[2023-03-16 11:12:36,965] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:12:36,965] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:12:36,965] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a5f27f1-cab5-4cb4-a5dc-c61e355199a6/dqc_reference
[2023-03-16 11:12:38,202] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:12:38,203] [INFO] Task started: Prodigal
[2023-03-16 11:12:38,203] [INFO] Running command: cat /var/lib/cwl/stge5976e58-dd67-49ad-bf83-66029b50ef86/OceanDNA-b9096.fa | prodigal -d OceanDNA-b9096/cds.fna -a OceanDNA-b9096/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:12:47,756] [INFO] Task succeeded: Prodigal
[2023-03-16 11:12:47,757] [INFO] Task started: HMMsearch
[2023-03-16 11:12:47,757] [INFO] Running command: hmmsearch --tblout OceanDNA-b9096/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a5f27f1-cab5-4cb4-a5dc-c61e355199a6/dqc_reference/reference_markers.hmm OceanDNA-b9096/protein.faa > /dev/null
[2023-03-16 11:12:48,002] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:12:48,002] [INFO] Found 6/6 markers.
[2023-03-16 11:12:48,020] [INFO] Query marker FASTA was written to OceanDNA-b9096/markers.fasta
[2023-03-16 11:12:48,022] [INFO] Task started: Blastn
[2023-03-16 11:12:48,022] [INFO] Running command: blastn -query OceanDNA-b9096/markers.fasta -db /var/lib/cwl/stg1a5f27f1-cab5-4cb4-a5dc-c61e355199a6/dqc_reference/reference_markers.fasta -out OceanDNA-b9096/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:12:49,049] [INFO] Task succeeded: Blastn
[2023-03-16 11:12:49,050] [INFO] Selected 31 target genomes.
[2023-03-16 11:12:49,050] [INFO] Target genome list was writen to OceanDNA-b9096/target_genomes.txt
[2023-03-16 11:12:49,065] [INFO] Task started: fastANI
[2023-03-16 11:12:49,065] [INFO] Running command: fastANI --query /var/lib/cwl/stge5976e58-dd67-49ad-bf83-66029b50ef86/OceanDNA-b9096.fa --refList OceanDNA-b9096/target_genomes.txt --output OceanDNA-b9096/fastani_result.tsv --threads 1
[2023-03-16 11:13:13,612] [INFO] Task succeeded: fastANI
[2023-03-16 11:13:13,613] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a5f27f1-cab5-4cb4-a5dc-c61e355199a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 11:13:13,613] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a5f27f1-cab5-4cb4-a5dc-c61e355199a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 11:13:13,613] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 11:13:13,613] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 11:13:13,613] [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 11:13:13,613] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9096/tc_result.tsv
[2023-03-16 11:13:13,613] [INFO] ===== Taxonomy check completed =====
[2023-03-16 11:13:13,613] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:13:13,614] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a5f27f1-cab5-4cb4-a5dc-c61e355199a6/dqc_reference/checkm_data
[2023-03-16 11:13:13,617] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:13:13,645] [INFO] Task started: CheckM
[2023-03-16 11:13:13,645] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9096/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9096/checkm_input OceanDNA-b9096/checkm_result
[2023-03-16 11:13:42,783] [INFO] Task succeeded: CheckM
[2023-03-16 11:13:42,784] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 11:13:42,786] [INFO] ===== Completeness check finished =====
[2023-03-16 11:13:42,786] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:13:42,787] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9096/markers.fasta)
[2023-03-16 11:13:42,788] [INFO] Task started: Blastn
[2023-03-16 11:13:42,788] [INFO] Running command: blastn -query OceanDNA-b9096/markers.fasta -db /var/lib/cwl/stg1a5f27f1-cab5-4cb4-a5dc-c61e355199a6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9096/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:13:43,718] [INFO] Task succeeded: Blastn
[2023-03-16 11:13:43,719] [INFO] Selected 19 target genomes.
[2023-03-16 11:13:43,719] [INFO] Target genome list was writen to OceanDNA-b9096/target_genomes_gtdb.txt
[2023-03-16 11:13:43,835] [INFO] Task started: fastANI
[2023-03-16 11:13:43,836] [INFO] Running command: fastANI --query /var/lib/cwl/stge5976e58-dd67-49ad-bf83-66029b50ef86/OceanDNA-b9096.fa --refList OceanDNA-b9096/target_genomes_gtdb.txt --output OceanDNA-b9096/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:13:51,189] [INFO] Task succeeded: fastANI
[2023-03-16 11:13:51,197] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 11:13:51,197] [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_902512755.1	s__MS024-2A sp902512755	83.1019	243	505	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_902517245.1	s__MS024-2A sp902517245	80.0813	248	505	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_902606525.1	s__MS024-2A sp902606525	79.7818	188	505	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	77.9241	146	505	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_905182305.1	s__MS024-2A sp905182305	77.4056	124	505	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_009886625.1	s__MS024-2A sp009886625	77.3113	107	505	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_000173095.1	s__MS024-2A sp000173095	77.0438	97	505	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_905181895.1	s__MS024-2A sp905181895	76.9596	74	505	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_017852075.1	s__MS024-2A sp017852075	76.8738	112	505	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_002714815.1	s__MS024-2A sp002714815	76.7416	161	505	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	76.5534	107	505	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_002167525.1	s__MS024-2A sp002167525	76.5484	93	505	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	98.89	98.89	0.72	0.72	2	-
GCA_902561795.1	s__MS024-2A sp902561795	76.5366	86	505	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_003130815.1	s__MS024-2A sp003130815	76.2603	108	505	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 11:13:51,197] [INFO] GTDB search result was written to OceanDNA-b9096/result_gtdb.tsv
[2023-03-16 11:13:51,197] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:13:51,198] [INFO] DFAST_QC result json was written to OceanDNA-b9096/dqc_result.json
[2023-03-16 11:13:51,199] [INFO] DFAST_QC completed!
[2023-03-16 11:13:51,199] [INFO] Total running time: 0h1m14s