[2023-03-17 08:39:27,336] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:39:27,336] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:39:27,336] [INFO] DQC Reference Directory: /var/lib/cwl/stg7de5da07-1f87-434f-840d-4f9b05f79f7a/dqc_reference
[2023-03-17 08:39:28,533] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:39:28,534] [INFO] Task started: Prodigal
[2023-03-17 08:39:28,534] [INFO] Running command: cat /var/lib/cwl/stgeb4c598c-de0a-4f3a-bd5a-50ea8a0cd154/OceanDNA-b22616.fa | prodigal -d OceanDNA-b22616/cds.fna -a OceanDNA-b22616/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:40:15,708] [INFO] Task succeeded: Prodigal
[2023-03-17 08:40:15,708] [INFO] Task started: HMMsearch
[2023-03-17 08:40:15,709] [INFO] Running command: hmmsearch --tblout OceanDNA-b22616/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7de5da07-1f87-434f-840d-4f9b05f79f7a/dqc_reference/reference_markers.hmm OceanDNA-b22616/protein.faa > /dev/null
[2023-03-17 08:40:15,984] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:40:15,984] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgeb4c598c-de0a-4f3a-bd5a-50ea8a0cd154/OceanDNA-b22616.fa]
[2023-03-17 08:40:16,026] [INFO] Query marker FASTA was written to OceanDNA-b22616/markers.fasta
[2023-03-17 08:40:16,027] [INFO] Task started: Blastn
[2023-03-17 08:40:16,027] [INFO] Running command: blastn -query OceanDNA-b22616/markers.fasta -db /var/lib/cwl/stg7de5da07-1f87-434f-840d-4f9b05f79f7a/dqc_reference/reference_markers.fasta -out OceanDNA-b22616/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:40:16,550] [INFO] Task succeeded: Blastn
[2023-03-17 08:40:16,550] [INFO] Selected 15 target genomes.
[2023-03-17 08:40:16,551] [INFO] Target genome list was writen to OceanDNA-b22616/target_genomes.txt
[2023-03-17 08:40:16,789] [INFO] Task started: fastANI
[2023-03-17 08:40:16,789] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb4c598c-de0a-4f3a-bd5a-50ea8a0cd154/OceanDNA-b22616.fa --refList OceanDNA-b22616/target_genomes.txt --output OceanDNA-b22616/fastani_result.tsv --threads 1
[2023-03-17 08:40:28,043] [INFO] Task succeeded: fastANI
[2023-03-17 08:40:28,044] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7de5da07-1f87-434f-840d-4f9b05f79f7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:40:28,044] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7de5da07-1f87-434f-840d-4f9b05f79f7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:40:28,044] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:40:28,044] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 08:40:28,044] [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 08:40:28,044] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22616/tc_result.tsv
[2023-03-17 08:40:28,044] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:40:28,044] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:40:28,044] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7de5da07-1f87-434f-840d-4f9b05f79f7a/dqc_reference/checkm_data
[2023-03-17 08:40:28,047] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:40:28,056] [INFO] Task started: CheckM
[2023-03-17 08:40:28,056] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22616/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22616/checkm_input OceanDNA-b22616/checkm_result
[2023-03-17 08:42:16,839] [INFO] Task succeeded: CheckM
[2023-03-17 08:42:16,840] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:42:16,844] [INFO] ===== Completeness check finished =====
[2023-03-17 08:42:16,845] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:42:16,845] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22616/markers.fasta)
[2023-03-17 08:42:16,846] [INFO] Task started: Blastn
[2023-03-17 08:42:16,846] [INFO] Running command: blastn -query OceanDNA-b22616/markers.fasta -db /var/lib/cwl/stg7de5da07-1f87-434f-840d-4f9b05f79f7a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22616/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:42:17,556] [INFO] Task succeeded: Blastn
[2023-03-17 08:42:17,557] [INFO] Selected 15 target genomes.
[2023-03-17 08:42:17,557] [INFO] Target genome list was writen to OceanDNA-b22616/target_genomes_gtdb.txt
[2023-03-17 08:42:17,791] [INFO] Task started: fastANI
[2023-03-17 08:42:17,791] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb4c598c-de0a-4f3a-bd5a-50ea8a0cd154/OceanDNA-b22616.fa --refList OceanDNA-b22616/target_genomes_gtdb.txt --output OceanDNA-b22616/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:42:33,056] [INFO] Task succeeded: fastANI
[2023-03-17 08:42:33,059] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 08:42:33,059] [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_002724245.1	s__UBA9264 sp002724245	99.7365	2247	2433	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA9264	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002709225.1	s__UBA9264 sp002709225	83.6296	1465	2433	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA9264	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702965.1	s__UBA9264 sp002702965	76.9129	396	2433	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA9264	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 08:42:33,059] [INFO] GTDB search result was written to OceanDNA-b22616/result_gtdb.tsv
[2023-03-17 08:42:33,059] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:42:33,060] [INFO] DFAST_QC result json was written to OceanDNA-b22616/dqc_result.json
[2023-03-17 08:42:33,060] [INFO] DFAST_QC completed!
[2023-03-17 08:42:33,060] [INFO] Total running time: 0h3m6s