[2023-03-18 09:05:52,002] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:05:52,004] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:05:52,004] [INFO] DQC Reference Directory: /var/lib/cwl/stg442d1190-82b9-4d33-bb57-9a04a1347095/dqc_reference
[2023-03-18 09:05:53,102] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:05:53,104] [INFO] Task started: Prodigal
[2023-03-18 09:05:53,104] [INFO] Running command: cat /var/lib/cwl/stg8e2bb15c-8e27-40d3-849f-93f2107ee4de/OceanDNA-b46581.fa | prodigal -d OceanDNA-b46581/cds.fna -a OceanDNA-b46581/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:06:15,881] [INFO] Task succeeded: Prodigal
[2023-03-18 09:06:15,881] [INFO] Task started: HMMsearch
[2023-03-18 09:06:15,881] [INFO] Running command: hmmsearch --tblout OceanDNA-b46581/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg442d1190-82b9-4d33-bb57-9a04a1347095/dqc_reference/reference_markers.hmm OceanDNA-b46581/protein.faa > /dev/null
[2023-03-18 09:06:16,054] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:06:16,055] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8e2bb15c-8e27-40d3-849f-93f2107ee4de/OceanDNA-b46581.fa]
[2023-03-18 09:06:16,075] [INFO] Query marker FASTA was written to OceanDNA-b46581/markers.fasta
[2023-03-18 09:06:16,076] [INFO] Task started: Blastn
[2023-03-18 09:06:16,076] [INFO] Running command: blastn -query OceanDNA-b46581/markers.fasta -db /var/lib/cwl/stg442d1190-82b9-4d33-bb57-9a04a1347095/dqc_reference/reference_markers.fasta -out OceanDNA-b46581/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:06:16,734] [INFO] Task succeeded: Blastn
[2023-03-18 09:06:16,735] [INFO] Selected 17 target genomes.
[2023-03-18 09:06:16,735] [INFO] Target genome list was writen to OceanDNA-b46581/target_genomes.txt
[2023-03-18 09:06:16,749] [INFO] Task started: fastANI
[2023-03-18 09:06:16,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e2bb15c-8e27-40d3-849f-93f2107ee4de/OceanDNA-b46581.fa --refList OceanDNA-b46581/target_genomes.txt --output OceanDNA-b46581/fastani_result.tsv --threads 1
[2023-03-18 09:06:28,134] [INFO] Task succeeded: fastANI
[2023-03-18 09:06:28,134] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg442d1190-82b9-4d33-bb57-9a04a1347095/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:06:28,135] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg442d1190-82b9-4d33-bb57-9a04a1347095/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:06:28,135] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:06:28,135] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:06:28,135] [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 09:06:28,135] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46581/tc_result.tsv
[2023-03-18 09:06:28,135] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:06:28,135] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:06:28,135] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg442d1190-82b9-4d33-bb57-9a04a1347095/dqc_reference/checkm_data
[2023-03-18 09:06:28,145] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:06:28,150] [INFO] Task started: CheckM
[2023-03-18 09:06:28,150] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46581/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46581/checkm_input OceanDNA-b46581/checkm_result
[2023-03-18 09:07:28,915] [INFO] Task succeeded: CheckM
[2023-03-18 09:07:28,916] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.83%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 09:07:28,918] [INFO] ===== Completeness check finished =====
[2023-03-18 09:07:28,918] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:07:28,918] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46581/markers.fasta)
[2023-03-18 09:07:28,920] [INFO] Task started: Blastn
[2023-03-18 09:07:28,920] [INFO] Running command: blastn -query OceanDNA-b46581/markers.fasta -db /var/lib/cwl/stg442d1190-82b9-4d33-bb57-9a04a1347095/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46581/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:07:29,879] [INFO] Task succeeded: Blastn
[2023-03-18 09:07:29,880] [INFO] Selected 19 target genomes.
[2023-03-18 09:07:29,880] [INFO] Target genome list was writen to OceanDNA-b46581/target_genomes_gtdb.txt
[2023-03-18 09:07:29,993] [INFO] Task started: fastANI
[2023-03-18 09:07:29,993] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e2bb15c-8e27-40d3-849f-93f2107ee4de/OceanDNA-b46581.fa --refList OceanDNA-b46581/target_genomes_gtdb.txt --output OceanDNA-b46581/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:07:41,358] [INFO] Task succeeded: fastANI
[2023-03-18 09:07:41,363] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:07:41,363] [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_003517285.1	s__UBA1100 sp003517285	87.8131	406	708	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__UBA1100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523245.1	s__UBA1100 sp011523245	87.0101	395	708	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__UBA1100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382585.1	s__JACNJL01 sp014382585	81.7109	262	708	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__JACNJL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718935.1	s__UBA1100 sp002718935	79.1655	151	708	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__UBA1100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239365.1	s__JACNJL01 sp014239365	77.749	185	708	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__JACNJL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:07:41,363] [INFO] GTDB search result was written to OceanDNA-b46581/result_gtdb.tsv
[2023-03-18 09:07:41,363] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:07:41,364] [INFO] DFAST_QC result json was written to OceanDNA-b46581/dqc_result.json
[2023-03-18 09:07:41,364] [INFO] DFAST_QC completed!
[2023-03-18 09:07:41,364] [INFO] Total running time: 0h1m49s