[2023-03-18 09:58:36,591] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:58:36,591] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:58:36,591] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a516f46-d24b-4a8f-9602-692b6929cfd5/dqc_reference
[2023-03-18 09:58:38,402] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:58:38,403] [INFO] Task started: Prodigal
[2023-03-18 09:58:38,403] [INFO] Running command: cat /var/lib/cwl/stg743688a5-bf43-47ad-9176-fe616f596b97/OceanDNA-b46474.fa | prodigal -d OceanDNA-b46474/cds.fna -a OceanDNA-b46474/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:58:59,939] [INFO] Task succeeded: Prodigal
[2023-03-18 09:58:59,940] [INFO] Task started: HMMsearch
[2023-03-18 09:58:59,940] [INFO] Running command: hmmsearch --tblout OceanDNA-b46474/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a516f46-d24b-4a8f-9602-692b6929cfd5/dqc_reference/reference_markers.hmm OceanDNA-b46474/protein.faa > /dev/null
[2023-03-18 09:59:00,150] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:59:00,151] [INFO] Found 6/6 markers.
[2023-03-18 09:59:00,169] [INFO] Query marker FASTA was written to OceanDNA-b46474/markers.fasta
[2023-03-18 09:59:00,170] [INFO] Task started: Blastn
[2023-03-18 09:59:00,170] [INFO] Running command: blastn -query OceanDNA-b46474/markers.fasta -db /var/lib/cwl/stg9a516f46-d24b-4a8f-9602-692b6929cfd5/dqc_reference/reference_markers.fasta -out OceanDNA-b46474/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:59:00,734] [INFO] Task succeeded: Blastn
[2023-03-18 09:59:00,735] [INFO] Selected 6 target genomes.
[2023-03-18 09:59:00,735] [INFO] Target genome list was writen to OceanDNA-b46474/target_genomes.txt
[2023-03-18 09:59:00,740] [INFO] Task started: fastANI
[2023-03-18 09:59:00,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg743688a5-bf43-47ad-9176-fe616f596b97/OceanDNA-b46474.fa --refList OceanDNA-b46474/target_genomes.txt --output OceanDNA-b46474/fastani_result.tsv --threads 1
[2023-03-18 09:59:02,934] [INFO] Task succeeded: fastANI
[2023-03-18 09:59:02,935] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a516f46-d24b-4a8f-9602-692b6929cfd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:59:02,935] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a516f46-d24b-4a8f-9602-692b6929cfd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:59:02,935] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:59:02,935] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:59:02,935] [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 09:59:02,935] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46474/tc_result.tsv
[2023-03-18 09:59:02,935] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:59:02,935] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:59:02,936] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a516f46-d24b-4a8f-9602-692b6929cfd5/dqc_reference/checkm_data
[2023-03-18 09:59:02,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:59:02,944] [INFO] Task started: CheckM
[2023-03-18 09:59:02,944] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46474/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46474/checkm_input OceanDNA-b46474/checkm_result
[2023-03-18 09:59:58,663] [INFO] Task succeeded: CheckM
[2023-03-18 09:59:58,663] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:59:58,666] [INFO] ===== Completeness check finished =====
[2023-03-18 09:59:58,666] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:59:58,666] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46474/markers.fasta)
[2023-03-18 09:59:58,667] [INFO] Task started: Blastn
[2023-03-18 09:59:58,667] [INFO] Running command: blastn -query OceanDNA-b46474/markers.fasta -db /var/lib/cwl/stg9a516f46-d24b-4a8f-9602-692b6929cfd5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46474/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:59:59,361] [INFO] Task succeeded: Blastn
[2023-03-18 09:59:59,361] [INFO] Selected 13 target genomes.
[2023-03-18 09:59:59,362] [INFO] Target genome list was writen to OceanDNA-b46474/target_genomes_gtdb.txt
[2023-03-18 09:59:59,373] [INFO] Task started: fastANI
[2023-03-18 09:59:59,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg743688a5-bf43-47ad-9176-fe616f596b97/OceanDNA-b46474.fa --refList OceanDNA-b46474/target_genomes_gtdb.txt --output OceanDNA-b46474/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:00:05,879] [INFO] Task succeeded: fastANI
[2023-03-18 10:00:05,883] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 10:00:05,883] [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_004213515.1	s__UBA1096 sp002170545	96.3254	758	1027	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	98.87	98.49	0.79	0.67	5	conclusive
GCA_002708005.1	s__UBA1096 sp002708005	82.1223	470	1027	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	97.71	97.68	0.70	0.66	3	-
GCA_002684915.1	s__UBA1096 sp002684915	81.913	622	1027	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	98.82	98.82	0.77	0.77	2	-
GCA_002453165.1	s__UBA1096 sp002453165	76.5477	56	1027	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	96.70	95.18	0.81	0.76	7	-
--------------------------------------------------------------------------------
[2023-03-18 10:00:05,883] [INFO] GTDB search result was written to OceanDNA-b46474/result_gtdb.tsv
[2023-03-18 10:00:05,883] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:00:05,884] [INFO] DFAST_QC result json was written to OceanDNA-b46474/dqc_result.json
[2023-03-18 10:00:05,884] [INFO] DFAST_QC completed!
[2023-03-18 10:00:05,884] [INFO] Total running time: 0h1m29s