[2023-03-18 02:48:49,204] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:48:49,204] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:48:49,205] [INFO] DQC Reference Directory: /var/lib/cwl/stg718fa73d-b933-40aa-8e3d-1b463e3321dc/dqc_reference
[2023-03-18 02:48:50,340] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:48:50,340] [INFO] Task started: Prodigal
[2023-03-18 02:48:50,341] [INFO] Running command: cat /var/lib/cwl/stgf08107ee-334a-4dba-b813-f1b37e35cb8e/OceanDNA-a4057.fa | prodigal -d OceanDNA-a4057/cds.fna -a OceanDNA-a4057/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:48:56,826] [INFO] Task succeeded: Prodigal
[2023-03-18 02:48:56,826] [INFO] Task started: HMMsearch
[2023-03-18 02:48:56,826] [INFO] Running command: hmmsearch --tblout OceanDNA-a4057/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg718fa73d-b933-40aa-8e3d-1b463e3321dc/dqc_reference/reference_markers.hmm OceanDNA-a4057/protein.faa > /dev/null
[2023-03-18 02:48:57,025] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:48:57,026] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf08107ee-334a-4dba-b813-f1b37e35cb8e/OceanDNA-a4057.fa]
[2023-03-18 02:48:57,035] [INFO] Query marker FASTA was written to OceanDNA-a4057/markers.fasta
[2023-03-18 02:48:57,036] [INFO] Task started: Blastn
[2023-03-18 02:48:57,036] [INFO] Running command: blastn -query OceanDNA-a4057/markers.fasta -db /var/lib/cwl/stg718fa73d-b933-40aa-8e3d-1b463e3321dc/dqc_reference/reference_markers.fasta -out OceanDNA-a4057/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:48:57,481] [INFO] Task succeeded: Blastn
[2023-03-18 02:48:57,482] [INFO] Selected 5 target genomes.
[2023-03-18 02:48:57,482] [INFO] Target genome list was writen to OceanDNA-a4057/target_genomes.txt
[2023-03-18 02:48:57,486] [INFO] Task started: fastANI
[2023-03-18 02:48:57,486] [INFO] Running command: fastANI --query /var/lib/cwl/stgf08107ee-334a-4dba-b813-f1b37e35cb8e/OceanDNA-a4057.fa --refList OceanDNA-a4057/target_genomes.txt --output OceanDNA-a4057/fastani_result.tsv --threads 1
[2023-03-18 02:48:59,433] [INFO] Task succeeded: fastANI
[2023-03-18 02:48:59,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg718fa73d-b933-40aa-8e3d-1b463e3321dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:48:59,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg718fa73d-b933-40aa-8e3d-1b463e3321dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:48:59,434] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:48:59,434] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:48:59,434] [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 02:48:59,434] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4057/tc_result.tsv
[2023-03-18 02:48:59,435] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:48:59,435] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:48:59,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg718fa73d-b933-40aa-8e3d-1b463e3321dc/dqc_reference/checkm_data
[2023-03-18 02:48:59,437] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:48:59,440] [INFO] Task started: CheckM
[2023-03-18 02:48:59,440] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4057/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4057/checkm_input OceanDNA-a4057/checkm_result
[2023-03-18 02:49:21,872] [INFO] Task succeeded: CheckM
[2023-03-18 02:49:21,873] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:49:21,875] [INFO] ===== Completeness check finished =====
[2023-03-18 02:49:21,875] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:49:21,875] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4057/markers.fasta)
[2023-03-18 02:49:21,876] [INFO] Task started: Blastn
[2023-03-18 02:49:21,876] [INFO] Running command: blastn -query OceanDNA-a4057/markers.fasta -db /var/lib/cwl/stg718fa73d-b933-40aa-8e3d-1b463e3321dc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4057/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:49:22,358] [INFO] Task succeeded: Blastn
[2023-03-18 02:49:22,359] [INFO] Selected 8 target genomes.
[2023-03-18 02:49:22,359] [INFO] Target genome list was writen to OceanDNA-a4057/target_genomes_gtdb.txt
[2023-03-18 02:49:22,390] [INFO] Task started: fastANI
[2023-03-18 02:49:22,390] [INFO] Running command: fastANI --query /var/lib/cwl/stgf08107ee-334a-4dba-b813-f1b37e35cb8e/OceanDNA-a4057.fa --refList OceanDNA-a4057/target_genomes_gtdb.txt --output OceanDNA-a4057/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:49:24,617] [INFO] Task succeeded: fastANI
[2023-03-18 02:49:24,622] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:49:24,622] [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_002457145.1	s__MGIIb-O3 sp002457145	91.3185	351	410	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.76	99.72	0.89	0.85	3	-
GCA_002731195.1	s__MGIIb-O3 sp002731195	80.669	231	410	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002172375.1	s__MGIIb-O3 sp002172375	80.027	224	410	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719615.1	s__MGIIb-O3 sp002719615	79.823	256	410	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712575.1	s__MGIIb-O3 sp002712575	79.6643	248	410	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003602595.1	s__MGIIb-O3 sp003602595	79.5998	246	410	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:49:24,622] [INFO] GTDB search result was written to OceanDNA-a4057/result_gtdb.tsv
[2023-03-18 02:49:24,622] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:49:24,623] [INFO] DFAST_QC result json was written to OceanDNA-a4057/dqc_result.json
[2023-03-18 02:49:24,623] [INFO] DFAST_QC completed!
[2023-03-18 02:49:24,623] [INFO] Total running time: 0h0m35s