[2023-03-19 02:37:51,619] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:37:51,619] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:37:51,619] [INFO] DQC Reference Directory: /var/lib/cwl/stg60d022f1-6330-46ac-8519-2ca3af7b8c35/dqc_reference
[2023-03-19 02:37:52,760] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:37:52,761] [INFO] Task started: Prodigal
[2023-03-19 02:37:52,761] [INFO] Running command: cat /var/lib/cwl/stg3f0be628-fc77-4529-8a60-807e82070780/OceanDNA-b4760.fa | prodigal -d OceanDNA-b4760/cds.fna -a OceanDNA-b4760/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:38:07,449] [INFO] Task succeeded: Prodigal
[2023-03-19 02:38:07,449] [INFO] Task started: HMMsearch
[2023-03-19 02:38:07,449] [INFO] Running command: hmmsearch --tblout OceanDNA-b4760/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60d022f1-6330-46ac-8519-2ca3af7b8c35/dqc_reference/reference_markers.hmm OceanDNA-b4760/protein.faa > /dev/null
[2023-03-19 02:38:07,654] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:38:07,655] [INFO] Found 6/6 markers.
[2023-03-19 02:38:07,671] [INFO] Query marker FASTA was written to OceanDNA-b4760/markers.fasta
[2023-03-19 02:38:07,672] [INFO] Task started: Blastn
[2023-03-19 02:38:07,672] [INFO] Running command: blastn -query OceanDNA-b4760/markers.fasta -db /var/lib/cwl/stg60d022f1-6330-46ac-8519-2ca3af7b8c35/dqc_reference/reference_markers.fasta -out OceanDNA-b4760/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:38:08,255] [INFO] Task succeeded: Blastn
[2023-03-19 02:38:08,257] [INFO] Selected 22 target genomes.
[2023-03-19 02:38:08,257] [INFO] Target genome list was writen to OceanDNA-b4760/target_genomes.txt
[2023-03-19 02:38:08,276] [INFO] Task started: fastANI
[2023-03-19 02:38:08,277] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f0be628-fc77-4529-8a60-807e82070780/OceanDNA-b4760.fa --refList OceanDNA-b4760/target_genomes.txt --output OceanDNA-b4760/fastani_result.tsv --threads 1
[2023-03-19 02:38:20,438] [INFO] Task succeeded: fastANI
[2023-03-19 02:38:20,438] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60d022f1-6330-46ac-8519-2ca3af7b8c35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:38:20,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60d022f1-6330-46ac-8519-2ca3af7b8c35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:38:20,449] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:38:20,449] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:38:20,449] [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
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	75.6375	57	752	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	75.2837	57	752	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:38:20,451] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4760/tc_result.tsv
[2023-03-19 02:38:20,451] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:38:20,451] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:38:20,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60d022f1-6330-46ac-8519-2ca3af7b8c35/dqc_reference/checkm_data
[2023-03-19 02:38:20,452] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:38:20,455] [INFO] Task started: CheckM
[2023-03-19 02:38:20,456] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4760/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4760/checkm_input OceanDNA-b4760/checkm_result
[2023-03-19 02:39:00,405] [INFO] Task succeeded: CheckM
[2023-03-19 02:39:00,405] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:39:00,410] [INFO] ===== Completeness check finished =====
[2023-03-19 02:39:00,410] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:39:00,410] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4760/markers.fasta)
[2023-03-19 02:39:00,412] [INFO] Task started: Blastn
[2023-03-19 02:39:00,412] [INFO] Running command: blastn -query OceanDNA-b4760/markers.fasta -db /var/lib/cwl/stg60d022f1-6330-46ac-8519-2ca3af7b8c35/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4760/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:39:01,297] [INFO] Task succeeded: Blastn
[2023-03-19 02:39:01,298] [INFO] Selected 21 target genomes.
[2023-03-19 02:39:01,298] [INFO] Target genome list was writen to OceanDNA-b4760/target_genomes_gtdb.txt
[2023-03-19 02:39:01,335] [INFO] Task started: fastANI
[2023-03-19 02:39:01,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f0be628-fc77-4529-8a60-807e82070780/OceanDNA-b4760.fa --refList OceanDNA-b4760/target_genomes_gtdb.txt --output OceanDNA-b4760/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:39:12,235] [INFO] Task succeeded: fastANI
[2023-03-19 02:39:12,238] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 02:39:12,239] [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_905182785.1	s__CAJJDF01 sp905182785	98.8871	685	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__CAJJDF01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018609055.1	s__CAJJDF01 sp018609055	79.3495	401	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__CAJJDF01	95.0	99.81	99.81	0.88	0.88	2	-
GCF_014784055.1	s__Polaribacter haliotis	75.4002	57	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-19 02:39:12,240] [INFO] GTDB search result was written to OceanDNA-b4760/result_gtdb.tsv
[2023-03-19 02:39:12,242] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:39:12,244] [INFO] DFAST_QC result json was written to OceanDNA-b4760/dqc_result.json
[2023-03-19 02:39:12,244] [INFO] DFAST_QC completed!
[2023-03-19 02:39:12,244] [INFO] Total running time: 0h1m21s