[2023-03-16 08:47:19,703] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:47:19,703] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:47:19,703] [INFO] DQC Reference Directory: /var/lib/cwl/stg56bc2e52-2754-46ed-82c5-12c3ee3c4dbb/dqc_reference
[2023-03-16 08:47:20,909] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:47:20,910] [INFO] Task started: Prodigal
[2023-03-16 08:47:20,910] [INFO] Running command: cat /var/lib/cwl/stg114f4117-ea22-477d-8d36-966071305e3e/OceanDNA-b9791.fa | prodigal -d OceanDNA-b9791/cds.fna -a OceanDNA-b9791/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:47:43,199] [INFO] Task succeeded: Prodigal
[2023-03-16 08:47:43,199] [INFO] Task started: HMMsearch
[2023-03-16 08:47:43,199] [INFO] Running command: hmmsearch --tblout OceanDNA-b9791/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56bc2e52-2754-46ed-82c5-12c3ee3c4dbb/dqc_reference/reference_markers.hmm OceanDNA-b9791/protein.faa > /dev/null
[2023-03-16 08:47:43,410] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:47:43,411] [INFO] Found 6/6 markers.
[2023-03-16 08:47:43,429] [INFO] Query marker FASTA was written to OceanDNA-b9791/markers.fasta
[2023-03-16 08:47:43,430] [INFO] Task started: Blastn
[2023-03-16 08:47:43,430] [INFO] Running command: blastn -query OceanDNA-b9791/markers.fasta -db /var/lib/cwl/stg56bc2e52-2754-46ed-82c5-12c3ee3c4dbb/dqc_reference/reference_markers.fasta -out OceanDNA-b9791/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:47:43,974] [INFO] Task succeeded: Blastn
[2023-03-16 08:47:43,975] [INFO] Selected 19 target genomes.
[2023-03-16 08:47:43,975] [INFO] Target genome list was writen to OceanDNA-b9791/target_genomes.txt
[2023-03-16 08:47:43,993] [INFO] Task started: fastANI
[2023-03-16 08:47:43,993] [INFO] Running command: fastANI --query /var/lib/cwl/stg114f4117-ea22-477d-8d36-966071305e3e/OceanDNA-b9791.fa --refList OceanDNA-b9791/target_genomes.txt --output OceanDNA-b9791/fastani_result.tsv --threads 1
[2023-03-16 08:47:55,420] [INFO] Task succeeded: fastANI
[2023-03-16 08:47:55,421] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56bc2e52-2754-46ed-82c5-12c3ee3c4dbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:47:55,421] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56bc2e52-2754-46ed-82c5-12c3ee3c4dbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:47:55,426] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:47:55,426] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:47:55,426] [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
Nonlabens marinus	strain=S1-08	GCA_000831385.1	930802	930802	type	True	79.572	451	1007	95	below_threshold
Nonlabens antarcticus	strain=JCM 14068	GCA_015356755.1	392714	392714	type	True	78.9864	375	1007	95	below_threshold
Nonlabens agnitus	strain=JCM 17109	GCA_002994045.1	870484	870484	type	True	78.6052	362	1007	95	below_threshold
Nonlabens ponticola	strain=MJ115	GCA_003966335.1	2496866	2496866	type	True	77.4081	206	1007	95	below_threshold
Nonlabens spongiae	strain=JCM 13191	GCA_002117125.1	331648	331648	type	True	76.708	96	1007	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:47:55,426] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9791/tc_result.tsv
[2023-03-16 08:47:55,426] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:47:55,426] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:47:55,426] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56bc2e52-2754-46ed-82c5-12c3ee3c4dbb/dqc_reference/checkm_data
[2023-03-16 08:47:55,427] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:47:55,435] [INFO] Task started: CheckM
[2023-03-16 08:47:55,435] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9791/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9791/checkm_input OceanDNA-b9791/checkm_result
[2023-03-16 08:48:54,251] [INFO] Task succeeded: CheckM
[2023-03-16 08:48:54,251] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 08:48:54,254] [INFO] ===== Completeness check finished =====
[2023-03-16 08:48:54,254] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:48:54,254] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9791/markers.fasta)
[2023-03-16 08:48:54,256] [INFO] Task started: Blastn
[2023-03-16 08:48:54,256] [INFO] Running command: blastn -query OceanDNA-b9791/markers.fasta -db /var/lib/cwl/stg56bc2e52-2754-46ed-82c5-12c3ee3c4dbb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9791/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:48:55,141] [INFO] Task succeeded: Blastn
[2023-03-16 08:48:55,142] [INFO] Selected 14 target genomes.
[2023-03-16 08:48:55,142] [INFO] Target genome list was writen to OceanDNA-b9791/target_genomes_gtdb.txt
[2023-03-16 08:48:55,179] [INFO] Task started: fastANI
[2023-03-16 08:48:55,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg114f4117-ea22-477d-8d36-966071305e3e/OceanDNA-b9791.fa --refList OceanDNA-b9791/target_genomes_gtdb.txt --output OceanDNA-b9791/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:49:03,569] [INFO] Task succeeded: fastANI
[2023-03-16 08:49:03,575] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:49:03,575] [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
GCF_000831385.1	s__Nonlabens marinus	79.5713	451	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015356755.1	s__Nonlabens antarcticus	78.9864	375	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001413925.1	s__Nonlabens sp001413925	78.7588	358	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994045.1	s__Nonlabens agnitus	78.6168	361	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101765.1	s__Nonlabens sp900101765	78.3904	338	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966335.1	s__Nonlabens ponticola	77.4081	206	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401815.1	s__Nonlabens sp018401815	77.1037	123	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	99.14	99.12	0.97	0.97	3	-
GCF_012974865.1	s__Nonlabens sp012974865	77.0653	148	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:49:03,576] [INFO] GTDB search result was written to OceanDNA-b9791/result_gtdb.tsv
[2023-03-16 08:49:03,576] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:49:03,579] [INFO] DFAST_QC result json was written to OceanDNA-b9791/dqc_result.json
[2023-03-16 08:49:03,579] [INFO] DFAST_QC completed!
[2023-03-16 08:49:03,579] [INFO] Total running time: 0h1m44s