[2023-03-15 13:00:04,932] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:00:04,932] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:00:04,932] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a63235c-076b-49f4-98e9-9f7c3d6acf6f/dqc_reference
[2023-03-15 13:00:06,090] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:00:06,091] [INFO] Task started: Prodigal
[2023-03-15 13:00:06,091] [INFO] Running command: cat /var/lib/cwl/stg31888534-7ec3-47b3-9525-eb42e8537d9a/OceanDNA-b25087.fa | prodigal -d OceanDNA-b25087/cds.fna -a OceanDNA-b25087/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:00:14,920] [INFO] Task succeeded: Prodigal
[2023-03-15 13:00:14,920] [INFO] Task started: HMMsearch
[2023-03-15 13:00:14,920] [INFO] Running command: hmmsearch --tblout OceanDNA-b25087/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a63235c-076b-49f4-98e9-9f7c3d6acf6f/dqc_reference/reference_markers.hmm OceanDNA-b25087/protein.faa > /dev/null
[2023-03-15 13:00:15,074] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:00:15,075] [INFO] Found 6/6 markers.
[2023-03-15 13:00:15,087] [INFO] Query marker FASTA was written to OceanDNA-b25087/markers.fasta
[2023-03-15 13:00:15,087] [INFO] Task started: Blastn
[2023-03-15 13:00:15,087] [INFO] Running command: blastn -query OceanDNA-b25087/markers.fasta -db /var/lib/cwl/stg5a63235c-076b-49f4-98e9-9f7c3d6acf6f/dqc_reference/reference_markers.fasta -out OceanDNA-b25087/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:00:15,665] [INFO] Task succeeded: Blastn
[2023-03-15 13:00:15,666] [INFO] Selected 37 target genomes.
[2023-03-15 13:00:15,666] [INFO] Target genome list was writen to OceanDNA-b25087/target_genomes.txt
[2023-03-15 13:00:15,685] [INFO] Task started: fastANI
[2023-03-15 13:00:15,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg31888534-7ec3-47b3-9525-eb42e8537d9a/OceanDNA-b25087.fa --refList OceanDNA-b25087/target_genomes.txt --output OceanDNA-b25087/fastani_result.tsv --threads 1
[2023-03-15 13:00:40,271] [INFO] Task succeeded: fastANI
[2023-03-15 13:00:40,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a63235c-076b-49f4-98e9-9f7c3d6acf6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:00:40,272] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a63235c-076b-49f4-98e9-9f7c3d6acf6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:00:40,272] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:00:40,272] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:00:40,272] [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 13:00:40,400] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25087/tc_result.tsv
[2023-03-15 13:00:40,400] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:00:40,400] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:00:40,400] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a63235c-076b-49f4-98e9-9f7c3d6acf6f/dqc_reference/checkm_data
[2023-03-15 13:00:40,403] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:00:40,475] [INFO] Task started: CheckM
[2023-03-15 13:00:40,476] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25087/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25087/checkm_input OceanDNA-b25087/checkm_result
[2023-03-15 13:01:08,056] [INFO] Task succeeded: CheckM
[2023-03-15 13:01:08,056] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.42%
Contamintation: 7.86%
Strain heterogeneity: 88.89%
--------------------------------------------------------------------------------
[2023-03-15 13:01:08,059] [INFO] ===== Completeness check finished =====
[2023-03-15 13:01:08,059] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:01:08,059] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25087/markers.fasta)
[2023-03-15 13:01:08,060] [INFO] Task started: Blastn
[2023-03-15 13:01:08,060] [INFO] Running command: blastn -query OceanDNA-b25087/markers.fasta -db /var/lib/cwl/stg5a63235c-076b-49f4-98e9-9f7c3d6acf6f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25087/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:01:09,009] [INFO] Task succeeded: Blastn
[2023-03-15 13:01:09,010] [INFO] Selected 14 target genomes.
[2023-03-15 13:01:09,010] [INFO] Target genome list was writen to OceanDNA-b25087/target_genomes_gtdb.txt
[2023-03-15 13:01:09,122] [INFO] Task started: fastANI
[2023-03-15 13:01:09,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg31888534-7ec3-47b3-9525-eb42e8537d9a/OceanDNA-b25087.fa --refList OceanDNA-b25087/target_genomes_gtdb.txt --output OceanDNA-b25087/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:01:14,940] [INFO] Task succeeded: fastANI
[2023-03-15 13:01:14,945] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:01:14,946] [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_002721725.1	s__UBA8337 sp002721725	91.9609	406	456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	99.29	99.29	0.93	0.93	2	-
GCA_009920875.1	s__UBA8337 sp009920875	86.5573	297	456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	97.55	97.55	0.89	0.89	2	-
GCA_900197605.1	s__UBA8337 sp900197605	80.5608	295	456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	96.88	95.59	0.86	0.84	6	-
GCA_016779015.1	s__UBA8337 sp016779015	79.9397	201	456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018660505.1	s__UBA8337 sp018660505	77.013	162	456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	99.75	99.71	0.96	0.95	3	-
GCA_002689195.1	s__UBA7378 sp002689195	76.8501	91	456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA7378	95.0	98.73	98.05	0.85	0.80	4	-
GCA_018673175.1	s__UBA8337 sp018673175	76.5772	146	456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902624095.1	s__UBA7378 sp902624095	76.0986	78	456	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA7378	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:01:14,946] [INFO] GTDB search result was written to OceanDNA-b25087/result_gtdb.tsv
[2023-03-15 13:01:14,946] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:01:14,947] [INFO] DFAST_QC result json was written to OceanDNA-b25087/dqc_result.json
[2023-03-15 13:01:14,947] [INFO] DFAST_QC completed!
[2023-03-15 13:01:14,947] [INFO] Total running time: 0h1m10s