[2023-03-14 11:17:27,809] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:17:27,809] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:17:27,809] [INFO] DQC Reference Directory: /var/lib/cwl/stg6026c67b-89bb-419d-bbff-a9c5a7cd9142/dqc_reference
[2023-03-14 11:17:28,971] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:17:28,971] [INFO] Task started: Prodigal
[2023-03-14 11:17:28,972] [INFO] Running command: cat /var/lib/cwl/stg78233925-0333-42d1-b263-ad81399aeeae/OceanDNA-b5654.fa | prodigal -d OceanDNA-b5654/cds.fna -a OceanDNA-b5654/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:17:38,163] [INFO] Task succeeded: Prodigal
[2023-03-14 11:17:38,164] [INFO] Task started: HMMsearch
[2023-03-14 11:17:38,164] [INFO] Running command: hmmsearch --tblout OceanDNA-b5654/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6026c67b-89bb-419d-bbff-a9c5a7cd9142/dqc_reference/reference_markers.hmm OceanDNA-b5654/protein.faa > /dev/null
[2023-03-14 11:17:38,339] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:17:38,340] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg78233925-0333-42d1-b263-ad81399aeeae/OceanDNA-b5654.fa]
[2023-03-14 11:17:38,352] [INFO] Query marker FASTA was written to OceanDNA-b5654/markers.fasta
[2023-03-14 11:17:38,353] [INFO] Task started: Blastn
[2023-03-14 11:17:38,354] [INFO] Running command: blastn -query OceanDNA-b5654/markers.fasta -db /var/lib/cwl/stg6026c67b-89bb-419d-bbff-a9c5a7cd9142/dqc_reference/reference_markers.fasta -out OceanDNA-b5654/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:17:38,872] [INFO] Task succeeded: Blastn
[2023-03-14 11:17:38,873] [INFO] Selected 22 target genomes.
[2023-03-14 11:17:38,873] [INFO] Target genome list was writen to OceanDNA-b5654/target_genomes.txt
[2023-03-14 11:17:38,889] [INFO] Task started: fastANI
[2023-03-14 11:17:38,889] [INFO] Running command: fastANI --query /var/lib/cwl/stg78233925-0333-42d1-b263-ad81399aeeae/OceanDNA-b5654.fa --refList OceanDNA-b5654/target_genomes.txt --output OceanDNA-b5654/fastani_result.tsv --threads 1
[2023-03-14 11:17:51,340] [INFO] Task succeeded: fastANI
[2023-03-14 11:17:51,340] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6026c67b-89bb-419d-bbff-a9c5a7cd9142/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:17:51,340] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6026c67b-89bb-419d-bbff-a9c5a7cd9142/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:17:51,341] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:17:51,341] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:17:51,341] [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
--------------------------------------------------------------------------------
[2023-03-14 11:17:51,341] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5654/tc_result.tsv
[2023-03-14 11:17:51,343] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:17:51,343] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:17:51,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6026c67b-89bb-419d-bbff-a9c5a7cd9142/dqc_reference/checkm_data
[2023-03-14 11:17:51,345] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:17:51,350] [INFO] Task started: CheckM
[2023-03-14 11:17:51,350] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5654/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5654/checkm_input OceanDNA-b5654/checkm_result
[2023-03-14 11:18:19,583] [INFO] Task succeeded: CheckM
[2023-03-14 11:18:19,583] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.88%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 11:18:19,586] [INFO] ===== Completeness check finished =====
[2023-03-14 11:18:19,586] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:18:19,586] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5654/markers.fasta)
[2023-03-14 11:18:19,587] [INFO] Task started: Blastn
[2023-03-14 11:18:19,587] [INFO] Running command: blastn -query OceanDNA-b5654/markers.fasta -db /var/lib/cwl/stg6026c67b-89bb-419d-bbff-a9c5a7cd9142/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5654/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:18:20,283] [INFO] Task succeeded: Blastn
[2023-03-14 11:18:20,286] [INFO] Selected 22 target genomes.
[2023-03-14 11:18:20,286] [INFO] Target genome list was writen to OceanDNA-b5654/target_genomes_gtdb.txt
[2023-03-14 11:18:20,361] [INFO] Task started: fastANI
[2023-03-14 11:18:20,361] [INFO] Running command: fastANI --query /var/lib/cwl/stg78233925-0333-42d1-b263-ad81399aeeae/OceanDNA-b5654.fa --refList OceanDNA-b5654/target_genomes_gtdb.txt --output OceanDNA-b5654/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:18:31,788] [INFO] Task succeeded: fastANI
[2023-03-14 11:18:31,790] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:18:31,791] [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_002682945.1	s__TMED14 sp002682945	88.869	388	458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167805.1	s__TMED14 sp002167805	88.199	410	458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	95.87	95.87	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-14 11:18:31,791] [INFO] GTDB search result was written to OceanDNA-b5654/result_gtdb.tsv
[2023-03-14 11:18:31,792] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:18:31,793] [INFO] DFAST_QC result json was written to OceanDNA-b5654/dqc_result.json
[2023-03-14 11:18:31,794] [INFO] DFAST_QC completed!
[2023-03-14 11:18:31,794] [INFO] Total running time: 0h1m4s