[2023-03-15 18:20:15,201] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:20:15,201] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:20:15,202] [INFO] DQC Reference Directory: /var/lib/cwl/stgd20e5cee-cba4-4ff6-99c7-98ee8718db12/dqc_reference
[2023-03-15 18:20:16,845] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:20:16,845] [INFO] Task started: Prodigal
[2023-03-15 18:20:16,845] [INFO] Running command: cat /var/lib/cwl/stg35641eb2-3c6d-4f84-98e1-7baba42f81be/OceanDNA-b11780.fa | prodigal -d OceanDNA-b11780/cds.fna -a OceanDNA-b11780/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:20:38,102] [INFO] Task succeeded: Prodigal
[2023-03-15 18:20:38,102] [INFO] Task started: HMMsearch
[2023-03-15 18:20:38,102] [INFO] Running command: hmmsearch --tblout OceanDNA-b11780/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd20e5cee-cba4-4ff6-99c7-98ee8718db12/dqc_reference/reference_markers.hmm OceanDNA-b11780/protein.faa > /dev/null
[2023-03-15 18:20:38,278] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:20:38,279] [INFO] Found 6/6 markers.
[2023-03-15 18:20:38,292] [INFO] Query marker FASTA was written to OceanDNA-b11780/markers.fasta
[2023-03-15 18:20:38,292] [INFO] Task started: Blastn
[2023-03-15 18:20:38,292] [INFO] Running command: blastn -query OceanDNA-b11780/markers.fasta -db /var/lib/cwl/stgd20e5cee-cba4-4ff6-99c7-98ee8718db12/dqc_reference/reference_markers.fasta -out OceanDNA-b11780/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:20:38,807] [INFO] Task succeeded: Blastn
[2023-03-15 18:20:38,808] [INFO] Selected 26 target genomes.
[2023-03-15 18:20:38,808] [INFO] Target genome list was writen to OceanDNA-b11780/target_genomes.txt
[2023-03-15 18:20:39,036] [INFO] Task started: fastANI
[2023-03-15 18:20:39,036] [INFO] Running command: fastANI --query /var/lib/cwl/stg35641eb2-3c6d-4f84-98e1-7baba42f81be/OceanDNA-b11780.fa --refList OceanDNA-b11780/target_genomes.txt --output OceanDNA-b11780/fastani_result.tsv --threads 1
[2023-03-15 18:20:53,915] [INFO] Task succeeded: fastANI
[2023-03-15 18:20:53,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd20e5cee-cba4-4ff6-99c7-98ee8718db12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:20:53,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd20e5cee-cba4-4ff6-99c7-98ee8718db12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:20:53,916] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:20:53,916] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 18:20:53,916] [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 18:20:53,916] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11780/tc_result.tsv
[2023-03-15 18:20:53,916] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:20:53,917] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:20:53,917] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd20e5cee-cba4-4ff6-99c7-98ee8718db12/dqc_reference/checkm_data
[2023-03-15 18:20:53,920] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:20:53,923] [INFO] Task started: CheckM
[2023-03-15 18:20:53,923] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11780/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11780/checkm_input OceanDNA-b11780/checkm_result
[2023-03-15 18:21:50,625] [INFO] Task succeeded: CheckM
[2023-03-15 18:21:50,625] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:21:50,627] [INFO] ===== Completeness check finished =====
[2023-03-15 18:21:50,628] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:21:50,628] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11780/markers.fasta)
[2023-03-15 18:21:50,629] [INFO] Task started: Blastn
[2023-03-15 18:21:50,629] [INFO] Running command: blastn -query OceanDNA-b11780/markers.fasta -db /var/lib/cwl/stgd20e5cee-cba4-4ff6-99c7-98ee8718db12/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11780/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:21:51,329] [INFO] Task succeeded: Blastn
[2023-03-15 18:21:51,330] [INFO] Selected 22 target genomes.
[2023-03-15 18:21:51,331] [INFO] Target genome list was writen to OceanDNA-b11780/target_genomes_gtdb.txt
[2023-03-15 18:21:51,447] [INFO] Task started: fastANI
[2023-03-15 18:21:51,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg35641eb2-3c6d-4f84-98e1-7baba42f81be/OceanDNA-b11780.fa --refList OceanDNA-b11780/target_genomes_gtdb.txt --output OceanDNA-b11780/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:22:04,105] [INFO] Task succeeded: fastANI
[2023-03-15 18:22:04,110] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 18:22:04,110] [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_905478325.1	s__UA16 sp002390615	99.8812	719	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	99.70	99.69	0.88	0.83	4	conclusive
GCA_905479395.1	s__UA16 sp905479395	77.0497	89	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	98.40	98.40	0.84	0.84	2	-
GCA_002336085.1	s__UA16 sp002336085	76.9036	74	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479115.1	s__UA16 sp002390405	76.5444	87	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	99.82	99.82	0.92	0.92	2	-
GCA_002448555.1	s__UA16 sp002448555	76.4286	60	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	99.35	99.35	0.96	0.96	2	-
GCA_002477505.1	s__UA16 sp002477505	76.0834	74	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	99.58	99.42	0.88	0.80	7	-
--------------------------------------------------------------------------------
[2023-03-15 18:22:04,110] [INFO] GTDB search result was written to OceanDNA-b11780/result_gtdb.tsv
[2023-03-15 18:22:04,110] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:22:04,111] [INFO] DFAST_QC result json was written to OceanDNA-b11780/dqc_result.json
[2023-03-15 18:22:04,111] [INFO] DFAST_QC completed!
[2023-03-15 18:22:04,111] [INFO] Total running time: 0h1m49s