_QC result json was written to OceanDNA-a3364/dqc_result.json
[2023-03-14 12:26:26,666] [INFO] DFAST_QC completed!
[2023-03-14 12:26:26,666] [INFO] Total running time: 0h0m45s