[2023-03-15 20:34:26,740] [INFO] DFAST_QC pipeline started.
[2023-03-15 20:34:26,741] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 20:34:26,741] [INFO] DQC Reference Directory: /var/lib/cwl/stga9cbe28b-4317-4241-abae-9386e659d8af/dqc_reference
[2023-03-15 20:34:28,459] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 20:34:28,459] [INFO] Task started: Prodigal
[2023-03-15 20:34:28,460] [INFO] Running command: cat /var/lib/cwl/stgb87a53a0-56f7-43a7-ad92-ea217f00cf9a/OceanDNA-a1044.fa | prodigal -d OceanDNA-a1044/cds.fna -a OceanDNA-a1044/protein.faa -g 11 -q > /dev/null
[2023-03-15 20:34:32,710] [INFO] Task succeeded: Prodigal
[2023-03-15 20:34:32,711] [INFO] Task started: HMMsearch
[2023-03-15 20:34:32,711] [INFO] Running command: hmmsearch --tblout OceanDNA-a1044/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9cbe28b-4317-4241-abae-9386e659d8af/dqc_reference/reference_markers.hmm OceanDNA-a1044/protein.faa > /dev/null
[2023-03-15 20:34:32,848] [INFO] Task succeeded: HMMsearch
[2023-03-15 20:34:32,849] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgb87a53a0-56f7-43a7-ad92-ea217f00cf9a/OceanDNA-a1044.fa]
[2023-03-15 20:34:32,853] [INFO] Query marker FASTA was written to OceanDNA-a1044/markers.fasta
[2023-03-15 20:34:32,854] [INFO] Task started: Blastn
[2023-03-15 20:34:32,854] [INFO] Running command: blastn -query OceanDNA-a1044/markers.fasta -db /var/lib/cwl/stga9cbe28b-4317-4241-abae-9386e659d8af/dqc_reference/reference_markers.fasta -out OceanDNA-a1044/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:34:33,913] [INFO] Task succeeded: Blastn
[2023-03-15 20:34:33,914] [INFO] Selected 2 target genomes.
[2023-03-15 20:34:33,914] [INFO] Target genome list was writen to OceanDNA-a1044/target_genomes.txt
[2023-03-15 20:34:33,916] [INFO] Task started: fastANI
[2023-03-15 20:34:33,916] [INFO] Running command: fastANI --query /var/lib/cwl/stgb87a53a0-56f7-43a7-ad92-ea217f00cf9a/OceanDNA-a1044.fa --refList OceanDNA-a1044/target_genomes.txt --output OceanDNA-a1044/fastani_result.tsv --threads 1
[2023-03-15 20:34:34,959] [INFO] Task succeeded: fastANI
[2023-03-15 20:34:34,960] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9cbe28b-4317-4241-abae-9386e659d8af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 20:34:34,960] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9cbe28b-4317-4241-abae-9386e659d8af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 20:34:34,960] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 20:34:34,960] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 20:34:34,960] [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 20:34:34,960] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1044/tc_result.tsv
[2023-03-15 20:34:34,961] [INFO] ===== Taxonomy check completed =====
[2023-03-15 20:34:34,961] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 20:34:34,961] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9cbe28b-4317-4241-abae-9386e659d8af/dqc_reference/checkm_data
[2023-03-15 20:34:34,963] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 20:34:34,965] [INFO] Task started: CheckM
[2023-03-15 20:34:34,965] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1044/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1044/checkm_input OceanDNA-a1044/checkm_result
[2023-03-15 20:34:54,883] [INFO] Task succeeded: CheckM
[2023-03-15 20:34:54,883] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 20:34:54,884] [INFO] ===== Completeness check finished =====
[2023-03-15 20:34:54,884] [INFO] ===== Start GTDB Search =====
[2023-03-15 20:34:54,884] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1044/markers.fasta)
[2023-03-15 20:34:54,886] [INFO] Task started: Blastn
[2023-03-15 20:34:54,886] [INFO] Running command: blastn -query OceanDNA-a1044/markers.fasta -db /var/lib/cwl/stga9cbe28b-4317-4241-abae-9386e659d8af/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1044/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:34:56,489] [INFO] Task succeeded: Blastn
[2023-03-15 20:34:56,490] [INFO] Selected 8 target genomes.
[2023-03-15 20:34:56,490] [INFO] Target genome list was writen to OceanDNA-a1044/target_genomes_gtdb.txt
[2023-03-15 20:34:56,788] [INFO] Task started: fastANI
[2023-03-15 20:34:56,788] [INFO] Running command: fastANI --query /var/lib/cwl/stgb87a53a0-56f7-43a7-ad92-ea217f00cf9a/OceanDNA-a1044.fa --refList OceanDNA-a1044/target_genomes_gtdb.txt --output OceanDNA-a1044/fastani_result_gtdb.tsv --threads 1
[2023-03-15 20:34:58,314] [INFO] Task succeeded: fastANI
[2023-03-15 20:34:58,318] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 20:34:58,318] [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_018693315.1	s__JAGVXH01 sp018693315	99.8591	172	183	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Pacearchaeales;f__GW2011-AR1;g__JAGVXH01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018697035.1	s__JAGVXH01 sp018697035	77.8841	78	183	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Pacearchaeales;f__GW2011-AR1;g__JAGVXH01	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018901375.1	s__JAGVXH01 sp018901375	77.654	73	183	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Pacearchaeales;f__GW2011-AR1;g__JAGVXH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018303845.1	s__JAGVXH01 sp018303845	76.9905	55	183	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Pacearchaeales;f__GW2011-AR1;g__JAGVXH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018830525.1	s__JAGVXH01 sp018830525	76.7566	61	183	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Pacearchaeales;f__GW2011-AR1;g__JAGVXH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 20:34:58,319] [INFO] GTDB search result was written to OceanDNA-a1044/result_gtdb.tsv
[2023-03-15 20:34:58,319] [INFO] ===== GTDB Search completed =====
[2023-03-15 20:34:58,319] [INFO] DFAST_QC result json was written to OceanDNA-a1044/dqc_result.json
[2023-03-15 20:34:58,319] [INFO] DFAST_QC completed!
[2023-03-15 20:34:58,319] [INFO] Total running time: 0h0m32s