[2023-03-18 20:40:39,434] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:40:39,435] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:40:39,435] [INFO] DQC Reference Directory: /var/lib/cwl/stg3773a574-1b82-4935-8ddc-0a276de6a116/dqc_reference
[2023-03-18 20:40:41,209] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:40:41,209] [INFO] Task started: Prodigal
[2023-03-18 20:40:41,209] [INFO] Running command: cat /var/lib/cwl/stg890b81ea-c0de-414d-ae12-b8231eae510a/OceanDNA-b5103.fa | prodigal -d OceanDNA-b5103/cds.fna -a OceanDNA-b5103/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:40:48,880] [INFO] Task succeeded: Prodigal
[2023-03-18 20:40:48,881] [INFO] Task started: HMMsearch
[2023-03-18 20:40:48,881] [INFO] Running command: hmmsearch --tblout OceanDNA-b5103/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3773a574-1b82-4935-8ddc-0a276de6a116/dqc_reference/reference_markers.hmm OceanDNA-b5103/protein.faa > /dev/null
[2023-03-18 20:40:49,025] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:40:49,026] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg890b81ea-c0de-414d-ae12-b8231eae510a/OceanDNA-b5103.fa]
[2023-03-18 20:40:49,034] [INFO] Query marker FASTA was written to OceanDNA-b5103/markers.fasta
[2023-03-18 20:40:49,034] [INFO] Task started: Blastn
[2023-03-18 20:40:49,035] [INFO] Running command: blastn -query OceanDNA-b5103/markers.fasta -db /var/lib/cwl/stg3773a574-1b82-4935-8ddc-0a276de6a116/dqc_reference/reference_markers.fasta -out OceanDNA-b5103/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:40:49,532] [INFO] Task succeeded: Blastn
[2023-03-18 20:40:49,533] [INFO] Selected 19 target genomes.
[2023-03-18 20:40:49,533] [INFO] Target genome list was writen to OceanDNA-b5103/target_genomes.txt
[2023-03-18 20:40:49,539] [INFO] Task started: fastANI
[2023-03-18 20:40:49,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg890b81ea-c0de-414d-ae12-b8231eae510a/OceanDNA-b5103.fa --refList OceanDNA-b5103/target_genomes.txt --output OceanDNA-b5103/fastani_result.tsv --threads 1
[2023-03-18 20:40:58,653] [INFO] Task succeeded: fastANI
[2023-03-18 20:40:58,653] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3773a574-1b82-4935-8ddc-0a276de6a116/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:40:58,653] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3773a574-1b82-4935-8ddc-0a276de6a116/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:40:58,653] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:40:58,653] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 20:40:58,654] [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
--------------------------------------------------------------------------------
[2023-03-18 20:40:58,654] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5103/tc_result.tsv
[2023-03-18 20:40:58,654] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:40:58,654] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:40:58,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3773a574-1b82-4935-8ddc-0a276de6a116/dqc_reference/checkm_data
[2023-03-18 20:40:58,657] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:40:58,659] [INFO] Task started: CheckM
[2023-03-18 20:40:58,660] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5103/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5103/checkm_input OceanDNA-b5103/checkm_result
[2023-03-18 20:41:23,286] [INFO] Task succeeded: CheckM
[2023-03-18 20:41:23,287] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.02%
Contamintation: 2.08%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 20:41:23,289] [INFO] ===== Completeness check finished =====
[2023-03-18 20:41:23,289] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:41:23,289] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5103/markers.fasta)
[2023-03-18 20:41:23,289] [INFO] Task started: Blastn
[2023-03-18 20:41:23,289] [INFO] Running command: blastn -query OceanDNA-b5103/markers.fasta -db /var/lib/cwl/stg3773a574-1b82-4935-8ddc-0a276de6a116/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5103/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:41:23,942] [INFO] Task succeeded: Blastn
[2023-03-18 20:41:23,943] [INFO] Selected 16 target genomes.
[2023-03-18 20:41:23,943] [INFO] Target genome list was writen to OceanDNA-b5103/target_genomes_gtdb.txt
[2023-03-18 20:41:23,996] [INFO] Task started: fastANI
[2023-03-18 20:41:23,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg890b81ea-c0de-414d-ae12-b8231eae510a/OceanDNA-b5103.fa --refList OceanDNA-b5103/target_genomes_gtdb.txt --output OceanDNA-b5103/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:41:28,690] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:28,698] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:41:28,698] [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_002705205.1	s__GCA-2705205 sp002705205	89.4913	268	415	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_905479165.1	s__UWMA-0277 sp905479165	78.0847	152	415	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_905478185.1	s__UWMA-0277 sp905478185	77.8767	182	415	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_905478765.1	s__UWMA-0277 sp905478765	77.6696	183	415	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_002730985.1	s__BACL11 sp002730985	77.6438	124	415	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	97.22	97.22	0.84	0.84	2	-
GCA_014384505.1	s__UWMA-0277 sp014384505	77.4237	128	415	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	77.404	103	415	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	77.2197	103	415	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_018645865.1	s__UWMA-0277 sp018645865	77.2056	98	415	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	99.24	99.14	0.74	0.70	3	-
GCA_002693745.1	s__BACL11 sp002693745	77.1875	122	415	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	98.58	98.58	0.90	0.90	2	-
GCA_902514225.1	s__GCA-002697625 sp902514225	76.4854	62	415	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:41:28,698] [INFO] GTDB search result was written to OceanDNA-b5103/result_gtdb.tsv
[2023-03-18 20:41:28,698] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:41:28,699] [INFO] DFAST_QC result json was written to OceanDNA-b5103/dqc_result.json
[2023-03-18 20:41:28,699] [INFO] DFAST_QC completed!
[2023-03-18 20:41:28,699] [INFO] Total running time: 0h0m49s