[2023-03-17 09:33:09,863] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:33:09,863] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:33:09,863] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfdbc946-b99f-42fb-b72b-9e9232053804/dqc_reference
[2023-03-17 09:33:10,964] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:33:10,964] [INFO] Task started: Prodigal
[2023-03-17 09:33:10,964] [INFO] Running command: cat /var/lib/cwl/stg0dc75903-36df-4e67-a60a-509a4cc372ae/OceanDNA-b5659.fa | prodigal -d OceanDNA-b5659/cds.fna -a OceanDNA-b5659/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:33:19,790] [INFO] Task succeeded: Prodigal
[2023-03-17 09:33:19,790] [INFO] Task started: HMMsearch
[2023-03-17 09:33:19,790] [INFO] Running command: hmmsearch --tblout OceanDNA-b5659/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfdbc946-b99f-42fb-b72b-9e9232053804/dqc_reference/reference_markers.hmm OceanDNA-b5659/protein.faa > /dev/null
[2023-03-17 09:33:19,919] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:33:19,920] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg0dc75903-36df-4e67-a60a-509a4cc372ae/OceanDNA-b5659.fa]
[2023-03-17 09:33:19,930] [INFO] Query marker FASTA was written to OceanDNA-b5659/markers.fasta
[2023-03-17 09:33:19,930] [INFO] Task started: Blastn
[2023-03-17 09:33:19,930] [INFO] Running command: blastn -query OceanDNA-b5659/markers.fasta -db /var/lib/cwl/stgcfdbc946-b99f-42fb-b72b-9e9232053804/dqc_reference/reference_markers.fasta -out OceanDNA-b5659/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:33:20,357] [INFO] Task succeeded: Blastn
[2023-03-17 09:33:20,358] [INFO] Selected 6 target genomes.
[2023-03-17 09:33:20,358] [INFO] Target genome list was writen to OceanDNA-b5659/target_genomes.txt
[2023-03-17 09:33:20,382] [INFO] Task started: fastANI
[2023-03-17 09:33:20,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dc75903-36df-4e67-a60a-509a4cc372ae/OceanDNA-b5659.fa --refList OceanDNA-b5659/target_genomes.txt --output OceanDNA-b5659/fastani_result.tsv --threads 1
[2023-03-17 09:33:24,753] [INFO] Task succeeded: fastANI
[2023-03-17 09:33:24,753] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfdbc946-b99f-42fb-b72b-9e9232053804/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:33:24,754] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfdbc946-b99f-42fb-b72b-9e9232053804/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:33:24,754] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:33:24,754] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:33:24,754] [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 09:33:24,754] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5659/tc_result.tsv
[2023-03-17 09:33:24,754] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:33:24,754] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:33:24,754] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfdbc946-b99f-42fb-b72b-9e9232053804/dqc_reference/checkm_data
[2023-03-17 09:33:24,757] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:33:24,806] [INFO] Task started: CheckM
[2023-03-17 09:33:24,807] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5659/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5659/checkm_input OceanDNA-b5659/checkm_result
[2023-03-17 09:33:52,717] [INFO] Task succeeded: CheckM
[2023-03-17 09:33:52,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:33:52,720] [INFO] ===== Completeness check finished =====
[2023-03-17 09:33:52,720] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:33:52,720] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5659/markers.fasta)
[2023-03-17 09:33:52,721] [INFO] Task started: Blastn
[2023-03-17 09:33:52,721] [INFO] Running command: blastn -query OceanDNA-b5659/markers.fasta -db /var/lib/cwl/stgcfdbc946-b99f-42fb-b72b-9e9232053804/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5659/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:33:53,151] [INFO] Task succeeded: Blastn
[2023-03-17 09:33:53,152] [INFO] Selected 9 target genomes.
[2023-03-17 09:33:53,152] [INFO] Target genome list was writen to OceanDNA-b5659/target_genomes_gtdb.txt
[2023-03-17 09:33:53,586] [INFO] Task started: fastANI
[2023-03-17 09:33:53,586] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dc75903-36df-4e67-a60a-509a4cc372ae/OceanDNA-b5659.fa --refList OceanDNA-b5659/target_genomes_gtdb.txt --output OceanDNA-b5659/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:33:57,431] [INFO] Task succeeded: fastANI
[2023-03-17 09:33:57,434] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 09:33:57,434] [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_002381225.1	s__TMED14 sp002381225	79.9473	147	266	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	98.92	98.57	0.92	0.89	11	-
GCA_003507115.1	s__TMED14 sp003507115	79.6349	122	266	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	98.82	98.50	0.76	0.76	3	-
GCA_001438205.1	s__TMED14 sp001438205	77.8922	89	266	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	99.81	99.57	0.95	0.91	8	-
--------------------------------------------------------------------------------
[2023-03-17 09:33:57,434] [INFO] GTDB search result was written to OceanDNA-b5659/result_gtdb.tsv
[2023-03-17 09:33:57,434] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:33:57,435] [INFO] DFAST_QC result json was written to OceanDNA-b5659/dqc_result.json
[2023-03-17 09:33:57,435] [INFO] DFAST_QC completed!
[2023-03-17 09:33:57,435] [INFO] Total running time: 0h0m48s