[2023-03-18 00:22:36,356] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:22:36,357] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:22:36,357] [INFO] DQC Reference Directory: /var/lib/cwl/stg173fa2c8-9abc-4649-a7fd-b4c28edd854d/dqc_reference
[2023-03-18 00:22:38,781] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:22:38,782] [INFO] Task started: Prodigal
[2023-03-18 00:22:38,782] [INFO] Running command: cat /var/lib/cwl/stgef8251c5-0fe7-4a7e-8775-bbf5fa2107d0/OceanDNA-a4140.fa | prodigal -d OceanDNA-a4140/cds.fna -a OceanDNA-a4140/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:22:43,112] [INFO] Task succeeded: Prodigal
[2023-03-18 00:22:43,113] [INFO] Task started: HMMsearch
[2023-03-18 00:22:43,113] [INFO] Running command: hmmsearch --tblout OceanDNA-a4140/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg173fa2c8-9abc-4649-a7fd-b4c28edd854d/dqc_reference/reference_markers.hmm OceanDNA-a4140/protein.faa > /dev/null
[2023-03-18 00:22:43,288] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:22:43,289] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgef8251c5-0fe7-4a7e-8775-bbf5fa2107d0/OceanDNA-a4140.fa]
[2023-03-18 00:22:43,295] [INFO] Query marker FASTA was written to OceanDNA-a4140/markers.fasta
[2023-03-18 00:22:43,295] [INFO] Task started: Blastn
[2023-03-18 00:22:43,296] [INFO] Running command: blastn -query OceanDNA-a4140/markers.fasta -db /var/lib/cwl/stg173fa2c8-9abc-4649-a7fd-b4c28edd854d/dqc_reference/reference_markers.fasta -out OceanDNA-a4140/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:22:45,319] [INFO] Task succeeded: Blastn
[2023-03-18 00:22:45,320] [INFO] Selected 5 target genomes.
[2023-03-18 00:22:45,320] [INFO] Target genome list was writen to OceanDNA-a4140/target_genomes.txt
[2023-03-18 00:22:45,325] [INFO] Task started: fastANI
[2023-03-18 00:22:45,325] [INFO] Running command: fastANI --query /var/lib/cwl/stgef8251c5-0fe7-4a7e-8775-bbf5fa2107d0/OceanDNA-a4140.fa --refList OceanDNA-a4140/target_genomes.txt --output OceanDNA-a4140/fastani_result.tsv --threads 1
[2023-03-18 00:22:49,384] [INFO] Task succeeded: fastANI
[2023-03-18 00:22:49,384] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg173fa2c8-9abc-4649-a7fd-b4c28edd854d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:22:49,385] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg173fa2c8-9abc-4649-a7fd-b4c28edd854d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:22:49,385] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:22:49,385] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:22:49,385] [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 00:22:49,385] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4140/tc_result.tsv
[2023-03-18 00:22:49,385] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:22:49,385] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:22:49,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg173fa2c8-9abc-4649-a7fd-b4c28edd854d/dqc_reference/checkm_data
[2023-03-18 00:22:49,396] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:22:49,779] [INFO] Task started: CheckM
[2023-03-18 00:22:49,779] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4140/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4140/checkm_input OceanDNA-a4140/checkm_result
[2023-03-18 00:23:08,217] [INFO] Task succeeded: CheckM
[2023-03-18 00:23:08,218] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.38%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:23:08,219] [INFO] ===== Completeness check finished =====
[2023-03-18 00:23:08,219] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:23:08,219] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4140/markers.fasta)
[2023-03-18 00:23:08,221] [INFO] Task started: Blastn
[2023-03-18 00:23:08,221] [INFO] Running command: blastn -query OceanDNA-a4140/markers.fasta -db /var/lib/cwl/stg173fa2c8-9abc-4649-a7fd-b4c28edd854d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4140/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:23:08,935] [INFO] Task succeeded: Blastn
[2023-03-18 00:23:08,936] [INFO] Selected 10 target genomes.
[2023-03-18 00:23:08,936] [INFO] Target genome list was writen to OceanDNA-a4140/target_genomes_gtdb.txt
[2023-03-18 00:23:08,944] [INFO] Task started: fastANI
[2023-03-18 00:23:08,944] [INFO] Running command: fastANI --query /var/lib/cwl/stgef8251c5-0fe7-4a7e-8775-bbf5fa2107d0/OceanDNA-a4140.fa --refList OceanDNA-a4140/target_genomes_gtdb.txt --output OceanDNA-a4140/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:23:10,877] [INFO] Task succeeded: fastANI
[2023-03-18 00:23:10,881] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:23:10,881] [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_001629235.1	s__MGIIb-O3 sp001629235	79.9509	133	233	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	97.45	95.03	0.80	0.68	7	-
GCA_902601345.1	s__MGIIb-O3 sp902601345	79.5273	115	233	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_902625325.1	s__MGIIb-O3 sp902625325	79.4499	139	233	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_001629255.1	s__MGIIb-O3 sp001629255	79.433	142	233	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	98.42	97.36	0.80	0.70	6	-
--------------------------------------------------------------------------------
[2023-03-18 00:23:10,881] [INFO] GTDB search result was written to OceanDNA-a4140/result_gtdb.tsv
[2023-03-18 00:23:10,881] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:23:10,882] [INFO] DFAST_QC result json was written to OceanDNA-a4140/dqc_result.json
[2023-03-18 00:23:10,882] [INFO] DFAST_QC completed!
[2023-03-18 00:23:10,882] [INFO] Total running time: 0h0m35s