[2023-03-19 04:29:38,147] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:38,147] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:38,147] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc1f6ce9-7d7e-482d-91ed-4b3359cb4419/dqc_reference
[2023-03-19 04:29:39,832] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:39,833] [INFO] Task started: Prodigal
[2023-03-19 04:29:39,833] [INFO] Running command: cat /var/lib/cwl/stg39df8cac-eb7a-41b9-b0bb-f26cb2e32c4a/OceanDNA-b886.fa | prodigal -d OceanDNA-b886/cds.fna -a OceanDNA-b886/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:29:47,682] [INFO] Task succeeded: Prodigal
[2023-03-19 04:29:47,682] [INFO] Task started: HMMsearch
[2023-03-19 04:29:47,682] [INFO] Running command: hmmsearch --tblout OceanDNA-b886/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc1f6ce9-7d7e-482d-91ed-4b3359cb4419/dqc_reference/reference_markers.hmm OceanDNA-b886/protein.faa > /dev/null
[2023-03-19 04:29:47,854] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:29:47,854] [INFO] Found 6/6 markers.
[2023-03-19 04:29:47,866] [INFO] Query marker FASTA was written to OceanDNA-b886/markers.fasta
[2023-03-19 04:29:47,867] [INFO] Task started: Blastn
[2023-03-19 04:29:47,867] [INFO] Running command: blastn -query OceanDNA-b886/markers.fasta -db /var/lib/cwl/stgfc1f6ce9-7d7e-482d-91ed-4b3359cb4419/dqc_reference/reference_markers.fasta -out OceanDNA-b886/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:29:48,380] [INFO] Task succeeded: Blastn
[2023-03-19 04:29:48,381] [INFO] Selected 21 target genomes.
[2023-03-19 04:29:48,381] [INFO] Target genome list was writen to OceanDNA-b886/target_genomes.txt
[2023-03-19 04:29:48,392] [INFO] Task started: fastANI
[2023-03-19 04:29:48,393] [INFO] Running command: fastANI --query /var/lib/cwl/stg39df8cac-eb7a-41b9-b0bb-f26cb2e32c4a/OceanDNA-b886.fa --refList OceanDNA-b886/target_genomes.txt --output OceanDNA-b886/fastani_result.tsv --threads 1
[2023-03-19 04:29:56,666] [INFO] Task succeeded: fastANI
[2023-03-19 04:29:56,666] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc1f6ce9-7d7e-482d-91ed-4b3359cb4419/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:29:56,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc1f6ce9-7d7e-482d-91ed-4b3359cb4419/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:29:56,667] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:29:56,667] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:29:56,667] [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
--------------------------------------------------------------------------------
[2023-03-19 04:29:56,667] [INFO] DFAST Taxonomy check result was written to OceanDNA-b886/tc_result.tsv
[2023-03-19 04:29:56,667] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:29:56,667] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:29:56,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc1f6ce9-7d7e-482d-91ed-4b3359cb4419/dqc_reference/checkm_data
[2023-03-19 04:29:56,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:29:56,673] [INFO] Task started: CheckM
[2023-03-19 04:29:56,673] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b886/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b886/checkm_input OceanDNA-b886/checkm_result
[2023-03-19 04:30:21,578] [INFO] Task succeeded: CheckM
[2023-03-19 04:30:21,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 2.81%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 04:30:21,580] [INFO] ===== Completeness check finished =====
[2023-03-19 04:30:21,581] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:30:21,581] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b886/markers.fasta)
[2023-03-19 04:30:21,581] [INFO] Task started: Blastn
[2023-03-19 04:30:21,581] [INFO] Running command: blastn -query OceanDNA-b886/markers.fasta -db /var/lib/cwl/stgfc1f6ce9-7d7e-482d-91ed-4b3359cb4419/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b886/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:22,343] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:22,344] [INFO] Selected 28 target genomes.
[2023-03-19 04:30:22,344] [INFO] Target genome list was writen to OceanDNA-b886/target_genomes_gtdb.txt
[2023-03-19 04:30:22,397] [INFO] Task started: fastANI
[2023-03-19 04:30:22,397] [INFO] Running command: fastANI --query /var/lib/cwl/stg39df8cac-eb7a-41b9-b0bb-f26cb2e32c4a/OceanDNA-b886.fa --refList OceanDNA-b886/target_genomes_gtdb.txt --output OceanDNA-b886/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:30:30,964] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:30,966] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:30:30,966] [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_000817115.1	s__MedAcidi-G2B sp000817115	92.5287	346	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G2B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902634555.1	s__MedAcidi-G2B sp902634555	91.8203	285	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G2B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:30:30,967] [INFO] GTDB search result was written to OceanDNA-b886/result_gtdb.tsv
[2023-03-19 04:30:30,967] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:30:30,967] [INFO] DFAST_QC result json was written to OceanDNA-b886/dqc_result.json
[2023-03-19 04:30:30,967] [INFO] DFAST_QC completed!
[2023-03-19 04:30:30,967] [INFO] Total running time: 0h0m53s