[2023-03-15 07:11:33,427] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:11:33,427] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:11:33,427] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b78a73c-33d8-4dee-989e-c63390fc644b/dqc_reference
[2023-03-15 07:11:34,521] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:11:34,521] [INFO] Task started: Prodigal
[2023-03-15 07:11:34,522] [INFO] Running command: cat /var/lib/cwl/stg75de010d-1734-4f2b-86db-e38f9d967226/OceanDNA-b23200.fa | prodigal -d OceanDNA-b23200/cds.fna -a OceanDNA-b23200/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:11:50,335] [INFO] Task succeeded: Prodigal
[2023-03-15 07:11:50,336] [INFO] Task started: HMMsearch
[2023-03-15 07:11:50,336] [INFO] Running command: hmmsearch --tblout OceanDNA-b23200/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b78a73c-33d8-4dee-989e-c63390fc644b/dqc_reference/reference_markers.hmm OceanDNA-b23200/protein.faa > /dev/null
[2023-03-15 07:11:50,588] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:11:50,589] [INFO] Found 6/6 markers.
[2023-03-15 07:11:50,614] [INFO] Query marker FASTA was written to OceanDNA-b23200/markers.fasta
[2023-03-15 07:11:50,615] [INFO] Task started: Blastn
[2023-03-15 07:11:50,615] [INFO] Running command: blastn -query OceanDNA-b23200/markers.fasta -db /var/lib/cwl/stg5b78a73c-33d8-4dee-989e-c63390fc644b/dqc_reference/reference_markers.fasta -out OceanDNA-b23200/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:11:51,143] [INFO] Task succeeded: Blastn
[2023-03-15 07:11:51,144] [INFO] Selected 16 target genomes.
[2023-03-15 07:11:51,145] [INFO] Target genome list was writen to OceanDNA-b23200/target_genomes.txt
[2023-03-15 07:11:51,155] [INFO] Task started: fastANI
[2023-03-15 07:11:51,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg75de010d-1734-4f2b-86db-e38f9d967226/OceanDNA-b23200.fa --refList OceanDNA-b23200/target_genomes.txt --output OceanDNA-b23200/fastani_result.tsv --threads 1
[2023-03-15 07:11:57,274] [INFO] Task succeeded: fastANI
[2023-03-15 07:11:57,275] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b78a73c-33d8-4dee-989e-c63390fc644b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:11:57,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b78a73c-33d8-4dee-989e-c63390fc644b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:11:57,275] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:11:57,275] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:11:57,275] [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
--------------------------------------------------------------------------------
[2023-03-15 07:11:57,285] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23200/tc_result.tsv
[2023-03-15 07:11:57,307] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:11:57,307] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:11:57,307] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b78a73c-33d8-4dee-989e-c63390fc644b/dqc_reference/checkm_data
[2023-03-15 07:11:57,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:11:57,397] [INFO] Task started: CheckM
[2023-03-15 07:11:57,397] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23200/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23200/checkm_input OceanDNA-b23200/checkm_result
[2023-03-15 07:12:40,292] [INFO] Task succeeded: CheckM
[2023-03-15 07:12:40,293] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.08%
Contamintation: 1.50%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-15 07:12:40,420] [INFO] ===== Completeness check finished =====
[2023-03-15 07:12:40,421] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:12:40,421] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23200/markers.fasta)
[2023-03-15 07:12:40,422] [INFO] Task started: Blastn
[2023-03-15 07:12:40,422] [INFO] Running command: blastn -query OceanDNA-b23200/markers.fasta -db /var/lib/cwl/stg5b78a73c-33d8-4dee-989e-c63390fc644b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23200/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:12:41,098] [INFO] Task succeeded: Blastn
[2023-03-15 07:12:41,101] [INFO] Selected 19 target genomes.
[2023-03-15 07:12:41,101] [INFO] Target genome list was writen to OceanDNA-b23200/target_genomes_gtdb.txt
[2023-03-15 07:12:41,165] [INFO] Task started: fastANI
[2023-03-15 07:12:41,165] [INFO] Running command: fastANI --query /var/lib/cwl/stg75de010d-1734-4f2b-86db-e38f9d967226/OceanDNA-b23200.fa --refList OceanDNA-b23200/target_genomes_gtdb.txt --output OceanDNA-b23200/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:12:51,907] [INFO] Task succeeded: fastANI
[2023-03-15 07:12:51,910] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:12:51,910] [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_002729015.1	s__TMED15 sp002729015	77.5803	399	969	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__UBA9662;g__TMED15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714785.1	s__TMED15 sp002714785	77.4809	388	969	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__UBA9662;g__TMED15	95.0	97.64	97.01	0.88	0.83	5	-
GCA_002699335.1	s__GCA-2699335 sp002699335	77.0122	74	969	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__UBA9662;g__GCA-2699335	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:12:51,912] [INFO] GTDB search result was written to OceanDNA-b23200/result_gtdb.tsv
[2023-03-15 07:12:51,913] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:12:51,916] [INFO] DFAST_QC result json was written to OceanDNA-b23200/dqc_result.json
[2023-03-15 07:12:51,916] [INFO] DFAST_QC completed!
[2023-03-15 07:12:51,916] [INFO] Total running time: 0h1m18s