[2023-03-14 11:14:12,738] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:14:12,739] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:14:12,739] [INFO] DQC Reference Directory: /var/lib/cwl/stg43a2f978-9d49-43e3-b138-7e10347916ca/dqc_reference
[2023-03-14 11:14:14,208] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:14,208] [INFO] Task started: Prodigal
[2023-03-14 11:14:14,209] [INFO] Running command: cat /var/lib/cwl/stgd06bcc08-1389-41cb-a6e1-b4f7ff2dfb04/OceanDNA-b5955.fa | prodigal -d OceanDNA-b5955/cds.fna -a OceanDNA-b5955/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:27,741] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:27,741] [INFO] Task started: HMMsearch
[2023-03-14 11:14:27,741] [INFO] Running command: hmmsearch --tblout OceanDNA-b5955/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43a2f978-9d49-43e3-b138-7e10347916ca/dqc_reference/reference_markers.hmm OceanDNA-b5955/protein.faa > /dev/null
[2023-03-14 11:14:27,961] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:27,961] [INFO] Found 6/6 markers.
[2023-03-14 11:14:27,979] [INFO] Query marker FASTA was written to OceanDNA-b5955/markers.fasta
[2023-03-14 11:14:27,981] [INFO] Task started: Blastn
[2023-03-14 11:14:27,982] [INFO] Running command: blastn -query OceanDNA-b5955/markers.fasta -db /var/lib/cwl/stg43a2f978-9d49-43e3-b138-7e10347916ca/dqc_reference/reference_markers.fasta -out OceanDNA-b5955/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:28,560] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:28,561] [INFO] Selected 28 target genomes.
[2023-03-14 11:14:28,561] [INFO] Target genome list was writen to OceanDNA-b5955/target_genomes.txt
[2023-03-14 11:14:28,579] [INFO] Task started: fastANI
[2023-03-14 11:14:28,579] [INFO] Running command: fastANI --query /var/lib/cwl/stgd06bcc08-1389-41cb-a6e1-b4f7ff2dfb04/OceanDNA-b5955.fa --refList OceanDNA-b5955/target_genomes.txt --output OceanDNA-b5955/fastani_result.tsv --threads 1
[2023-03-14 11:14:43,709] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:43,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43a2f978-9d49-43e3-b138-7e10347916ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:43,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43a2f978-9d49-43e3-b138-7e10347916ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:43,710] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:14:43,710] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:14:43,710] [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
--------------------------------------------------------------------------------
[2023-03-14 11:14:43,710] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5955/tc_result.tsv
[2023-03-14 11:14:43,710] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:43,711] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:43,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43a2f978-9d49-43e3-b138-7e10347916ca/dqc_reference/checkm_data
[2023-03-14 11:14:43,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:43,739] [INFO] Task started: CheckM
[2023-03-14 11:14:43,739] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5955/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5955/checkm_input OceanDNA-b5955/checkm_result
[2023-03-14 11:15:22,050] [INFO] Task succeeded: CheckM
[2023-03-14 11:15:22,050] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:15:22,052] [INFO] ===== Completeness check finished =====
[2023-03-14 11:15:22,052] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:15:22,052] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5955/markers.fasta)
[2023-03-14 11:15:22,057] [INFO] Task started: Blastn
[2023-03-14 11:15:22,057] [INFO] Running command: blastn -query OceanDNA-b5955/markers.fasta -db /var/lib/cwl/stg43a2f978-9d49-43e3-b138-7e10347916ca/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5955/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:15:22,959] [INFO] Task succeeded: Blastn
[2023-03-14 11:15:22,960] [INFO] Selected 19 target genomes.
[2023-03-14 11:15:22,960] [INFO] Target genome list was writen to OceanDNA-b5955/target_genomes_gtdb.txt
[2023-03-14 11:15:23,006] [INFO] Task started: fastANI
[2023-03-14 11:15:23,006] [INFO] Running command: fastANI --query /var/lib/cwl/stgd06bcc08-1389-41cb-a6e1-b4f7ff2dfb04/OceanDNA-b5955.fa --refList OceanDNA-b5955/target_genomes_gtdb.txt --output OceanDNA-b5955/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:15:30,651] [INFO] Task succeeded: fastANI
[2023-03-14 11:15:30,657] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:15:30,658] [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_002707525.1	s__UBA10364 sp002707525	99.8439	581	626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003023665.1	s__UBA10364 sp003023665	84.0026	435	626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	98.70	98.70	0.79	0.79	2	-
GCA_902614915.1	s__UBA10364 sp902614915	80.1701	345	626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525035.1	s__UBA10364 sp011525035	78.4839	183	626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003385605.1	s__UBA10364 sp003385605	78.3675	193	626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.63	99.63	0.71	0.71	2	-
GCA_012269745.1	s__UBA10364 sp012269745	78.256	180	626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623275.1	s__UBA10364 sp018623275	77.7756	128	626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003445735.1	s__UBA10364 sp003445735	77.5981	54	626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	97.99	97.76	0.85	0.77	3	-
GCA_003487785.1	s__UBA10364 sp003487785	76.8643	51	626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.22	99.20	0.81	0.80	3	-
GCA_905182675.1	s__UBA10364 sp905182675	76.5962	58	626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:15:30,658] [INFO] GTDB search result was written to OceanDNA-b5955/result_gtdb.tsv
[2023-03-14 11:15:30,658] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:15:30,659] [INFO] DFAST_QC result json was written to OceanDNA-b5955/dqc_result.json
[2023-03-14 11:15:30,659] [INFO] DFAST_QC completed!
[2023-03-14 11:15:30,659] [INFO] Total running time: 0h1m18s