[2023-03-15 11:20:29,258] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:20:29,260] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:20:29,260] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e7cda11-9b3f-4cfe-8e40-de5eb4e361f2/dqc_reference
[2023-03-15 11:20:30,378] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:20:30,378] [INFO] Task started: Prodigal
[2023-03-15 11:20:30,378] [INFO] Running command: cat /var/lib/cwl/stg22c9fc90-3a0f-4f20-bc4a-f182a7ab61a9/OceanDNA-b46829.fa | prodigal -d OceanDNA-b46829/cds.fna -a OceanDNA-b46829/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:20:51,025] [INFO] Task succeeded: Prodigal
[2023-03-15 11:20:51,025] [INFO] Task started: HMMsearch
[2023-03-15 11:20:51,025] [INFO] Running command: hmmsearch --tblout OceanDNA-b46829/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e7cda11-9b3f-4cfe-8e40-de5eb4e361f2/dqc_reference/reference_markers.hmm OceanDNA-b46829/protein.faa > /dev/null
[2023-03-15 11:20:51,200] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:20:51,201] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg22c9fc90-3a0f-4f20-bc4a-f182a7ab61a9/OceanDNA-b46829.fa]
[2023-03-15 11:20:51,246] [INFO] Query marker FASTA was written to OceanDNA-b46829/markers.fasta
[2023-03-15 11:20:51,247] [INFO] Task started: Blastn
[2023-03-15 11:20:51,248] [INFO] Running command: blastn -query OceanDNA-b46829/markers.fasta -db /var/lib/cwl/stg3e7cda11-9b3f-4cfe-8e40-de5eb4e361f2/dqc_reference/reference_markers.fasta -out OceanDNA-b46829/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:20:51,692] [INFO] Task succeeded: Blastn
[2023-03-15 11:20:51,698] [INFO] Selected 15 target genomes.
[2023-03-15 11:20:51,698] [INFO] Target genome list was writen to OceanDNA-b46829/target_genomes.txt
[2023-03-15 11:20:51,718] [INFO] Task started: fastANI
[2023-03-15 11:20:51,719] [INFO] Running command: fastANI --query /var/lib/cwl/stg22c9fc90-3a0f-4f20-bc4a-f182a7ab61a9/OceanDNA-b46829.fa --refList OceanDNA-b46829/target_genomes.txt --output OceanDNA-b46829/fastani_result.tsv --threads 1
[2023-03-15 11:21:04,770] [INFO] Task succeeded: fastANI
[2023-03-15 11:21:04,771] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e7cda11-9b3f-4cfe-8e40-de5eb4e361f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:21:04,771] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e7cda11-9b3f-4cfe-8e40-de5eb4e361f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:21:04,771] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:21:04,771] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:21:04,771] [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 11:21:04,775] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46829/tc_result.tsv
[2023-03-15 11:21:04,779] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:21:04,779] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:21:04,779] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e7cda11-9b3f-4cfe-8e40-de5eb4e361f2/dqc_reference/checkm_data
[2023-03-15 11:21:04,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:21:04,797] [INFO] Task started: CheckM
[2023-03-15 11:21:04,797] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46829/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46829/checkm_input OceanDNA-b46829/checkm_result
[2023-03-15 11:21:59,933] [INFO] Task succeeded: CheckM
[2023-03-15 11:21:59,933] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:21:59,975] [INFO] ===== Completeness check finished =====
[2023-03-15 11:21:59,975] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:21:59,975] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46829/markers.fasta)
[2023-03-15 11:21:59,977] [INFO] Task started: Blastn
[2023-03-15 11:21:59,977] [INFO] Running command: blastn -query OceanDNA-b46829/markers.fasta -db /var/lib/cwl/stg3e7cda11-9b3f-4cfe-8e40-de5eb4e361f2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46829/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:22:00,405] [INFO] Task succeeded: Blastn
[2023-03-15 11:22:00,408] [INFO] Selected 15 target genomes.
[2023-03-15 11:22:00,408] [INFO] Target genome list was writen to OceanDNA-b46829/target_genomes_gtdb.txt
[2023-03-15 11:22:00,421] [INFO] Task started: fastANI
[2023-03-15 11:22:00,421] [INFO] Running command: fastANI --query /var/lib/cwl/stg22c9fc90-3a0f-4f20-bc4a-f182a7ab61a9/OceanDNA-b46829.fa --refList OceanDNA-b46829/target_genomes_gtdb.txt --output OceanDNA-b46829/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:22:10,338] [INFO] Task succeeded: fastANI
[2023-03-15 11:22:10,341] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:22:10,341] [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_002172625.1	s__SW10 sp002172625	79.0859	268	657	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	98.72	98.72	0.89	0.89	2	-
GCA_018222765.1	s__SW10 sp018222765	79.0083	304	657	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729295.1	s__SW10 sp002729295	78.8991	224	657	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	99.31	99.31	0.79	0.79	2	-
GCA_905182405.1	s__SW10 sp905182405	76.7448	72	657	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:22:10,346] [INFO] GTDB search result was written to OceanDNA-b46829/result_gtdb.tsv
[2023-03-15 11:22:10,354] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:22:10,360] [INFO] DFAST_QC result json was written to OceanDNA-b46829/dqc_result.json
[2023-03-15 11:22:10,360] [INFO] DFAST_QC completed!
[2023-03-15 11:22:10,360] [INFO] Total running time: 0h1m41s