[2023-03-16 04:05:20,067] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:05:20,067] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:05:20,067] [INFO] DQC Reference Directory: /var/lib/cwl/stg26e14d4e-f7f6-4c23-96c7-acc9f08c189c/dqc_reference
[2023-03-16 04:05:21,169] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:05:21,170] [INFO] Task started: Prodigal
[2023-03-16 04:05:21,170] [INFO] Running command: cat /var/lib/cwl/stg5885da7f-28ff-43ef-876c-105ecef9f5b5/OceanDNA-b4870.fa | prodigal -d OceanDNA-b4870/cds.fna -a OceanDNA-b4870/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:05:28,257] [INFO] Task succeeded: Prodigal
[2023-03-16 04:05:28,257] [INFO] Task started: HMMsearch
[2023-03-16 04:05:28,257] [INFO] Running command: hmmsearch --tblout OceanDNA-b4870/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26e14d4e-f7f6-4c23-96c7-acc9f08c189c/dqc_reference/reference_markers.hmm OceanDNA-b4870/protein.faa > /dev/null
[2023-03-16 04:05:28,424] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:05:28,425] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5885da7f-28ff-43ef-876c-105ecef9f5b5/OceanDNA-b4870.fa]
[2023-03-16 04:05:28,434] [INFO] Query marker FASTA was written to OceanDNA-b4870/markers.fasta
[2023-03-16 04:05:28,435] [INFO] Task started: Blastn
[2023-03-16 04:05:28,435] [INFO] Running command: blastn -query OceanDNA-b4870/markers.fasta -db /var/lib/cwl/stg26e14d4e-f7f6-4c23-96c7-acc9f08c189c/dqc_reference/reference_markers.fasta -out OceanDNA-b4870/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:28,967] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:28,968] [INFO] Selected 22 target genomes.
[2023-03-16 04:05:28,968] [INFO] Target genome list was writen to OceanDNA-b4870/target_genomes.txt
[2023-03-16 04:05:28,978] [INFO] Task started: fastANI
[2023-03-16 04:05:28,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg5885da7f-28ff-43ef-876c-105ecef9f5b5/OceanDNA-b4870.fa --refList OceanDNA-b4870/target_genomes.txt --output OceanDNA-b4870/fastani_result.tsv --threads 1
[2023-03-16 04:05:39,576] [INFO] Task succeeded: fastANI
[2023-03-16 04:05:39,576] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26e14d4e-f7f6-4c23-96c7-acc9f08c189c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:05:39,577] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26e14d4e-f7f6-4c23-96c7-acc9f08c189c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:05:39,577] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:05:39,577] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:05:39,577] [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 04:05:39,577] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4870/tc_result.tsv
[2023-03-16 04:05:39,577] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:05:39,577] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:05:39,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26e14d4e-f7f6-4c23-96c7-acc9f08c189c/dqc_reference/checkm_data
[2023-03-16 04:05:39,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:05:39,582] [INFO] Task started: CheckM
[2023-03-16 04:05:39,582] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4870/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4870/checkm_input OceanDNA-b4870/checkm_result
[2023-03-16 04:06:02,298] [INFO] Task succeeded: CheckM
[2023-03-16 04:06:02,298] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.35%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:06:02,300] [INFO] ===== Completeness check finished =====
[2023-03-16 04:06:02,300] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:06:02,300] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4870/markers.fasta)
[2023-03-16 04:06:02,300] [INFO] Task started: Blastn
[2023-03-16 04:06:02,300] [INFO] Running command: blastn -query OceanDNA-b4870/markers.fasta -db /var/lib/cwl/stg26e14d4e-f7f6-4c23-96c7-acc9f08c189c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4870/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:06:03,101] [INFO] Task succeeded: Blastn
[2023-03-16 04:06:03,102] [INFO] Selected 20 target genomes.
[2023-03-16 04:06:03,102] [INFO] Target genome list was writen to OceanDNA-b4870/target_genomes_gtdb.txt
[2023-03-16 04:06:03,147] [INFO] Task started: fastANI
[2023-03-16 04:06:03,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg5885da7f-28ff-43ef-876c-105ecef9f5b5/OceanDNA-b4870.fa --refList OceanDNA-b4870/target_genomes_gtdb.txt --output OceanDNA-b4870/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:06:09,116] [INFO] Task succeeded: fastANI
[2023-03-16 04:06:09,125] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:06:09,125] [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_002715565.1	s__GCA-2715565 sp002715565	77.4945	110	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2715565	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002728175.1	s__GCA-2697505 sp002728175	77.0441	132	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2697505	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002697505.1	s__GCA-2697505 sp002697505	77.0137	106	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2697505	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724895.1	s__GCA-2693335 sp002724895	76.8611	98	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2693335	95.0	97.78	97.48	0.81	0.76	3	-
GCA_002693745.1	s__BACL11 sp002693745	76.6008	58	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	98.58	98.58	0.90	0.90	2	-
GCA_014384505.1	s__UWMA-0277 sp014384505	76.4405	59	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018664745.1	s__UWMA-0277 sp018664745	76.4293	61	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478765.1	s__UWMA-0277 sp905478765	76.4123	72	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479165.1	s__UWMA-0277 sp905479165	76.3473	63	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902579065.1	s__GCA-002715885 sp902579065	76.2917	52	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002705205.1	s__GCA-2705205 sp002705205	76.2823	66	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2705205	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960805.1	s__UWMA-0277 sp012960805	76.1136	69	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181585.1	s__CAJIYG01 sp905181585	76.074	66	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__CAJIYG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712715.1	s__GCA-2712715 sp002712715	75.6647	59	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2712715	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:06:09,125] [INFO] GTDB search result was written to OceanDNA-b4870/result_gtdb.tsv
[2023-03-16 04:06:09,125] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:06:09,126] [INFO] DFAST_QC result json was written to OceanDNA-b4870/dqc_result.json
[2023-03-16 04:06:09,126] [INFO] DFAST_QC completed!
[2023-03-16 04:06:09,126] [INFO] Total running time: 0h0m49s