[2023-03-16 00:33:46,669] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:33:46,669] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:33:46,669] [INFO] DQC Reference Directory: /var/lib/cwl/stgbea19cc6-fb65-4b0a-ace0-57649d2568dc/dqc_reference
[2023-03-16 00:33:47,849] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:33:47,849] [INFO] Task started: Prodigal
[2023-03-16 00:33:47,850] [INFO] Running command: cat /var/lib/cwl/stg8f911aab-12c4-46a3-93f9-bf3ce9bc1386/OceanDNA-b9008.fa | prodigal -d OceanDNA-b9008/cds.fna -a OceanDNA-b9008/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:33:53,162] [INFO] Task succeeded: Prodigal
[2023-03-16 00:33:53,162] [INFO] Task started: HMMsearch
[2023-03-16 00:33:53,162] [INFO] Running command: hmmsearch --tblout OceanDNA-b9008/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbea19cc6-fb65-4b0a-ace0-57649d2568dc/dqc_reference/reference_markers.hmm OceanDNA-b9008/protein.faa > /dev/null
[2023-03-16 00:33:53,333] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:33:53,333] [INFO] Found 6/6 markers.
[2023-03-16 00:33:53,342] [INFO] Query marker FASTA was written to OceanDNA-b9008/markers.fasta
[2023-03-16 00:33:53,345] [INFO] Task started: Blastn
[2023-03-16 00:33:53,345] [INFO] Running command: blastn -query OceanDNA-b9008/markers.fasta -db /var/lib/cwl/stgbea19cc6-fb65-4b0a-ace0-57649d2568dc/dqc_reference/reference_markers.fasta -out OceanDNA-b9008/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:33:54,347] [INFO] Task succeeded: Blastn
[2023-03-16 00:33:54,348] [INFO] Selected 24 target genomes.
[2023-03-16 00:33:54,348] [INFO] Target genome list was writen to OceanDNA-b9008/target_genomes.txt
[2023-03-16 00:33:54,597] [INFO] Task started: fastANI
[2023-03-16 00:33:54,597] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f911aab-12c4-46a3-93f9-bf3ce9bc1386/OceanDNA-b9008.fa --refList OceanDNA-b9008/target_genomes.txt --output OceanDNA-b9008/fastani_result.tsv --threads 1
[2023-03-16 00:34:07,506] [INFO] Task succeeded: fastANI
[2023-03-16 00:34:07,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbea19cc6-fb65-4b0a-ace0-57649d2568dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:34:07,507] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbea19cc6-fb65-4b0a-ace0-57649d2568dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:34:07,507] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:34:07,507] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 00:34:07,507] [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 00:34:07,508] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9008/tc_result.tsv
[2023-03-16 00:34:07,508] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:34:07,508] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:34:07,508] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbea19cc6-fb65-4b0a-ace0-57649d2568dc/dqc_reference/checkm_data
[2023-03-16 00:34:07,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:34:07,579] [INFO] Task started: CheckM
[2023-03-16 00:34:07,579] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9008/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9008/checkm_input OceanDNA-b9008/checkm_result
[2023-03-16 00:34:27,020] [INFO] Task succeeded: CheckM
[2023-03-16 00:34:27,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 4.69%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 00:34:27,022] [INFO] ===== Completeness check finished =====
[2023-03-16 00:34:27,022] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:34:27,022] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9008/markers.fasta)
[2023-03-16 00:34:27,024] [INFO] Task started: Blastn
[2023-03-16 00:34:27,024] [INFO] Running command: blastn -query OceanDNA-b9008/markers.fasta -db /var/lib/cwl/stgbea19cc6-fb65-4b0a-ace0-57649d2568dc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9008/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:34:27,774] [INFO] Task succeeded: Blastn
[2023-03-16 00:34:27,775] [INFO] Selected 9 target genomes.
[2023-03-16 00:34:27,775] [INFO] Target genome list was writen to OceanDNA-b9008/target_genomes_gtdb.txt
[2023-03-16 00:34:27,864] [INFO] Task started: fastANI
[2023-03-16 00:34:27,864] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f911aab-12c4-46a3-93f9-bf3ce9bc1386/OceanDNA-b9008.fa --refList OceanDNA-b9008/target_genomes_gtdb.txt --output OceanDNA-b9008/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:34:30,813] [INFO] Task succeeded: fastANI
[2023-03-16 00:34:30,818] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 00:34:30,818] [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_902613595.1	s__MS024-2A sp902613595	96.2142	230	253	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_003130815.1	s__MS024-2A sp003130815	84.8292	207	253	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_902618245.1	s__MS024-2A sp902618245	84.5004	201	253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	98.05	96.19	0.87	0.86	3	-
GCA_902561795.1	s__MS024-2A sp902561795	84.4414	202	253	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	84.3105	160	253	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_902616905.1	s__MS024-2A sp902616905	77.8849	54	253	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 00:34:30,818] [INFO] GTDB search result was written to OceanDNA-b9008/result_gtdb.tsv
[2023-03-16 00:34:30,819] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:34:30,819] [INFO] DFAST_QC result json was written to OceanDNA-b9008/dqc_result.json
[2023-03-16 00:34:30,819] [INFO] DFAST_QC completed!
[2023-03-16 00:34:30,819] [INFO] Total running time: 0h0m44s