[2023-03-16 19:49:08,464] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:49:08,464] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:49:08,465] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e1887db-c839-4cf9-b782-392a43d6a210/dqc_reference
[2023-03-16 19:49:09,654] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:49:09,655] [INFO] Task started: Prodigal
[2023-03-16 19:49:09,655] [INFO] Running command: cat /var/lib/cwl/stg11d462ff-ebca-4927-8169-90f6e13abdb5/OceanDNA-b8315.fa | prodigal -d OceanDNA-b8315/cds.fna -a OceanDNA-b8315/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:49:15,046] [INFO] Task succeeded: Prodigal
[2023-03-16 19:49:15,046] [INFO] Task started: HMMsearch
[2023-03-16 19:49:15,046] [INFO] Running command: hmmsearch --tblout OceanDNA-b8315/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e1887db-c839-4cf9-b782-392a43d6a210/dqc_reference/reference_markers.hmm OceanDNA-b8315/protein.faa > /dev/null
[2023-03-16 19:49:15,224] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:49:15,225] [INFO] Found 6/6 markers.
[2023-03-16 19:49:15,234] [INFO] Query marker FASTA was written to OceanDNA-b8315/markers.fasta
[2023-03-16 19:49:15,235] [INFO] Task started: Blastn
[2023-03-16 19:49:15,235] [INFO] Running command: blastn -query OceanDNA-b8315/markers.fasta -db /var/lib/cwl/stg2e1887db-c839-4cf9-b782-392a43d6a210/dqc_reference/reference_markers.fasta -out OceanDNA-b8315/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:49:15,815] [INFO] Task succeeded: Blastn
[2023-03-16 19:49:15,816] [INFO] Selected 35 target genomes.
[2023-03-16 19:49:15,817] [INFO] Target genome list was writen to OceanDNA-b8315/target_genomes.txt
[2023-03-16 19:49:15,838] [INFO] Task started: fastANI
[2023-03-16 19:49:15,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg11d462ff-ebca-4927-8169-90f6e13abdb5/OceanDNA-b8315.fa --refList OceanDNA-b8315/target_genomes.txt --output OceanDNA-b8315/fastani_result.tsv --threads 1
[2023-03-16 19:49:33,866] [INFO] Task succeeded: fastANI
[2023-03-16 19:49:33,867] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e1887db-c839-4cf9-b782-392a43d6a210/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:49:33,867] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e1887db-c839-4cf9-b782-392a43d6a210/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:49:33,867] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 19:49:33,867] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 19:49:33,867] [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
--------------------------------------------------------------------------------
[2023-03-16 19:49:33,868] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8315/tc_result.tsv
[2023-03-16 19:49:33,868] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:49:33,868] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:49:33,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e1887db-c839-4cf9-b782-392a43d6a210/dqc_reference/checkm_data
[2023-03-16 19:49:33,871] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:49:33,873] [INFO] Task started: CheckM
[2023-03-16 19:49:33,874] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8315/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8315/checkm_input OceanDNA-b8315/checkm_result
[2023-03-16 19:49:53,123] [INFO] Task succeeded: CheckM
[2023-03-16 19:49:53,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 19:49:53,127] [INFO] ===== Completeness check finished =====
[2023-03-16 19:49:53,127] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:49:53,127] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8315/markers.fasta)
[2023-03-16 19:49:53,128] [INFO] Task started: Blastn
[2023-03-16 19:49:53,129] [INFO] Running command: blastn -query OceanDNA-b8315/markers.fasta -db /var/lib/cwl/stg2e1887db-c839-4cf9-b782-392a43d6a210/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8315/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:49:54,097] [INFO] Task succeeded: Blastn
[2023-03-16 19:49:54,098] [INFO] Selected 15 target genomes.
[2023-03-16 19:49:54,098] [INFO] Target genome list was writen to OceanDNA-b8315/target_genomes_gtdb.txt
[2023-03-16 19:49:54,110] [INFO] Task started: fastANI
[2023-03-16 19:49:54,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg11d462ff-ebca-4927-8169-90f6e13abdb5/OceanDNA-b8315.fa --refList OceanDNA-b8315/target_genomes_gtdb.txt --output OceanDNA-b8315/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:49:57,618] [INFO] Task succeeded: fastANI
[2023-03-16 19:49:57,626] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 19:49:57,626] [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_004213645.1	s__MED-G11 sp004213645	99.3232	265	307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.96	97.96	0.74	0.74	2	conclusive
GCA_002457075.1	s__MED-G11 sp002457075	80.6636	165	307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	98.35	98.35	0.79	0.79	2	-
GCA_004214015.1	s__MED-G11 sp004214015	80.5661	145	307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.90	97.77	0.83	0.80	4	-
GCA_014239665.1	s__MED-G11 sp014239665	80.561	194	307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.49	96.27	0.81	0.77	10	-
GCA_902516925.1	s__MED-G11 sp902516925	80.2298	156	307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016777325.1	s__MED-G11 sp016777325	80.1406	142	307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902593165.1	s__MED-G11 sp902593165	80.0356	192	307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.69	96.69	0.86	0.86	2	-
GCA_902519955.1	s__MED-G11 sp902519955	79.8864	171	307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.88	99.84	0.80	0.74	3	-
GCA_018646865.1	s__MED-G11 sp014239615	79.7195	204	307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.76	99.49	0.92	0.80	17	-
GCA_902509805.1	s__MED-G11 sp902509805	79.679	106	307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.79	97.79	0.58	0.58	2	-
GCA_902514615.1	s__MED-G11 sp902514615	79.6264	160	307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902523665.1	s__MED-G11 sp902523665	79.4575	159	307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622595.1	s__MED-G11 sp902622595	79.2244	193	307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.81	96.16	0.93	0.91	12	-
--------------------------------------------------------------------------------
[2023-03-16 19:49:57,627] [INFO] GTDB search result was written to OceanDNA-b8315/result_gtdb.tsv
[2023-03-16 19:49:57,628] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:49:57,629] [INFO] DFAST_QC result json was written to OceanDNA-b8315/dqc_result.json
[2023-03-16 19:49:57,629] [INFO] DFAST_QC completed!
[2023-03-16 19:49:57,629] [INFO] Total running time: 0h0m49s