[2023-03-18 01:35:16,924] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:35:16,925] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:35:16,925] [INFO] DQC Reference Directory: /var/lib/cwl/stg36df4c80-1517-4f6b-b2e6-d6e456e79cf5/dqc_reference
[2023-03-18 01:35:18,357] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:35:18,358] [INFO] Task started: Prodigal
[2023-03-18 01:35:18,358] [INFO] Running command: cat /var/lib/cwl/stg53cc4191-4a69-42a4-a6d6-af61745e9fd0/OceanDNA-b42446.fa | prodigal -d OceanDNA-b42446/cds.fna -a OceanDNA-b42446/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:35:24,419] [INFO] Task succeeded: Prodigal
[2023-03-18 01:35:24,419] [INFO] Task started: HMMsearch
[2023-03-18 01:35:24,419] [INFO] Running command: hmmsearch --tblout OceanDNA-b42446/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36df4c80-1517-4f6b-b2e6-d6e456e79cf5/dqc_reference/reference_markers.hmm OceanDNA-b42446/protein.faa > /dev/null
[2023-03-18 01:35:24,584] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:35:24,584] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg53cc4191-4a69-42a4-a6d6-af61745e9fd0/OceanDNA-b42446.fa]
[2023-03-18 01:35:24,596] [INFO] Query marker FASTA was written to OceanDNA-b42446/markers.fasta
[2023-03-18 01:35:24,597] [INFO] Task started: Blastn
[2023-03-18 01:35:24,598] [INFO] Running command: blastn -query OceanDNA-b42446/markers.fasta -db /var/lib/cwl/stg36df4c80-1517-4f6b-b2e6-d6e456e79cf5/dqc_reference/reference_markers.fasta -out OceanDNA-b42446/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:35:26,018] [INFO] Task succeeded: Blastn
[2023-03-18 01:35:26,019] [INFO] Selected 21 target genomes.
[2023-03-18 01:35:26,020] [INFO] Target genome list was writen to OceanDNA-b42446/target_genomes.txt
[2023-03-18 01:35:26,038] [INFO] Task started: fastANI
[2023-03-18 01:35:26,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg53cc4191-4a69-42a4-a6d6-af61745e9fd0/OceanDNA-b42446.fa --refList OceanDNA-b42446/target_genomes.txt --output OceanDNA-b42446/fastani_result.tsv --threads 1
[2023-03-18 01:35:36,689] [INFO] Task succeeded: fastANI
[2023-03-18 01:35:36,689] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36df4c80-1517-4f6b-b2e6-d6e456e79cf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:35:36,689] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36df4c80-1517-4f6b-b2e6-d6e456e79cf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:35:36,690] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:35:36,690] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:35:36,690] [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 01:35:36,690] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42446/tc_result.tsv
[2023-03-18 01:35:36,690] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:35:36,690] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:35:36,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36df4c80-1517-4f6b-b2e6-d6e456e79cf5/dqc_reference/checkm_data
[2023-03-18 01:35:36,694] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:35:36,870] [INFO] Task started: CheckM
[2023-03-18 01:35:36,870] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42446/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42446/checkm_input OceanDNA-b42446/checkm_result
[2023-03-18 01:35:57,833] [INFO] Task succeeded: CheckM
[2023-03-18 01:35:57,834] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.15%
Contamintation: 0.93%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 01:35:57,889] [INFO] ===== Completeness check finished =====
[2023-03-18 01:35:57,889] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:35:57,889] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42446/markers.fasta)
[2023-03-18 01:35:57,890] [INFO] Task started: Blastn
[2023-03-18 01:35:57,890] [INFO] Running command: blastn -query OceanDNA-b42446/markers.fasta -db /var/lib/cwl/stg36df4c80-1517-4f6b-b2e6-d6e456e79cf5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42446/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:35:58,699] [INFO] Task succeeded: Blastn
[2023-03-18 01:35:58,703] [INFO] Selected 22 target genomes.
[2023-03-18 01:35:58,703] [INFO] Target genome list was writen to OceanDNA-b42446/target_genomes_gtdb.txt
[2023-03-18 01:35:58,748] [INFO] Task started: fastANI
[2023-03-18 01:35:58,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg53cc4191-4a69-42a4-a6d6-af61745e9fd0/OceanDNA-b42446.fa --refList OceanDNA-b42446/target_genomes_gtdb.txt --output OceanDNA-b42446/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:36:04,210] [INFO] Task succeeded: fastANI
[2023-03-18 01:36:04,214] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:36:04,214] [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_905182235.1	s__CAJJAM01 sp905182235	99.4012	274	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__CAJJAM01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015660645.1	s__CAJJAM01 sp015660645	80.3582	233	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__CAJJAM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003212335.1	s__GCA-2707915 sp003212335	76.3007	53	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	96.12	95.05	0.82	0.77	11	-
--------------------------------------------------------------------------------
[2023-03-18 01:36:04,215] [INFO] GTDB search result was written to OceanDNA-b42446/result_gtdb.tsv
[2023-03-18 01:36:04,215] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:36:04,217] [INFO] DFAST_QC result json was written to OceanDNA-b42446/dqc_result.json
[2023-03-18 01:36:04,217] [INFO] DFAST_QC completed!
[2023-03-18 01:36:04,217] [INFO] Total running time: 0h0m47s