[2023-03-18 08:17:17,714] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:17,714] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:17,714] [INFO] DQC Reference Directory: /var/lib/cwl/stg04cf4492-cee9-4c49-bb45-b5d09a141757/dqc_reference
[2023-03-18 08:17:18,943] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:18,943] [INFO] Task started: Prodigal
[2023-03-18 08:17:18,943] [INFO] Running command: cat /var/lib/cwl/stg87e87812-98a3-41f6-b45a-5f496d2750ac/OceanDNA-b3089.fa | prodigal -d OceanDNA-b3089/cds.fna -a OceanDNA-b3089/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:24,488] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:24,488] [INFO] Task started: HMMsearch
[2023-03-18 08:17:24,488] [INFO] Running command: hmmsearch --tblout OceanDNA-b3089/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04cf4492-cee9-4c49-bb45-b5d09a141757/dqc_reference/reference_markers.hmm OceanDNA-b3089/protein.faa > /dev/null
[2023-03-18 08:17:24,665] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:24,666] [INFO] Found 6/6 markers.
[2023-03-18 08:17:24,674] [INFO] Query marker FASTA was written to OceanDNA-b3089/markers.fasta
[2023-03-18 08:17:24,674] [INFO] Task started: Blastn
[2023-03-18 08:17:24,674] [INFO] Running command: blastn -query OceanDNA-b3089/markers.fasta -db /var/lib/cwl/stg04cf4492-cee9-4c49-bb45-b5d09a141757/dqc_reference/reference_markers.fasta -out OceanDNA-b3089/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:25,226] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:25,226] [INFO] Selected 28 target genomes.
[2023-03-18 08:17:25,227] [INFO] Target genome list was writen to OceanDNA-b3089/target_genomes.txt
[2023-03-18 08:17:25,241] [INFO] Task started: fastANI
[2023-03-18 08:17:25,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg87e87812-98a3-41f6-b45a-5f496d2750ac/OceanDNA-b3089.fa --refList OceanDNA-b3089/target_genomes.txt --output OceanDNA-b3089/fastani_result.tsv --threads 1
[2023-03-18 08:17:41,235] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:41,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04cf4492-cee9-4c49-bb45-b5d09a141757/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:17:41,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04cf4492-cee9-4c49-bb45-b5d09a141757/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:17:41,236] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:17:41,236] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:17:41,236] [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 08:17:41,237] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3089/tc_result.tsv
[2023-03-18 08:17:41,237] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:17:41,237] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:17:41,237] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04cf4492-cee9-4c49-bb45-b5d09a141757/dqc_reference/checkm_data
[2023-03-18 08:17:41,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:17:41,242] [INFO] Task started: CheckM
[2023-03-18 08:17:41,242] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3089/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3089/checkm_input OceanDNA-b3089/checkm_result
[2023-03-18 08:18:01,216] [INFO] Task succeeded: CheckM
[2023-03-18 08:18:01,216] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:18:01,218] [INFO] ===== Completeness check finished =====
[2023-03-18 08:18:01,218] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:18:01,219] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3089/markers.fasta)
[2023-03-18 08:18:01,219] [INFO] Task started: Blastn
[2023-03-18 08:18:01,219] [INFO] Running command: blastn -query OceanDNA-b3089/markers.fasta -db /var/lib/cwl/stg04cf4492-cee9-4c49-bb45-b5d09a141757/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3089/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:18:02,124] [INFO] Task succeeded: Blastn
[2023-03-18 08:18:02,125] [INFO] Selected 8 target genomes.
[2023-03-18 08:18:02,125] [INFO] Target genome list was writen to OceanDNA-b3089/target_genomes_gtdb.txt
[2023-03-18 08:18:02,231] [INFO] Task started: fastANI
[2023-03-18 08:18:02,232] [INFO] Running command: fastANI --query /var/lib/cwl/stg87e87812-98a3-41f6-b45a-5f496d2750ac/OceanDNA-b3089.fa --refList OceanDNA-b3089/target_genomes_gtdb.txt --output OceanDNA-b3089/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:18:04,287] [INFO] Task succeeded: fastANI
[2023-03-18 08:18:04,293] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:18:04,293] [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_003569265.1	s__Planktophila sp003569265	89.1114	151	319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.55	99.55	0.94	0.94	2	-
GCF_002288185.1	s__Planktophila vernalis	87.4091	282	319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002284895.1	s__Planktophila sp002284895	86.8399	298	319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000378885.1	s__Planktophila sp000378885	86.5784	247	319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	96.66	96.52	0.78	0.69	3	-
GCA_005789205.1	s__Planktophila sp005789205	85.9502	225	319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010024385.1	s__Planktophila sp010024385	85.7002	262	319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.43	99.35	0.91	0.87	13	-
GCA_018969355.1	s__Planktophila sp018969355	84.232	265	319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903894425.1	s__Planktophila sp903894425	80.2675	173	319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:18:04,293] [INFO] GTDB search result was written to OceanDNA-b3089/result_gtdb.tsv
[2023-03-18 08:18:04,293] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:18:04,294] [INFO] DFAST_QC result json was written to OceanDNA-b3089/dqc_result.json
[2023-03-18 08:18:04,294] [INFO] DFAST_QC completed!
[2023-03-18 08:18:04,294] [INFO] Total running time: 0h0m47s