[2023-03-16 00:13:32,241] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:13:32,241] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:13:32,241] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2178c14-ac55-4681-b655-d42a517ee04d/dqc_reference
[2023-03-16 00:13:33,472] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:13:33,472] [INFO] Task started: Prodigal
[2023-03-16 00:13:33,473] [INFO] Running command: cat /var/lib/cwl/stg0485075d-e8ef-4862-bf24-af8f78342342/OceanDNA-b4869.fa | prodigal -d OceanDNA-b4869/cds.fna -a OceanDNA-b4869/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:13:40,585] [INFO] Task succeeded: Prodigal
[2023-03-16 00:13:40,586] [INFO] Task started: HMMsearch
[2023-03-16 00:13:40,586] [INFO] Running command: hmmsearch --tblout OceanDNA-b4869/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2178c14-ac55-4681-b655-d42a517ee04d/dqc_reference/reference_markers.hmm OceanDNA-b4869/protein.faa > /dev/null
[2023-03-16 00:13:40,760] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:13:40,761] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0485075d-e8ef-4862-bf24-af8f78342342/OceanDNA-b4869.fa]
[2023-03-16 00:13:40,775] [INFO] Query marker FASTA was written to OceanDNA-b4869/markers.fasta
[2023-03-16 00:13:40,777] [INFO] Task started: Blastn
[2023-03-16 00:13:40,777] [INFO] Running command: blastn -query OceanDNA-b4869/markers.fasta -db /var/lib/cwl/stgd2178c14-ac55-4681-b655-d42a517ee04d/dqc_reference/reference_markers.fasta -out OceanDNA-b4869/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:13:41,325] [INFO] Task succeeded: Blastn
[2023-03-16 00:13:41,329] [INFO] Selected 23 target genomes.
[2023-03-16 00:13:41,329] [INFO] Target genome list was writen to OceanDNA-b4869/target_genomes.txt
[2023-03-16 00:13:41,343] [INFO] Task started: fastANI
[2023-03-16 00:13:41,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg0485075d-e8ef-4862-bf24-af8f78342342/OceanDNA-b4869.fa --refList OceanDNA-b4869/target_genomes.txt --output OceanDNA-b4869/fastani_result.tsv --threads 1
[2023-03-16 00:13:53,987] [INFO] Task succeeded: fastANI
[2023-03-16 00:13:53,987] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2178c14-ac55-4681-b655-d42a517ee04d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:13:53,987] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2178c14-ac55-4681-b655-d42a517ee04d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:13:53,988] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:13:53,988] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 00:13:53,988] [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 00:13:54,129] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4869/tc_result.tsv
[2023-03-16 00:13:54,133] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:13:54,133] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:13:54,133] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2178c14-ac55-4681-b655-d42a517ee04d/dqc_reference/checkm_data
[2023-03-16 00:13:54,137] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:13:54,155] [INFO] Task started: CheckM
[2023-03-16 00:13:54,155] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4869/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4869/checkm_input OceanDNA-b4869/checkm_result
[2023-03-16 00:14:17,129] [INFO] Task succeeded: CheckM
[2023-03-16 00:14:17,130] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:14:17,142] [INFO] ===== Completeness check finished =====
[2023-03-16 00:14:17,142] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:14:17,142] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4869/markers.fasta)
[2023-03-16 00:14:17,144] [INFO] Task started: Blastn
[2023-03-16 00:14:17,144] [INFO] Running command: blastn -query OceanDNA-b4869/markers.fasta -db /var/lib/cwl/stgd2178c14-ac55-4681-b655-d42a517ee04d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4869/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:14:17,975] [INFO] Task succeeded: Blastn
[2023-03-16 00:14:17,978] [INFO] Selected 25 target genomes.
[2023-03-16 00:14:17,978] [INFO] Target genome list was writen to OceanDNA-b4869/target_genomes_gtdb.txt
[2023-03-16 00:14:17,999] [INFO] Task started: fastANI
[2023-03-16 00:14:17,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg0485075d-e8ef-4862-bf24-af8f78342342/OceanDNA-b4869.fa --refList OceanDNA-b4869/target_genomes_gtdb.txt --output OceanDNA-b4869/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:14:25,682] [INFO] Task succeeded: fastANI
[2023-03-16 00:14:25,692] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:14:25,692] [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_905479165.1	s__UWMA-0277 sp905479165	77.0508	90	393	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	76.9761	95	393	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_002711125.1	s__GCA-2711125 sp002711125	76.9532	86	393	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2711125	95.0	97.93	96.61	0.96	0.94	3	-
GCA_905478185.1	s__UWMA-0277 sp905478185	76.8724	89	393	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	96.67	96.67	0.88	0.88	2	-
GCA_012960805.1	s__UWMA-0277 sp012960805	76.8323	92	393	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_002705205.1	s__GCA-2705205 sp002705205	76.7464	69	393	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_018664745.1	s__UWMA-0277 sp018664745	76.6095	56	393	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_905181635.1	s__UWMA-0277 sp905181635	76.5994	63	393	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_002724895.1	s__GCA-2693335 sp002724895	76.5984	89	393	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_014384505.1	s__UWMA-0277 sp014384505	76.5426	72	393	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_002728175.1	s__GCA-2697505 sp002728175	76.4355	70	393	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_002693745.1	s__BACL11 sp002693745	76.397	62	393	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	98.58	98.58	0.90	0.90	2	-
GCA_002710495.1	s__GCA-002697625 sp002710495	76.3827	66	393	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002697505.1	s__GCA-2697505 sp002697505	76.3289	62	393	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_014381465.1	s__DUAL01 sp014381465	76.2657	57	393	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__DUAL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018675825.1	s__GCA-002715885 sp018675825	75.9912	54	393	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 00:14:25,694] [INFO] GTDB search result was written to OceanDNA-b4869/result_gtdb.tsv
[2023-03-16 00:14:25,696] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:14:25,699] [INFO] DFAST_QC result json was written to OceanDNA-b4869/dqc_result.json
[2023-03-16 00:14:25,699] [INFO] DFAST_QC completed!
[2023-03-16 00:14:25,699] [INFO] Total running time: 0h0m53s