[2023-03-18 06:15:37,928] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:15:37,929] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:15:37,929] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d09bd32-19fc-4c17-a8e1-52e4a4f81d1d/dqc_reference
[2023-03-18 06:15:39,035] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:15:39,036] [INFO] Task started: Prodigal
[2023-03-18 06:15:39,037] [INFO] Running command: cat /var/lib/cwl/stgf2a37f92-ced1-4355-b432-82e298baf55e/OceanDNA-b34923.fa | prodigal -d OceanDNA-b34923/cds.fna -a OceanDNA-b34923/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:15:49,790] [INFO] Task succeeded: Prodigal
[2023-03-18 06:15:49,790] [INFO] Task started: HMMsearch
[2023-03-18 06:15:49,790] [INFO] Running command: hmmsearch --tblout OceanDNA-b34923/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d09bd32-19fc-4c17-a8e1-52e4a4f81d1d/dqc_reference/reference_markers.hmm OceanDNA-b34923/protein.faa > /dev/null
[2023-03-18 06:15:49,985] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:15:49,986] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf2a37f92-ced1-4355-b432-82e298baf55e/OceanDNA-b34923.fa]
[2023-03-18 06:15:50,009] [INFO] Query marker FASTA was written to OceanDNA-b34923/markers.fasta
[2023-03-18 06:15:50,010] [INFO] Task started: Blastn
[2023-03-18 06:15:50,010] [INFO] Running command: blastn -query OceanDNA-b34923/markers.fasta -db /var/lib/cwl/stg3d09bd32-19fc-4c17-a8e1-52e4a4f81d1d/dqc_reference/reference_markers.fasta -out OceanDNA-b34923/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:15:50,589] [INFO] Task succeeded: Blastn
[2023-03-18 06:15:50,590] [INFO] Selected 20 target genomes.
[2023-03-18 06:15:50,590] [INFO] Target genome list was writen to OceanDNA-b34923/target_genomes.txt
[2023-03-18 06:15:50,621] [INFO] Task started: fastANI
[2023-03-18 06:15:50,621] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2a37f92-ced1-4355-b432-82e298baf55e/OceanDNA-b34923.fa --refList OceanDNA-b34923/target_genomes.txt --output OceanDNA-b34923/fastani_result.tsv --threads 1
[2023-03-18 06:16:04,208] [INFO] Task succeeded: fastANI
[2023-03-18 06:16:04,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d09bd32-19fc-4c17-a8e1-52e4a4f81d1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:16:04,208] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d09bd32-19fc-4c17-a8e1-52e4a4f81d1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:16:04,213] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 06:16:04,214] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 06:16:04,214] [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
Paraglaciecola hydrolytica	strain=S66	GCA_001565895.1	1799789	1799789	type	True	97.9605	415	455	95	conclusive
Paraglaciecola psychrophila	strain=170	GCA_000315075.1	326544	326544	type	True	77.5814	58	455	95	below_threshold
Paraglaciecola psychrophila	strain=170	GCA_000347635.1	326544	326544	type	True	77.4849	58	455	95	below_threshold
Paraglaciecola arctica	strain=BSs20135	GCA_000314995.1	1128911	1128911	type	True	77.3456	66	455	95	below_threshold
Paraglaciecola aquimarina	strain=GGW-M5	GCA_021532655.1	1235557	1235557	type	True	77.0884	60	455	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 06:16:04,214] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34923/tc_result.tsv
[2023-03-18 06:16:04,214] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:16:04,214] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:16:04,214] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d09bd32-19fc-4c17-a8e1-52e4a4f81d1d/dqc_reference/checkm_data
[2023-03-18 06:16:04,215] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:16:04,220] [INFO] Task started: CheckM
[2023-03-18 06:16:04,220] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34923/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34923/checkm_input OceanDNA-b34923/checkm_result
[2023-03-18 06:16:35,982] [INFO] Task succeeded: CheckM
[2023-03-18 06:16:35,982] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.69%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 06:16:36,013] [INFO] ===== Completeness check finished =====
[2023-03-18 06:16:36,013] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:16:36,013] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34923/markers.fasta)
[2023-03-18 06:16:36,014] [INFO] Task started: Blastn
[2023-03-18 06:16:36,014] [INFO] Running command: blastn -query OceanDNA-b34923/markers.fasta -db /var/lib/cwl/stg3d09bd32-19fc-4c17-a8e1-52e4a4f81d1d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34923/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:16:36,843] [INFO] Task succeeded: Blastn
[2023-03-18 06:16:36,844] [INFO] Selected 22 target genomes.
[2023-03-18 06:16:36,844] [INFO] Target genome list was writen to OceanDNA-b34923/target_genomes_gtdb.txt
[2023-03-18 06:16:36,907] [INFO] Task started: fastANI
[2023-03-18 06:16:36,907] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2a37f92-ced1-4355-b432-82e298baf55e/OceanDNA-b34923.fa --refList OceanDNA-b34923/target_genomes_gtdb.txt --output OceanDNA-b34923/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:16:53,211] [INFO] Task succeeded: fastANI
[2023-03-18 06:16:53,217] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 06:16:53,217] [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_001565895.1	s__Paraglaciecola hydrolytica	97.9605	415	455	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009993955.1	s__Paraglaciecola sp009993955	78.0098	77	455	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	99.98	99.98	0.98	0.98	2	-
GCF_002835935.1	s__Paraglaciecola sp002835935	77.5854	57	455	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000347635.1	s__Paraglaciecola psychrophila	77.4849	58	455	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000314995.1	s__Paraglaciecola arctica	77.3456	66	455	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796765.1	s__Paraglaciecola sp009796765	77.1114	59	455	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861065.1	s__Paraglaciecola arctica_B	76.9787	60	455	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014225.1	s__Paraglaciecola atlantica_A	76.4931	52	455	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 06:16:53,219] [INFO] GTDB search result was written to OceanDNA-b34923/result_gtdb.tsv
[2023-03-18 06:16:53,220] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:16:53,224] [INFO] DFAST_QC result json was written to OceanDNA-b34923/dqc_result.json
[2023-03-18 06:16:53,224] [INFO] DFAST_QC completed!
[2023-03-18 06:16:53,224] [INFO] Total running time: 0h1m15s