[2023-03-15 21:32:41,290] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:32:41,290] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:32:41,290] [INFO] DQC Reference Directory: /var/lib/cwl/stg04a97af5-6718-4504-af39-882dce7a4412/dqc_reference
[2023-03-15 21:32:42,945] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:32:42,946] [INFO] Task started: Prodigal
[2023-03-15 21:32:42,946] [INFO] Running command: cat /var/lib/cwl/stgf0af83af-840a-4902-9b0a-b53fc337caae/OceanDNA-a2321.fa | prodigal -d OceanDNA-a2321/cds.fna -a OceanDNA-a2321/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:32:50,969] [INFO] Task succeeded: Prodigal
[2023-03-15 21:32:50,969] [INFO] Task started: HMMsearch
[2023-03-15 21:32:50,969] [INFO] Running command: hmmsearch --tblout OceanDNA-a2321/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04a97af5-6718-4504-af39-882dce7a4412/dqc_reference/reference_markers.hmm OceanDNA-a2321/protein.faa > /dev/null
[2023-03-15 21:32:51,129] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:32:51,130] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf0af83af-840a-4902-9b0a-b53fc337caae/OceanDNA-a2321.fa]
[2023-03-15 21:32:51,144] [INFO] Query marker FASTA was written to OceanDNA-a2321/markers.fasta
[2023-03-15 21:32:51,146] [INFO] Task started: Blastn
[2023-03-15 21:32:51,146] [INFO] Running command: blastn -query OceanDNA-a2321/markers.fasta -db /var/lib/cwl/stg04a97af5-6718-4504-af39-882dce7a4412/dqc_reference/reference_markers.fasta -out OceanDNA-a2321/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:32:51,579] [INFO] Task succeeded: Blastn
[2023-03-15 21:32:51,579] [INFO] Selected 5 target genomes.
[2023-03-15 21:32:51,580] [INFO] Target genome list was writen to OceanDNA-a2321/target_genomes.txt
[2023-03-15 21:32:51,583] [INFO] Task started: fastANI
[2023-03-15 21:32:51,583] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0af83af-840a-4902-9b0a-b53fc337caae/OceanDNA-a2321.fa --refList OceanDNA-a2321/target_genomes.txt --output OceanDNA-a2321/fastani_result.tsv --threads 1
[2023-03-15 21:32:52,817] [INFO] Task succeeded: fastANI
[2023-03-15 21:32:52,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04a97af5-6718-4504-af39-882dce7a4412/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:32:52,817] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04a97af5-6718-4504-af39-882dce7a4412/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:32:52,818] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:32:52,818] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:32:52,818] [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 21:32:52,818] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2321/tc_result.tsv
[2023-03-15 21:32:52,818] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:32:52,818] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:32:52,818] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04a97af5-6718-4504-af39-882dce7a4412/dqc_reference/checkm_data
[2023-03-15 21:32:52,873] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:32:52,876] [INFO] Task started: CheckM
[2023-03-15 21:32:52,876] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2321/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2321/checkm_input OceanDNA-a2321/checkm_result
[2023-03-15 21:33:19,442] [INFO] Task succeeded: CheckM
[2023-03-15 21:33:19,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.73%
Contamintation: 1.56%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 21:33:19,445] [INFO] ===== Completeness check finished =====
[2023-03-15 21:33:19,445] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:33:19,445] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2321/markers.fasta)
[2023-03-15 21:33:19,446] [INFO] Task started: Blastn
[2023-03-15 21:33:19,446] [INFO] Running command: blastn -query OceanDNA-a2321/markers.fasta -db /var/lib/cwl/stg04a97af5-6718-4504-af39-882dce7a4412/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2321/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:33:19,870] [INFO] Task succeeded: Blastn
[2023-03-15 21:33:19,871] [INFO] Selected 8 target genomes.
[2023-03-15 21:33:19,871] [INFO] Target genome list was writen to OceanDNA-a2321/target_genomes_gtdb.txt
[2023-03-15 21:33:20,164] [INFO] Task started: fastANI
[2023-03-15 21:33:20,164] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0af83af-840a-4902-9b0a-b53fc337caae/OceanDNA-a2321.fa --refList OceanDNA-a2321/target_genomes_gtdb.txt --output OceanDNA-a2321/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:33:22,880] [INFO] Task succeeded: fastANI
[2023-03-15 21:33:22,885] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:33:22,885] [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_002727485.1	s__MGIIa-L1 sp002727485	98.6699	288	481	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002702945.1	s__MGIIa-L1 sp002702945	83.0584	388	481	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	98.55	98.53	0.86	0.86	3	-
GCA_002729095.1	s__MGIIa-L1 sp002729095	80.8292	324	481	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	98.94	98.73	0.83	0.79	6	-
GCA_003602575.1	s__MGIIa-L1 sp003602575	78.7326	240	481	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002172355.2	s__MGIIa-L1 sp002172355	78.4653	173	481	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.37	98.74	0.95	0.91	3	-
GCA_002726395.1	s__MGIIa-L1 sp002726395	76.5771	63	481	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.39	99.39	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-03-15 21:33:22,885] [INFO] GTDB search result was written to OceanDNA-a2321/result_gtdb.tsv
[2023-03-15 21:33:22,885] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:33:22,886] [INFO] DFAST_QC result json was written to OceanDNA-a2321/dqc_result.json
[2023-03-15 21:33:22,886] [INFO] DFAST_QC completed!
[2023-03-15 21:33:22,886] [INFO] Total running time: 0h0m42s