[2023-03-17 10:48:47,677] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:48:47,677] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:48:47,677] [INFO] DQC Reference Directory: /var/lib/cwl/stge8480218-83ca-4cbb-861d-f5e993b3c671/dqc_reference
[2023-03-17 10:48:48,960] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:48:48,961] [INFO] Task started: Prodigal
[2023-03-17 10:48:48,961] [INFO] Running command: cat /var/lib/cwl/stg570dc406-e6e9-46e8-8c67-473bab332f95/OceanDNA-b35712.fa | prodigal -d OceanDNA-b35712/cds.fna -a OceanDNA-b35712/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:49:02,864] [INFO] Task succeeded: Prodigal
[2023-03-17 10:49:02,864] [INFO] Task started: HMMsearch
[2023-03-17 10:49:02,864] [INFO] Running command: hmmsearch --tblout OceanDNA-b35712/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8480218-83ca-4cbb-861d-f5e993b3c671/dqc_reference/reference_markers.hmm OceanDNA-b35712/protein.faa > /dev/null
[2023-03-17 10:49:03,115] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:49:03,115] [INFO] Found 6/6 markers.
[2023-03-17 10:49:03,136] [INFO] Query marker FASTA was written to OceanDNA-b35712/markers.fasta
[2023-03-17 10:49:03,136] [INFO] Task started: Blastn
[2023-03-17 10:49:03,136] [INFO] Running command: blastn -query OceanDNA-b35712/markers.fasta -db /var/lib/cwl/stge8480218-83ca-4cbb-861d-f5e993b3c671/dqc_reference/reference_markers.fasta -out OceanDNA-b35712/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:49:03,697] [INFO] Task succeeded: Blastn
[2023-03-17 10:49:03,698] [INFO] Selected 40 target genomes.
[2023-03-17 10:49:03,698] [INFO] Target genome list was writen to OceanDNA-b35712/target_genomes.txt
[2023-03-17 10:49:03,722] [INFO] Task started: fastANI
[2023-03-17 10:49:03,722] [INFO] Running command: fastANI --query /var/lib/cwl/stg570dc406-e6e9-46e8-8c67-473bab332f95/OceanDNA-b35712.fa --refList OceanDNA-b35712/target_genomes.txt --output OceanDNA-b35712/fastani_result.tsv --threads 1
[2023-03-17 10:49:32,021] [INFO] Task succeeded: fastANI
[2023-03-17 10:49:32,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8480218-83ca-4cbb-861d-f5e993b3c671/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:49:32,021] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8480218-83ca-4cbb-861d-f5e993b3c671/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:49:32,022] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:49:32,022] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:49:32,022] [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 10:49:32,022] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35712/tc_result.tsv
[2023-03-17 10:49:32,022] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:49:32,022] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:49:32,022] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8480218-83ca-4cbb-861d-f5e993b3c671/dqc_reference/checkm_data
[2023-03-17 10:49:32,024] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:49:32,029] [INFO] Task started: CheckM
[2023-03-17 10:49:32,029] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35712/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35712/checkm_input OceanDNA-b35712/checkm_result
[2023-03-17 10:50:10,349] [INFO] Task succeeded: CheckM
[2023-03-17 10:50:10,349] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:50:10,352] [INFO] ===== Completeness check finished =====
[2023-03-17 10:50:10,352] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:50:10,352] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35712/markers.fasta)
[2023-03-17 10:50:10,354] [INFO] Task started: Blastn
[2023-03-17 10:50:10,354] [INFO] Running command: blastn -query OceanDNA-b35712/markers.fasta -db /var/lib/cwl/stge8480218-83ca-4cbb-861d-f5e993b3c671/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35712/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:50:11,140] [INFO] Task succeeded: Blastn
[2023-03-17 10:50:11,141] [INFO] Selected 25 target genomes.
[2023-03-17 10:50:11,141] [INFO] Target genome list was writen to OceanDNA-b35712/target_genomes_gtdb.txt
[2023-03-17 10:50:11,333] [INFO] Task started: fastANI
[2023-03-17 10:50:11,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg570dc406-e6e9-46e8-8c67-473bab332f95/OceanDNA-b35712.fa --refList OceanDNA-b35712/target_genomes_gtdb.txt --output OceanDNA-b35712/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:50:24,751] [INFO] Task succeeded: fastANI
[2023-03-17 10:50:24,755] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:50:24,755] [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_018648825.1	s__Thiopontia sp018648825	99.6425	586	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCF-002020875;f__GCF-002020875;g__Thiopontia	95.0	99.74	99.68	0.85	0.80	15	conclusive
GCA_013349825.1	s__Thiopontia sp013349825	79.3359	193	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCF-002020875;f__GCF-002020875;g__Thiopontia	95.0	99.78	99.58	0.88	0.82	21	-
GCA_018671205.1	s__Thiopontia sp018671205	77.3579	150	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCF-002020875;f__GCF-002020875;g__Thiopontia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384675.1	s__Thiopontia autotrophica	77.3358	96	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCF-002020875;f__GCF-002020875;g__Thiopontia	95.0	99.91	99.91	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-17 10:50:24,755] [INFO] GTDB search result was written to OceanDNA-b35712/result_gtdb.tsv
[2023-03-17 10:50:24,756] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:50:24,756] [INFO] DFAST_QC result json was written to OceanDNA-b35712/dqc_result.json
[2023-03-17 10:50:24,757] [INFO] DFAST_QC completed!
[2023-03-17 10:50:24,757] [INFO] Total running time: 0h1m37s