[2023-03-15 06:35:36,163] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:35:36,165] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:35:36,165] [INFO] DQC Reference Directory: /var/lib/cwl/stg28bc8615-b3c5-46f6-be26-3a736550737a/dqc_reference
[2023-03-15 06:35:37,285] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:35:37,286] [INFO] Task started: Prodigal
[2023-03-15 06:35:37,286] [INFO] Running command: cat /var/lib/cwl/stg6d4de7e7-61da-4e3f-99d6-ca20e50285ac/OceanDNA-b46625.fa | prodigal -d OceanDNA-b46625/cds.fna -a OceanDNA-b46625/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:35:58,986] [INFO] Task succeeded: Prodigal
[2023-03-15 06:35:58,986] [INFO] Task started: HMMsearch
[2023-03-15 06:35:58,986] [INFO] Running command: hmmsearch --tblout OceanDNA-b46625/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28bc8615-b3c5-46f6-be26-3a736550737a/dqc_reference/reference_markers.hmm OceanDNA-b46625/protein.faa > /dev/null
[2023-03-15 06:35:59,177] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:35:59,177] [INFO] Found 6/6 markers.
[2023-03-15 06:35:59,213] [INFO] Query marker FASTA was written to OceanDNA-b46625/markers.fasta
[2023-03-15 06:35:59,213] [INFO] Task started: Blastn
[2023-03-15 06:35:59,213] [INFO] Running command: blastn -query OceanDNA-b46625/markers.fasta -db /var/lib/cwl/stg28bc8615-b3c5-46f6-be26-3a736550737a/dqc_reference/reference_markers.fasta -out OceanDNA-b46625/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:35:59,725] [INFO] Task succeeded: Blastn
[2023-03-15 06:35:59,734] [INFO] Selected 13 target genomes.
[2023-03-15 06:35:59,734] [INFO] Target genome list was writen to OceanDNA-b46625/target_genomes.txt
[2023-03-15 06:35:59,741] [INFO] Task started: fastANI
[2023-03-15 06:35:59,741] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d4de7e7-61da-4e3f-99d6-ca20e50285ac/OceanDNA-b46625.fa --refList OceanDNA-b46625/target_genomes.txt --output OceanDNA-b46625/fastani_result.tsv --threads 1
[2023-03-15 06:36:07,223] [INFO] Task succeeded: fastANI
[2023-03-15 06:36:07,223] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28bc8615-b3c5-46f6-be26-3a736550737a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:36:07,224] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28bc8615-b3c5-46f6-be26-3a736550737a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:36:07,224] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:36:07,224] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 06:36:07,224] [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
--------------------------------------------------------------------------------
[2023-03-15 06:36:07,226] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46625/tc_result.tsv
[2023-03-15 06:36:07,229] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:36:07,229] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:36:07,230] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28bc8615-b3c5-46f6-be26-3a736550737a/dqc_reference/checkm_data
[2023-03-15 06:36:07,233] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:36:07,263] [INFO] Task started: CheckM
[2023-03-15 06:36:07,264] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46625/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46625/checkm_input OceanDNA-b46625/checkm_result
[2023-03-15 06:37:03,655] [INFO] Task succeeded: CheckM
[2023-03-15 06:37:03,656] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 06:37:03,687] [INFO] ===== Completeness check finished =====
[2023-03-15 06:37:03,688] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:37:03,688] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46625/markers.fasta)
[2023-03-15 06:37:03,689] [INFO] Task started: Blastn
[2023-03-15 06:37:03,689] [INFO] Running command: blastn -query OceanDNA-b46625/markers.fasta -db /var/lib/cwl/stg28bc8615-b3c5-46f6-be26-3a736550737a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46625/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:37:04,393] [INFO] Task succeeded: Blastn
[2023-03-15 06:37:04,398] [INFO] Selected 15 target genomes.
[2023-03-15 06:37:04,398] [INFO] Target genome list was writen to OceanDNA-b46625/target_genomes_gtdb.txt
[2023-03-15 06:37:04,420] [INFO] Task started: fastANI
[2023-03-15 06:37:04,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d4de7e7-61da-4e3f-99d6-ca20e50285ac/OceanDNA-b46625.fa --refList OceanDNA-b46625/target_genomes_gtdb.txt --output OceanDNA-b46625/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:37:12,205] [INFO] Task succeeded: fastANI
[2023-03-15 06:37:12,208] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 06:37:12,208] [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_002719595.1	s__UBA1100 sp002719595	98.685	496	874	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__UBA1100	95.0	97.74	95.96	0.58	0.55	4	conclusive
GCA_902551155.1	s__UBA1100 sp902551155	93.8983	381	874	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__UBA1100	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 06:37:12,210] [INFO] GTDB search result was written to OceanDNA-b46625/result_gtdb.tsv
[2023-03-15 06:37:12,215] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:37:12,219] [INFO] DFAST_QC result json was written to OceanDNA-b46625/dqc_result.json
[2023-03-15 06:37:12,219] [INFO] DFAST_QC completed!
[2023-03-15 06:37:12,219] [INFO] Total running time: 0h1m36s