[2023-03-18 10:24:55,194] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:24:55,194] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:24:55,194] [INFO] DQC Reference Directory: /var/lib/cwl/stg94d03192-4dcf-46ce-ab90-e89cc8020757/dqc_reference
[2023-03-18 10:24:56,333] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:24:56,333] [INFO] Task started: Prodigal
[2023-03-18 10:24:56,333] [INFO] Running command: cat /var/lib/cwl/stgaa415e3a-b31c-410a-9929-a8529bea620f/OceanDNA-b46505.fa | prodigal -d OceanDNA-b46505/cds.fna -a OceanDNA-b46505/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:25:27,774] [INFO] Task succeeded: Prodigal
[2023-03-18 10:25:27,774] [INFO] Task started: HMMsearch
[2023-03-18 10:25:27,774] [INFO] Running command: hmmsearch --tblout OceanDNA-b46505/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94d03192-4dcf-46ce-ab90-e89cc8020757/dqc_reference/reference_markers.hmm OceanDNA-b46505/protein.faa > /dev/null
[2023-03-18 10:25:27,959] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:25:27,960] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgaa415e3a-b31c-410a-9929-a8529bea620f/OceanDNA-b46505.fa]
[2023-03-18 10:25:27,982] [INFO] Query marker FASTA was written to OceanDNA-b46505/markers.fasta
[2023-03-18 10:25:27,983] [INFO] Task started: Blastn
[2023-03-18 10:25:27,983] [INFO] Running command: blastn -query OceanDNA-b46505/markers.fasta -db /var/lib/cwl/stg94d03192-4dcf-46ce-ab90-e89cc8020757/dqc_reference/reference_markers.fasta -out OceanDNA-b46505/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:25:28,496] [INFO] Task succeeded: Blastn
[2023-03-18 10:25:28,497] [INFO] Selected 25 target genomes.
[2023-03-18 10:25:28,497] [INFO] Target genome list was writen to OceanDNA-b46505/target_genomes.txt
[2023-03-18 10:25:28,539] [INFO] Task started: fastANI
[2023-03-18 10:25:28,539] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa415e3a-b31c-410a-9929-a8529bea620f/OceanDNA-b46505.fa --refList OceanDNA-b46505/target_genomes.txt --output OceanDNA-b46505/fastani_result.tsv --threads 1
[2023-03-18 10:25:45,906] [INFO] Task succeeded: fastANI
[2023-03-18 10:25:45,906] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94d03192-4dcf-46ce-ab90-e89cc8020757/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:25:45,906] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94d03192-4dcf-46ce-ab90-e89cc8020757/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:25:45,907] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:25:45,907] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:25:45,907] [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 10:25:45,907] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46505/tc_result.tsv
[2023-03-18 10:25:45,907] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:25:45,907] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:25:45,907] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94d03192-4dcf-46ce-ab90-e89cc8020757/dqc_reference/checkm_data
[2023-03-18 10:25:45,910] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:25:46,013] [INFO] Task started: CheckM
[2023-03-18 10:25:46,013] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46505/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46505/checkm_input OceanDNA-b46505/checkm_result
[2023-03-18 10:27:04,832] [INFO] Task succeeded: CheckM
[2023-03-18 10:27:04,833] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 10:27:04,840] [INFO] ===== Completeness check finished =====
[2023-03-18 10:27:04,840] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:27:04,840] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46505/markers.fasta)
[2023-03-18 10:27:04,841] [INFO] Task started: Blastn
[2023-03-18 10:27:04,841] [INFO] Running command: blastn -query OceanDNA-b46505/markers.fasta -db /var/lib/cwl/stg94d03192-4dcf-46ce-ab90-e89cc8020757/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46505/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:27:05,704] [INFO] Task succeeded: Blastn
[2023-03-18 10:27:05,707] [INFO] Selected 8 target genomes.
[2023-03-18 10:27:05,707] [INFO] Target genome list was writen to OceanDNA-b46505/target_genomes_gtdb.txt
[2023-03-18 10:27:05,714] [INFO] Task started: fastANI
[2023-03-18 10:27:05,714] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa415e3a-b31c-410a-9929-a8529bea620f/OceanDNA-b46505.fa --refList OceanDNA-b46505/target_genomes_gtdb.txt --output OceanDNA-b46505/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:27:10,591] [INFO] Task succeeded: fastANI
[2023-03-18 10:27:10,597] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 10:27:10,597] [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_002453165.1	s__UBA1096 sp002453165	95.4983	799	1121	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	96.70	95.18	0.81	0.76	7	conclusive
GCA_011523195.1	s__UBA1096 sp011523195	94.9204	553	1121	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689335.1	s__UBA1096 sp002689335	81.2755	465	1121	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686755.1	s__UBA1096 sp002686755	80.7043	454	1121	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382705.1	s__UBA1096 sp014382705	79.3002	538	1121	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003972865.1	s__UBA1096 sp003972865	78.918	363	1121	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015658765.1	s__UBA1096 sp015658765	78.5314	270	1121	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235585.1	s__JACRJY01 sp016235585	75.4039	70	1121	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__JACRJY01;g__JACRJY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:27:10,598] [INFO] GTDB search result was written to OceanDNA-b46505/result_gtdb.tsv
[2023-03-18 10:27:10,598] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:27:10,600] [INFO] DFAST_QC result json was written to OceanDNA-b46505/dqc_result.json
[2023-03-18 10:27:10,600] [INFO] DFAST_QC completed!
[2023-03-18 10:27:10,600] [INFO] Total running time: 0h2m15s