[2023-03-17 11:00:13,106] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:00:13,106] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:00:13,106] [INFO] DQC Reference Directory: /var/lib/cwl/stge098bf76-8ffb-4c62-8700-c8191b34aa68/dqc_reference
[2023-03-17 11:00:14,194] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:00:14,194] [INFO] Task started: Prodigal
[2023-03-17 11:00:14,194] [INFO] Running command: cat /var/lib/cwl/stg36039462-d782-4f26-9e55-e5d3fc94e6b7/OceanDNA-b15967.fa | prodigal -d OceanDNA-b15967/cds.fna -a OceanDNA-b15967/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:00:24,616] [INFO] Task succeeded: Prodigal
[2023-03-17 11:00:24,616] [INFO] Task started: HMMsearch
[2023-03-17 11:00:24,616] [INFO] Running command: hmmsearch --tblout OceanDNA-b15967/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge098bf76-8ffb-4c62-8700-c8191b34aa68/dqc_reference/reference_markers.hmm OceanDNA-b15967/protein.faa > /dev/null
[2023-03-17 11:00:24,790] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:00:24,790] [INFO] Found 6/6 markers.
[2023-03-17 11:00:24,812] [INFO] Query marker FASTA was written to OceanDNA-b15967/markers.fasta
[2023-03-17 11:00:24,813] [INFO] Task started: Blastn
[2023-03-17 11:00:24,813] [INFO] Running command: blastn -query OceanDNA-b15967/markers.fasta -db /var/lib/cwl/stge098bf76-8ffb-4c62-8700-c8191b34aa68/dqc_reference/reference_markers.fasta -out OceanDNA-b15967/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:00:25,385] [INFO] Task succeeded: Blastn
[2023-03-17 11:00:25,389] [INFO] Selected 17 target genomes.
[2023-03-17 11:00:25,389] [INFO] Target genome list was writen to OceanDNA-b15967/target_genomes.txt
[2023-03-17 11:00:25,460] [INFO] Task started: fastANI
[2023-03-17 11:00:25,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg36039462-d782-4f26-9e55-e5d3fc94e6b7/OceanDNA-b15967.fa --refList OceanDNA-b15967/target_genomes.txt --output OceanDNA-b15967/fastani_result.tsv --threads 1
[2023-03-17 11:00:40,075] [INFO] Task succeeded: fastANI
[2023-03-17 11:00:40,075] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge098bf76-8ffb-4c62-8700-c8191b34aa68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:00:40,075] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge098bf76-8ffb-4c62-8700-c8191b34aa68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:00:40,076] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:00:40,076] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:00:40,076] [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 11:00:40,076] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15967/tc_result.tsv
[2023-03-17 11:00:40,076] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:00:40,076] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:00:40,076] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge098bf76-8ffb-4c62-8700-c8191b34aa68/dqc_reference/checkm_data
[2023-03-17 11:00:40,079] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:00:40,092] [INFO] Task started: CheckM
[2023-03-17 11:00:40,092] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15967/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15967/checkm_input OceanDNA-b15967/checkm_result
[2023-03-17 11:01:10,550] [INFO] Task succeeded: CheckM
[2023-03-17 11:01:10,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.59%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:01:10,576] [INFO] ===== Completeness check finished =====
[2023-03-17 11:01:10,576] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:01:10,576] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15967/markers.fasta)
[2023-03-17 11:01:10,577] [INFO] Task started: Blastn
[2023-03-17 11:01:10,577] [INFO] Running command: blastn -query OceanDNA-b15967/markers.fasta -db /var/lib/cwl/stge098bf76-8ffb-4c62-8700-c8191b34aa68/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15967/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:01:11,494] [INFO] Task succeeded: Blastn
[2023-03-17 11:01:11,495] [INFO] Selected 15 target genomes.
[2023-03-17 11:01:11,495] [INFO] Target genome list was writen to OceanDNA-b15967/target_genomes_gtdb.txt
[2023-03-17 11:01:11,510] [INFO] Task started: fastANI
[2023-03-17 11:01:11,510] [INFO] Running command: fastANI --query /var/lib/cwl/stg36039462-d782-4f26-9e55-e5d3fc94e6b7/OceanDNA-b15967.fa --refList OceanDNA-b15967/target_genomes_gtdb.txt --output OceanDNA-b15967/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:01:21,354] [INFO] Task succeeded: fastANI
[2023-03-17 11:01:21,357] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:01:21,358] [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_002347925.1	s__UBA12225 sp002347925	98.9965	450	479	d__Bacteria;p__Chloroflexota;c__UBA2235;o__UBA12225;f__UBA12225;g__UBA12225	95.0	98.21	95.05	0.90	0.85	18	conclusive
GCA_009693165.1	s__UBA12225 sp009693165	84.5238	259	479	d__Bacteria;p__Chloroflexota;c__UBA2235;o__UBA12225;f__UBA12225;g__UBA12225	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903836285.1	s__CAILQO01 sp903836285	77.3427	80	479	d__Bacteria;p__Chloroflexota;c__UBA2235;o__UBA12225;f__UBA12225;g__CAILQO01	95.0	98.79	98.57	0.84	0.81	6	-
--------------------------------------------------------------------------------
[2023-03-17 11:01:21,358] [INFO] GTDB search result was written to OceanDNA-b15967/result_gtdb.tsv
[2023-03-17 11:01:21,358] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:01:21,358] [INFO] DFAST_QC result json was written to OceanDNA-b15967/dqc_result.json
[2023-03-17 11:01:21,359] [INFO] DFAST_QC completed!
[2023-03-17 11:01:21,359] [INFO] Total running time: 0h1m8s