[2023-03-16 04:24:46,332] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:24:46,332] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:24:46,332] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b794ea3-dab2-4dbc-9aa1-528edfc2451d/dqc_reference
[2023-03-16 04:24:48,114] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:24:48,115] [INFO] Task started: Prodigal
[2023-03-16 04:24:48,115] [INFO] Running command: cat /var/lib/cwl/stg2d62f263-8b5c-418a-867d-0d6f61b712b2/OceanDNA-b19633.fa | prodigal -d OceanDNA-b19633/cds.fna -a OceanDNA-b19633/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:24:57,449] [INFO] Task succeeded: Prodigal
[2023-03-16 04:24:57,449] [INFO] Task started: HMMsearch
[2023-03-16 04:24:57,449] [INFO] Running command: hmmsearch --tblout OceanDNA-b19633/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b794ea3-dab2-4dbc-9aa1-528edfc2451d/dqc_reference/reference_markers.hmm OceanDNA-b19633/protein.faa > /dev/null
[2023-03-16 04:24:57,696] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:24:57,697] [INFO] Found 6/6 markers.
[2023-03-16 04:24:57,710] [INFO] Query marker FASTA was written to OceanDNA-b19633/markers.fasta
[2023-03-16 04:24:57,710] [INFO] Task started: Blastn
[2023-03-16 04:24:57,710] [INFO] Running command: blastn -query OceanDNA-b19633/markers.fasta -db /var/lib/cwl/stg1b794ea3-dab2-4dbc-9aa1-528edfc2451d/dqc_reference/reference_markers.fasta -out OceanDNA-b19633/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:24:58,237] [INFO] Task succeeded: Blastn
[2023-03-16 04:24:58,238] [INFO] Selected 17 target genomes.
[2023-03-16 04:24:58,239] [INFO] Target genome list was writen to OceanDNA-b19633/target_genomes.txt
[2023-03-16 04:24:58,247] [INFO] Task started: fastANI
[2023-03-16 04:24:58,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d62f263-8b5c-418a-867d-0d6f61b712b2/OceanDNA-b19633.fa --refList OceanDNA-b19633/target_genomes.txt --output OceanDNA-b19633/fastani_result.tsv --threads 1
[2023-03-16 04:25:06,822] [INFO] Task succeeded: fastANI
[2023-03-16 04:25:06,823] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b794ea3-dab2-4dbc-9aa1-528edfc2451d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:25:06,823] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b794ea3-dab2-4dbc-9aa1-528edfc2451d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:25:06,823] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:25:06,823] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:25:06,823] [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
--------------------------------------------------------------------------------
[2023-03-16 04:25:06,823] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19633/tc_result.tsv
[2023-03-16 04:25:06,823] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:25:06,824] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:25:06,824] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b794ea3-dab2-4dbc-9aa1-528edfc2451d/dqc_reference/checkm_data
[2023-03-16 04:25:06,826] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:25:06,830] [INFO] Task started: CheckM
[2023-03-16 04:25:06,830] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19633/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19633/checkm_input OceanDNA-b19633/checkm_result
[2023-03-16 04:25:35,635] [INFO] Task succeeded: CheckM
[2023-03-16 04:25:35,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.91%
Strain heterogeneity: 80.00%
--------------------------------------------------------------------------------
[2023-03-16 04:25:35,637] [INFO] ===== Completeness check finished =====
[2023-03-16 04:25:35,637] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:25:35,637] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19633/markers.fasta)
[2023-03-16 04:25:35,638] [INFO] Task started: Blastn
[2023-03-16 04:25:35,638] [INFO] Running command: blastn -query OceanDNA-b19633/markers.fasta -db /var/lib/cwl/stg1b794ea3-dab2-4dbc-9aa1-528edfc2451d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19633/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:25:36,353] [INFO] Task succeeded: Blastn
[2023-03-16 04:25:36,354] [INFO] Selected 23 target genomes.
[2023-03-16 04:25:36,354] [INFO] Target genome list was writen to OceanDNA-b19633/target_genomes_gtdb.txt
[2023-03-16 04:25:36,379] [INFO] Task started: fastANI
[2023-03-16 04:25:36,379] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d62f263-8b5c-418a-867d-0d6f61b712b2/OceanDNA-b19633.fa --refList OceanDNA-b19633/target_genomes_gtdb.txt --output OceanDNA-b19633/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:25:43,454] [INFO] Task succeeded: fastANI
[2023-03-16 04:25:43,457] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:25:43,457] [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_018649625.1	s__GCA-2722105 sp018649625	76.099	51	611	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	99.96	99.90	0.93	0.85	15	-
GCA_002167345.2	s__CACEUX01 sp002167345	76.0297	55	611	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__CACEUX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708715.1	s__GCA-002708715 sp002708715	75.9038	72	611	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-002708715	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:25:43,457] [INFO] GTDB search result was written to OceanDNA-b19633/result_gtdb.tsv
[2023-03-16 04:25:43,458] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:25:43,458] [INFO] DFAST_QC result json was written to OceanDNA-b19633/dqc_result.json
[2023-03-16 04:25:43,458] [INFO] DFAST_QC completed!
[2023-03-16 04:25:43,458] [INFO] Total running time: 0h0m57s