[2023-03-17 09:33:09,985] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:33:09,985] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:33:09,985] [INFO] DQC Reference Directory: /var/lib/cwl/stg0bf38867-e0d7-4fed-80ba-01d9deb3e99e/dqc_reference
[2023-03-17 09:33:11,104] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:33:11,104] [INFO] Task started: Prodigal
[2023-03-17 09:33:11,104] [INFO] Running command: cat /var/lib/cwl/stg082a54bf-06f8-41c8-b672-e46097414d09/OceanDNA-b1316.fa | prodigal -d OceanDNA-b1316/cds.fna -a OceanDNA-b1316/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:33:24,438] [INFO] Task succeeded: Prodigal
[2023-03-17 09:33:24,438] [INFO] Task started: HMMsearch
[2023-03-17 09:33:24,438] [INFO] Running command: hmmsearch --tblout OceanDNA-b1316/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0bf38867-e0d7-4fed-80ba-01d9deb3e99e/dqc_reference/reference_markers.hmm OceanDNA-b1316/protein.faa > /dev/null
[2023-03-17 09:33:24,607] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:33:24,607] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg082a54bf-06f8-41c8-b672-e46097414d09/OceanDNA-b1316.fa]
[2023-03-17 09:33:24,621] [INFO] Query marker FASTA was written to OceanDNA-b1316/markers.fasta
[2023-03-17 09:33:24,622] [INFO] Task started: Blastn
[2023-03-17 09:33:24,622] [INFO] Running command: blastn -query OceanDNA-b1316/markers.fasta -db /var/lib/cwl/stg0bf38867-e0d7-4fed-80ba-01d9deb3e99e/dqc_reference/reference_markers.fasta -out OceanDNA-b1316/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:33:25,134] [INFO] Task succeeded: Blastn
[2023-03-17 09:33:25,135] [INFO] Selected 26 target genomes.
[2023-03-17 09:33:25,135] [INFO] Target genome list was writen to OceanDNA-b1316/target_genomes.txt
[2023-03-17 09:33:25,338] [INFO] Task started: fastANI
[2023-03-17 09:33:25,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg082a54bf-06f8-41c8-b672-e46097414d09/OceanDNA-b1316.fa --refList OceanDNA-b1316/target_genomes.txt --output OceanDNA-b1316/fastani_result.tsv --threads 1
[2023-03-17 09:33:41,182] [INFO] Task succeeded: fastANI
[2023-03-17 09:33:41,183] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0bf38867-e0d7-4fed-80ba-01d9deb3e99e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:33:41,183] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0bf38867-e0d7-4fed-80ba-01d9deb3e99e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:33:41,183] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:33:41,183] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:33:41,183] [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 09:33:41,249] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1316/tc_result.tsv
[2023-03-17 09:33:41,250] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:33:41,250] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:33:41,250] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0bf38867-e0d7-4fed-80ba-01d9deb3e99e/dqc_reference/checkm_data
[2023-03-17 09:33:41,253] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:33:41,274] [INFO] Task started: CheckM
[2023-03-17 09:33:41,274] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1316/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1316/checkm_input OceanDNA-b1316/checkm_result
[2023-03-17 09:34:17,981] [INFO] Task succeeded: CheckM
[2023-03-17 09:34:17,982] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:34:17,984] [INFO] ===== Completeness check finished =====
[2023-03-17 09:34:17,984] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:34:17,984] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1316/markers.fasta)
[2023-03-17 09:34:17,985] [INFO] Task started: Blastn
[2023-03-17 09:34:17,986] [INFO] Running command: blastn -query OceanDNA-b1316/markers.fasta -db /var/lib/cwl/stg0bf38867-e0d7-4fed-80ba-01d9deb3e99e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1316/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:34:18,718] [INFO] Task succeeded: Blastn
[2023-03-17 09:34:18,719] [INFO] Selected 17 target genomes.
[2023-03-17 09:34:18,719] [INFO] Target genome list was writen to OceanDNA-b1316/target_genomes_gtdb.txt
[2023-03-17 09:34:19,237] [INFO] Task started: fastANI
[2023-03-17 09:34:19,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg082a54bf-06f8-41c8-b672-e46097414d09/OceanDNA-b1316.fa --refList OceanDNA-b1316/target_genomes_gtdb.txt --output OceanDNA-b1316/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:34:27,293] [INFO] Task succeeded: fastANI
[2023-03-17 09:34:27,300] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 09:34:27,300] [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_002348705.1	s__UBA9410 sp002348705	99.9562	716	730	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	99.53	98.86	0.93	0.89	6	conclusive
GCA_002727895.1	s__UBA9410 sp002727895	78.8	232	730	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	97.12	97.12	0.93	0.93	2	-
GCA_016845305.1	s__UBA9410 sp016845305	78.5855	312	730	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239855.1	s__UBA9410 sp014239855	77.6112	221	730	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714485.1	s__UBA9410 sp002714485	77.5724	149	730	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014237715.1	s__UBA9410 sp014237715	77.412	193	730	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.52	98.52	0.97	0.97	2	-
GCA_002717365.1	s__UBA9410 sp002717365	77.2908	125	730	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003541675.1	s__UBA9410 sp003541675	76.8754	111	730	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240365.1	s__UBA9410 sp014240365	76.5831	127	730	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.11	98.07	0.86	0.84	5	-
GCA_015658775.1	s__UBA3125 sp015658775	76.2292	94	730	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	98.89	98.89	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-03-17 09:34:27,300] [INFO] GTDB search result was written to OceanDNA-b1316/result_gtdb.tsv
[2023-03-17 09:34:27,301] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:34:27,301] [INFO] DFAST_QC result json was written to OceanDNA-b1316/dqc_result.json
[2023-03-17 09:34:27,301] [INFO] DFAST_QC completed!
[2023-03-17 09:34:27,302] [INFO] Total running time: 0h1m17s