[2023-03-15 13:54:06,139] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:54:06,140] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:54:06,140] [INFO] DQC Reference Directory: /var/lib/cwl/stg04b58b19-8e25-42a1-a337-6bdf28df2348/dqc_reference
[2023-03-15 13:54:07,236] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:54:07,237] [INFO] Task started: Prodigal
[2023-03-15 13:54:07,237] [INFO] Running command: cat /var/lib/cwl/stg1db71bc3-3988-4ae0-9881-3cd3cfa2f6bd/OceanDNA-b7295.fa | prodigal -d OceanDNA-b7295/cds.fna -a OceanDNA-b7295/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:54:16,363] [INFO] Task succeeded: Prodigal
[2023-03-15 13:54:16,363] [INFO] Task started: HMMsearch
[2023-03-15 13:54:16,363] [INFO] Running command: hmmsearch --tblout OceanDNA-b7295/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04b58b19-8e25-42a1-a337-6bdf28df2348/dqc_reference/reference_markers.hmm OceanDNA-b7295/protein.faa > /dev/null
[2023-03-15 13:54:16,523] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:54:16,523] [INFO] Found 6/6 markers.
[2023-03-15 13:54:16,562] [INFO] Query marker FASTA was written to OceanDNA-b7295/markers.fasta
[2023-03-15 13:54:16,564] [INFO] Task started: Blastn
[2023-03-15 13:54:16,565] [INFO] Running command: blastn -query OceanDNA-b7295/markers.fasta -db /var/lib/cwl/stg04b58b19-8e25-42a1-a337-6bdf28df2348/dqc_reference/reference_markers.fasta -out OceanDNA-b7295/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:54:17,137] [INFO] Task succeeded: Blastn
[2023-03-15 13:54:17,145] [INFO] Selected 27 target genomes.
[2023-03-15 13:54:17,146] [INFO] Target genome list was writen to OceanDNA-b7295/target_genomes.txt
[2023-03-15 13:54:17,161] [INFO] Task started: fastANI
[2023-03-15 13:54:17,161] [INFO] Running command: fastANI --query /var/lib/cwl/stg1db71bc3-3988-4ae0-9881-3cd3cfa2f6bd/OceanDNA-b7295.fa --refList OceanDNA-b7295/target_genomes.txt --output OceanDNA-b7295/fastani_result.tsv --threads 1
[2023-03-15 13:54:31,434] [INFO] Task succeeded: fastANI
[2023-03-15 13:54:31,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04b58b19-8e25-42a1-a337-6bdf28df2348/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:54:31,435] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04b58b19-8e25-42a1-a337-6bdf28df2348/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:54:31,439] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:54:31,439] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:54:31,439] [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
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.0627	51	366	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	76.001	50	366	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	75.794	64	366	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:54:31,441] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7295/tc_result.tsv
[2023-03-15 13:54:31,441] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:54:31,441] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:54:31,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04b58b19-8e25-42a1-a337-6bdf28df2348/dqc_reference/checkm_data
[2023-03-15 13:54:31,442] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:54:31,447] [INFO] Task started: CheckM
[2023-03-15 13:54:31,447] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7295/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7295/checkm_input OceanDNA-b7295/checkm_result
[2023-03-15 13:54:59,675] [INFO] Task succeeded: CheckM
[2023-03-15 13:54:59,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.53%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 13:54:59,736] [INFO] ===== Completeness check finished =====
[2023-03-15 13:54:59,736] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:54:59,736] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7295/markers.fasta)
[2023-03-15 13:54:59,737] [INFO] Task started: Blastn
[2023-03-15 13:54:59,737] [INFO] Running command: blastn -query OceanDNA-b7295/markers.fasta -db /var/lib/cwl/stg04b58b19-8e25-42a1-a337-6bdf28df2348/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7295/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:55:00,526] [INFO] Task succeeded: Blastn
[2023-03-15 13:55:00,540] [INFO] Selected 11 target genomes.
[2023-03-15 13:55:00,540] [INFO] Target genome list was writen to OceanDNA-b7295/target_genomes_gtdb.txt
[2023-03-15 13:55:00,549] [INFO] Task started: fastANI
[2023-03-15 13:55:00,549] [INFO] Running command: fastANI --query /var/lib/cwl/stg1db71bc3-3988-4ae0-9881-3cd3cfa2f6bd/OceanDNA-b7295.fa --refList OceanDNA-b7295/target_genomes_gtdb.txt --output OceanDNA-b7295/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:55:04,666] [INFO] Task succeeded: fastANI
[2023-03-15 13:55:04,673] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:55:04,673] [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_905479095.1	s__Hel1-33-131 sp905479095	89.5229	311	366	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001735745.1	s__Hel1-33-131 sp001735745	81.4374	289	366	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018673215.1	s__Hel1-33-131 sp018673215	80.9819	245	366	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608735.1	s__Hel1-33-131 sp018608735	80.1155	209	366	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608765.1	s__Hel1-33-131 sp018608765	79.9899	253	366	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608725.1	s__Hel1-33-131 sp018608725	79.9118	234	366	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181825.1	s__Hel1-33-131 sp905181825	78.2805	161	366	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	99.01	99.01	0.77	0.77	2	-
GCA_018608625.1	s__Hel1-33-131 sp018608625	78.1834	163	366	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	98.93	97.98	0.88	0.82	3	-
GCA_018608705.1	s__Hel1-33-131 sp018608705	77.1884	129	366	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	99.44	99.44	0.94	0.94	2	-
GCF_001971785.1	s__Seonamhaeicola sp001971785	76.0169	51	366	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:55:04,679] [INFO] GTDB search result was written to OceanDNA-b7295/result_gtdb.tsv
[2023-03-15 13:55:04,688] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:55:04,695] [INFO] DFAST_QC result json was written to OceanDNA-b7295/dqc_result.json
[2023-03-15 13:55:04,696] [INFO] DFAST_QC completed!
[2023-03-15 13:55:04,696] [INFO] Total running time: 0h0m59s