[2023-03-15 23:09:36,592] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:09:36,592] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:09:36,592] [INFO] DQC Reference Directory: /var/lib/cwl/stg01b2dece-1464-4f48-8b2f-b6d86e80dc24/dqc_reference
[2023-03-15 23:09:37,728] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:09:37,728] [INFO] Task started: Prodigal
[2023-03-15 23:09:37,728] [INFO] Running command: cat /var/lib/cwl/stg3ed8e2a8-dbb6-4b8c-b267-4aa3dd844838/OceanDNA-b5102.fa | prodigal -d OceanDNA-b5102/cds.fna -a OceanDNA-b5102/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:09:41,902] [INFO] Task succeeded: Prodigal
[2023-03-15 23:09:41,902] [INFO] Task started: HMMsearch
[2023-03-15 23:09:41,902] [INFO] Running command: hmmsearch --tblout OceanDNA-b5102/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01b2dece-1464-4f48-8b2f-b6d86e80dc24/dqc_reference/reference_markers.hmm OceanDNA-b5102/protein.faa > /dev/null
[2023-03-15 23:09:42,064] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:09:42,065] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg3ed8e2a8-dbb6-4b8c-b267-4aa3dd844838/OceanDNA-b5102.fa]
[2023-03-15 23:09:42,072] [INFO] Query marker FASTA was written to OceanDNA-b5102/markers.fasta
[2023-03-15 23:09:42,073] [INFO] Task started: Blastn
[2023-03-15 23:09:42,074] [INFO] Running command: blastn -query OceanDNA-b5102/markers.fasta -db /var/lib/cwl/stg01b2dece-1464-4f48-8b2f-b6d86e80dc24/dqc_reference/reference_markers.fasta -out OceanDNA-b5102/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:09:42,714] [INFO] Task succeeded: Blastn
[2023-03-15 23:09:42,724] [INFO] Selected 16 target genomes.
[2023-03-15 23:09:42,724] [INFO] Target genome list was writen to OceanDNA-b5102/target_genomes.txt
[2023-03-15 23:09:42,731] [INFO] Task started: fastANI
[2023-03-15 23:09:42,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ed8e2a8-dbb6-4b8c-b267-4aa3dd844838/OceanDNA-b5102.fa --refList OceanDNA-b5102/target_genomes.txt --output OceanDNA-b5102/fastani_result.tsv --threads 1
[2023-03-15 23:09:50,715] [INFO] Task succeeded: fastANI
[2023-03-15 23:09:50,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01b2dece-1464-4f48-8b2f-b6d86e80dc24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:09:50,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01b2dece-1464-4f48-8b2f-b6d86e80dc24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:09:50,715] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:09:50,715] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:09:50,715] [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 23:09:50,716] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5102/tc_result.tsv
[2023-03-15 23:09:50,716] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:09:50,716] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:09:50,716] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01b2dece-1464-4f48-8b2f-b6d86e80dc24/dqc_reference/checkm_data
[2023-03-15 23:09:50,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:09:50,722] [INFO] Task started: CheckM
[2023-03-15 23:09:50,722] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5102/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5102/checkm_input OceanDNA-b5102/checkm_result
[2023-03-15 23:10:07,479] [INFO] Task succeeded: CheckM
[2023-03-15 23:10:07,480] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.69%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:10:07,483] [INFO] ===== Completeness check finished =====
[2023-03-15 23:10:07,483] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:10:07,484] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5102/markers.fasta)
[2023-03-15 23:10:07,484] [INFO] Task started: Blastn
[2023-03-15 23:10:07,484] [INFO] Running command: blastn -query OceanDNA-b5102/markers.fasta -db /var/lib/cwl/stg01b2dece-1464-4f48-8b2f-b6d86e80dc24/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5102/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:10:07,933] [INFO] Task succeeded: Blastn
[2023-03-15 23:10:07,934] [INFO] Selected 11 target genomes.
[2023-03-15 23:10:07,935] [INFO] Target genome list was writen to OceanDNA-b5102/target_genomes_gtdb.txt
[2023-03-15 23:10:07,990] [INFO] Task started: fastANI
[2023-03-15 23:10:07,990] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ed8e2a8-dbb6-4b8c-b267-4aa3dd844838/OceanDNA-b5102.fa --refList OceanDNA-b5102/target_genomes_gtdb.txt --output OceanDNA-b5102/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:10:10,590] [INFO] Task succeeded: fastANI
[2023-03-15 23:10:10,595] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:10:10,595] [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_018664745.1	s__UWMA-0277 sp018664745	83.8337	97	149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384505.1	s__UWMA-0277 sp014384505	82.2721	100	149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960805.1	s__UWMA-0277 sp012960805	82.0437	93	149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018645865.1	s__UWMA-0277 sp018645865	81.2955	98	149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	99.24	99.14	0.74	0.70	3	-
GCA_905612305.1	s__UWMA-0277 sp905612305	80.6661	79	149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478185.1	s__UWMA-0277 sp905478185	80.5299	90	149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	96.67	96.67	0.88	0.88	2	-
GCA_905478765.1	s__UWMA-0277 sp905478765	80.0359	79	149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479165.1	s__UWMA-0277 sp905479165	79.7425	77	149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:10:10,596] [INFO] GTDB search result was written to OceanDNA-b5102/result_gtdb.tsv
[2023-03-15 23:10:10,596] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:10:10,597] [INFO] DFAST_QC result json was written to OceanDNA-b5102/dqc_result.json
[2023-03-15 23:10:10,597] [INFO] DFAST_QC completed!
[2023-03-15 23:10:10,597] [INFO] Total running time: 0h0m34s