[2023-03-16 04:38:30,085] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:38:30,085] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:38:30,085] [INFO] DQC Reference Directory: /var/lib/cwl/stg74cd5bb2-e924-458b-aa09-9bce175ead22/dqc_reference
[2023-03-16 04:38:31,197] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:38:31,197] [INFO] Task started: Prodigal
[2023-03-16 04:38:31,198] [INFO] Running command: cat /var/lib/cwl/stg21e2cef5-78ab-4768-958c-7fb6329998c9/OceanDNA-b34087.fa | prodigal -d OceanDNA-b34087/cds.fna -a OceanDNA-b34087/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:38:37,764] [INFO] Task succeeded: Prodigal
[2023-03-16 04:38:37,764] [INFO] Task started: HMMsearch
[2023-03-16 04:38:37,764] [INFO] Running command: hmmsearch --tblout OceanDNA-b34087/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74cd5bb2-e924-458b-aa09-9bce175ead22/dqc_reference/reference_markers.hmm OceanDNA-b34087/protein.faa > /dev/null
[2023-03-16 04:38:37,914] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:38:37,915] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg21e2cef5-78ab-4768-958c-7fb6329998c9/OceanDNA-b34087.fa]
[2023-03-16 04:38:37,929] [INFO] Query marker FASTA was written to OceanDNA-b34087/markers.fasta
[2023-03-16 04:38:37,930] [INFO] Task started: Blastn
[2023-03-16 04:38:37,930] [INFO] Running command: blastn -query OceanDNA-b34087/markers.fasta -db /var/lib/cwl/stg74cd5bb2-e924-458b-aa09-9bce175ead22/dqc_reference/reference_markers.fasta -out OceanDNA-b34087/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:38:38,373] [INFO] Task succeeded: Blastn
[2023-03-16 04:38:38,374] [INFO] Selected 23 target genomes.
[2023-03-16 04:38:38,374] [INFO] Target genome list was writen to OceanDNA-b34087/target_genomes.txt
[2023-03-16 04:38:38,388] [INFO] Task started: fastANI
[2023-03-16 04:38:38,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg21e2cef5-78ab-4768-958c-7fb6329998c9/OceanDNA-b34087.fa --refList OceanDNA-b34087/target_genomes.txt --output OceanDNA-b34087/fastani_result.tsv --threads 1
[2023-03-16 04:38:49,579] [INFO] Task succeeded: fastANI
[2023-03-16 04:38:49,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74cd5bb2-e924-458b-aa09-9bce175ead22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:38:49,580] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74cd5bb2-e924-458b-aa09-9bce175ead22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:38:49,580] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:38:49,580] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:38:49,580] [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
--------------------------------------------------------------------------------
[2023-03-16 04:38:49,580] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34087/tc_result.tsv
[2023-03-16 04:38:49,580] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:38:49,581] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:38:49,581] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74cd5bb2-e924-458b-aa09-9bce175ead22/dqc_reference/checkm_data
[2023-03-16 04:38:49,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:38:49,587] [INFO] Task started: CheckM
[2023-03-16 04:38:49,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34087/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34087/checkm_input OceanDNA-b34087/checkm_result
[2023-03-16 04:39:11,733] [INFO] Task succeeded: CheckM
[2023-03-16 04:39:11,733] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.40%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:39:11,735] [INFO] ===== Completeness check finished =====
[2023-03-16 04:39:11,735] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:39:11,735] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34087/markers.fasta)
[2023-03-16 04:39:11,738] [INFO] Task started: Blastn
[2023-03-16 04:39:11,738] [INFO] Running command: blastn -query OceanDNA-b34087/markers.fasta -db /var/lib/cwl/stg74cd5bb2-e924-458b-aa09-9bce175ead22/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34087/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:39:12,203] [INFO] Task succeeded: Blastn
[2023-03-16 04:39:12,204] [INFO] Selected 22 target genomes.
[2023-03-16 04:39:12,204] [INFO] Target genome list was writen to OceanDNA-b34087/target_genomes_gtdb.txt
[2023-03-16 04:39:12,219] [INFO] Task started: fastANI
[2023-03-16 04:39:12,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg21e2cef5-78ab-4768-958c-7fb6329998c9/OceanDNA-b34087.fa --refList OceanDNA-b34087/target_genomes_gtdb.txt --output OceanDNA-b34087/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:39:20,157] [INFO] Task succeeded: fastANI
[2023-03-16 04:39:20,161] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:39:20,161] [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_017857755.1	s__GCA-2401735 sp017857755	77.6602	64	338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__GCA-2401735	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006844635.1	s__GCA-2401735 sp006844635	77.5778	62	338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__GCA-2401735	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401735.1	s__GCA-2401735 sp002401735	77.5714	75	338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__GCA-2401735	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018398995.1	s__GCA-2401735 sp018398995	77.374	87	338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__GCA-2401735	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:39:20,161] [INFO] GTDB search result was written to OceanDNA-b34087/result_gtdb.tsv
[2023-03-16 04:39:20,161] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:39:20,162] [INFO] DFAST_QC result json was written to OceanDNA-b34087/dqc_result.json
[2023-03-16 04:39:20,162] [INFO] DFAST_QC completed!
[2023-03-16 04:39:20,162] [INFO] Total running time: 0h0m50s