[2023-03-17 23:10:23,649] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:10:23,649] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:10:23,650] [INFO] DQC Reference Directory: /var/lib/cwl/stg11810edb-5109-4242-b47a-9ead9d6fdd70/dqc_reference
[2023-03-17 23:10:24,813] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:10:24,813] [INFO] Task started: Prodigal
[2023-03-17 23:10:24,813] [INFO] Running command: cat /var/lib/cwl/stg81813eee-1d03-41e9-9a02-8233c095790b/OceanDNA-b45588.fa | prodigal -d OceanDNA-b45588/cds.fna -a OceanDNA-b45588/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:10:39,672] [INFO] Task succeeded: Prodigal
[2023-03-17 23:10:39,673] [INFO] Task started: HMMsearch
[2023-03-17 23:10:39,673] [INFO] Running command: hmmsearch --tblout OceanDNA-b45588/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11810edb-5109-4242-b47a-9ead9d6fdd70/dqc_reference/reference_markers.hmm OceanDNA-b45588/protein.faa > /dev/null
[2023-03-17 23:10:39,839] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:10:39,839] [INFO] Found 6/6 markers.
[2023-03-17 23:10:39,856] [INFO] Query marker FASTA was written to OceanDNA-b45588/markers.fasta
[2023-03-17 23:10:39,856] [INFO] Task started: Blastn
[2023-03-17 23:10:39,856] [INFO] Running command: blastn -query OceanDNA-b45588/markers.fasta -db /var/lib/cwl/stg11810edb-5109-4242-b47a-9ead9d6fdd70/dqc_reference/reference_markers.fasta -out OceanDNA-b45588/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:10:40,411] [INFO] Task succeeded: Blastn
[2023-03-17 23:10:40,413] [INFO] Selected 12 target genomes.
[2023-03-17 23:10:40,414] [INFO] Target genome list was writen to OceanDNA-b45588/target_genomes.txt
[2023-03-17 23:10:40,420] [INFO] Task started: fastANI
[2023-03-17 23:10:40,421] [INFO] Running command: fastANI --query /var/lib/cwl/stg81813eee-1d03-41e9-9a02-8233c095790b/OceanDNA-b45588.fa --refList OceanDNA-b45588/target_genomes.txt --output OceanDNA-b45588/fastani_result.tsv --threads 1
[2023-03-17 23:10:46,286] [INFO] Task succeeded: fastANI
[2023-03-17 23:10:46,286] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11810edb-5109-4242-b47a-9ead9d6fdd70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:10:46,287] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11810edb-5109-4242-b47a-9ead9d6fdd70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:10:46,287] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:10:46,287] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:10:46,287] [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
--------------------------------------------------------------------------------
[2023-03-17 23:10:46,288] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45588/tc_result.tsv
[2023-03-17 23:10:46,288] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:10:46,288] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:10:46,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11810edb-5109-4242-b47a-9ead9d6fdd70/dqc_reference/checkm_data
[2023-03-17 23:10:46,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:10:46,295] [INFO] Task started: CheckM
[2023-03-17 23:10:46,295] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45588/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45588/checkm_input OceanDNA-b45588/checkm_result
[2023-03-17 23:11:26,905] [INFO] Task succeeded: CheckM
[2023-03-17 23:11:26,905] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:11:26,907] [INFO] ===== Completeness check finished =====
[2023-03-17 23:11:26,907] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:11:26,907] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45588/markers.fasta)
[2023-03-17 23:11:26,908] [INFO] Task started: Blastn
[2023-03-17 23:11:26,908] [INFO] Running command: blastn -query OceanDNA-b45588/markers.fasta -db /var/lib/cwl/stg11810edb-5109-4242-b47a-9ead9d6fdd70/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45588/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:11:27,902] [INFO] Task succeeded: Blastn
[2023-03-17 23:11:27,903] [INFO] Selected 24 target genomes.
[2023-03-17 23:11:27,903] [INFO] Target genome list was writen to OceanDNA-b45588/target_genomes_gtdb.txt
[2023-03-17 23:11:27,925] [INFO] Task started: fastANI
[2023-03-17 23:11:27,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg81813eee-1d03-41e9-9a02-8233c095790b/OceanDNA-b45588.fa --refList OceanDNA-b45588/target_genomes_gtdb.txt --output OceanDNA-b45588/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:11:38,122] [INFO] Task succeeded: fastANI
[2023-03-17 23:11:38,126] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:11:38,126] [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_902615835.1	s__MB11C04 sp902615835	98.5024	296	570	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902612125.1	s__MB11C04 sp902612125	92.5116	381	570	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902569115.1	s__MB11C04 sp902569115	79.6962	153	570	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689665.1	s__MB11C04 sp002689665	79.2674	198	570	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002168015.1	s__MB11C04 sp002168015	77.5912	89	570	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692535.1	s__MB11C04 sp002692535	76.8825	70	570	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:11:38,127] [INFO] GTDB search result was written to OceanDNA-b45588/result_gtdb.tsv
[2023-03-17 23:11:38,128] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:11:38,129] [INFO] DFAST_QC result json was written to OceanDNA-b45588/dqc_result.json
[2023-03-17 23:11:38,129] [INFO] DFAST_QC completed!
[2023-03-17 23:11:38,129] [INFO] Total running time: 0h1m14s