[2023-03-15 07:29:11,758] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:29:11,759] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:29:11,759] [INFO] DQC Reference Directory: /var/lib/cwl/stg668f8979-7b65-4fc2-8ee1-e73684f0479e/dqc_reference
[2023-03-15 07:29:13,588] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:29:13,588] [INFO] Task started: Prodigal
[2023-03-15 07:29:13,588] [INFO] Running command: cat /var/lib/cwl/stg42be0101-f090-485e-8f4b-b3cee25f70e8/OceanDNA-b9182.fa | prodigal -d OceanDNA-b9182/cds.fna -a OceanDNA-b9182/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:29:25,373] [INFO] Task succeeded: Prodigal
[2023-03-15 07:29:25,374] [INFO] Task started: HMMsearch
[2023-03-15 07:29:25,374] [INFO] Running command: hmmsearch --tblout OceanDNA-b9182/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg668f8979-7b65-4fc2-8ee1-e73684f0479e/dqc_reference/reference_markers.hmm OceanDNA-b9182/protein.faa > /dev/null
[2023-03-15 07:29:25,574] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:29:25,575] [INFO] Found 6/6 markers.
[2023-03-15 07:29:25,588] [INFO] Query marker FASTA was written to OceanDNA-b9182/markers.fasta
[2023-03-15 07:29:25,588] [INFO] Task started: Blastn
[2023-03-15 07:29:25,589] [INFO] Running command: blastn -query OceanDNA-b9182/markers.fasta -db /var/lib/cwl/stg668f8979-7b65-4fc2-8ee1-e73684f0479e/dqc_reference/reference_markers.fasta -out OceanDNA-b9182/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:29:26,180] [INFO] Task succeeded: Blastn
[2023-03-15 07:29:26,181] [INFO] Selected 33 target genomes.
[2023-03-15 07:29:26,182] [INFO] Target genome list was writen to OceanDNA-b9182/target_genomes.txt
[2023-03-15 07:29:26,203] [INFO] Task started: fastANI
[2023-03-15 07:29:26,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg42be0101-f090-485e-8f4b-b3cee25f70e8/OceanDNA-b9182.fa --refList OceanDNA-b9182/target_genomes.txt --output OceanDNA-b9182/fastani_result.tsv --threads 1
[2023-03-15 07:29:44,967] [INFO] Task succeeded: fastANI
[2023-03-15 07:29:44,967] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg668f8979-7b65-4fc2-8ee1-e73684f0479e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:29:44,968] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg668f8979-7b65-4fc2-8ee1-e73684f0479e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:29:44,968] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:29:44,968] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:29:44,968] [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 07:29:44,968] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9182/tc_result.tsv
[2023-03-15 07:29:44,968] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:29:44,968] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:29:44,968] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg668f8979-7b65-4fc2-8ee1-e73684f0479e/dqc_reference/checkm_data
[2023-03-15 07:29:44,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:29:44,974] [INFO] Task started: CheckM
[2023-03-15 07:29:44,974] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9182/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9182/checkm_input OceanDNA-b9182/checkm_result
[2023-03-15 07:30:18,794] [INFO] Task succeeded: CheckM
[2023-03-15 07:30:18,794] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:30:18,796] [INFO] ===== Completeness check finished =====
[2023-03-15 07:30:18,796] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:30:18,796] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9182/markers.fasta)
[2023-03-15 07:30:18,797] [INFO] Task started: Blastn
[2023-03-15 07:30:18,797] [INFO] Running command: blastn -query OceanDNA-b9182/markers.fasta -db /var/lib/cwl/stg668f8979-7b65-4fc2-8ee1-e73684f0479e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9182/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:30:19,552] [INFO] Task succeeded: Blastn
[2023-03-15 07:30:19,553] [INFO] Selected 24 target genomes.
[2023-03-15 07:30:19,553] [INFO] Target genome list was writen to OceanDNA-b9182/target_genomes_gtdb.txt
[2023-03-15 07:30:19,569] [INFO] Task started: fastANI
[2023-03-15 07:30:19,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg42be0101-f090-485e-8f4b-b3cee25f70e8/OceanDNA-b9182.fa --refList OceanDNA-b9182/target_genomes_gtdb.txt --output OceanDNA-b9182/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:30:28,450] [INFO] Task succeeded: fastANI
[2023-03-15 07:30:28,459] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:30:28,459] [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_011525195.1	s__MS024-2A sp011525195	96.7529	457	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902546725.1	s__MS024-2A sp902546725	78.2271	179	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167945.1	s__MS024-2A sp002167945	77.934	182	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017851655.1	s__MS024-2A sp017851655	77.4186	144	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.55	99.53	0.87	0.86	3	-
GCA_000173095.1	s__MS024-2A sp000173095	77.0683	116	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.61	99.48	0.88	0.84	16	-
GCA_009886625.1	s__MS024-2A sp009886625	77.0586	118	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292265.1	s__MS024-2A sp002292265	76.9312	118	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.71	99.21	0.94	0.92	6	-
GCA_008081175.1	s__MS024-2A sp008081175	76.8713	74	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.02	98.61	0.90	0.80	6	-
GCA_017852075.1	s__MS024-2A sp017852075	76.8578	125	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.70	99.69	0.95	0.94	3	-
GCA_002705385.1	s__MS024-2A sp002705385	76.7885	98	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182305.1	s__MS024-2A sp905182305	76.5652	106	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480425.1	s__MS024-2A sp905480425	76.5444	96	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	95.11	95.11	0.87	0.87	2	-
GCA_902561795.1	s__MS024-2A sp902561795	75.981	52	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902613595.1	s__MS024-2A sp902613595	75.9543	61	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:30:28,459] [INFO] GTDB search result was written to OceanDNA-b9182/result_gtdb.tsv
[2023-03-15 07:30:28,459] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:30:28,460] [INFO] DFAST_QC result json was written to OceanDNA-b9182/dqc_result.json
[2023-03-15 07:30:28,461] [INFO] DFAST_QC completed!
[2023-03-15 07:30:28,461] [INFO] Total running time: 0h1m17s