[2023-03-16 08:50:59,684] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:50:59,685] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:50:59,685] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e33f32b-209c-49dd-b4cc-3c1c47b21911/dqc_reference
[2023-03-16 08:51:00,916] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:51:00,916] [INFO] Task started: Prodigal
[2023-03-16 08:51:00,916] [INFO] Running command: cat /var/lib/cwl/stg5452b6ba-0d79-49ad-a16d-0e131f6caef5/OceanDNA-b34885.fa | prodigal -d OceanDNA-b34885/cds.fna -a OceanDNA-b34885/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:51:22,892] [INFO] Task succeeded: Prodigal
[2023-03-16 08:51:22,893] [INFO] Task started: HMMsearch
[2023-03-16 08:51:22,893] [INFO] Running command: hmmsearch --tblout OceanDNA-b34885/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e33f32b-209c-49dd-b4cc-3c1c47b21911/dqc_reference/reference_markers.hmm OceanDNA-b34885/protein.faa > /dev/null
[2023-03-16 08:51:23,140] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:51:23,140] [INFO] Found 6/6 markers.
[2023-03-16 08:51:23,166] [INFO] Query marker FASTA was written to OceanDNA-b34885/markers.fasta
[2023-03-16 08:51:23,167] [INFO] Task started: Blastn
[2023-03-16 08:51:23,167] [INFO] Running command: blastn -query OceanDNA-b34885/markers.fasta -db /var/lib/cwl/stg1e33f32b-209c-49dd-b4cc-3c1c47b21911/dqc_reference/reference_markers.fasta -out OceanDNA-b34885/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:51:23,789] [INFO] Task succeeded: Blastn
[2023-03-16 08:51:23,793] [INFO] Selected 15 target genomes.
[2023-03-16 08:51:23,793] [INFO] Target genome list was writen to OceanDNA-b34885/target_genomes.txt
[2023-03-16 08:51:23,810] [INFO] Task started: fastANI
[2023-03-16 08:51:23,810] [INFO] Running command: fastANI --query /var/lib/cwl/stg5452b6ba-0d79-49ad-a16d-0e131f6caef5/OceanDNA-b34885.fa --refList OceanDNA-b34885/target_genomes.txt --output OceanDNA-b34885/fastani_result.tsv --threads 1
[2023-03-16 08:51:36,237] [INFO] Task succeeded: fastANI
[2023-03-16 08:51:36,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e33f32b-209c-49dd-b4cc-3c1c47b21911/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:51:36,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e33f32b-209c-49dd-b4cc-3c1c47b21911/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:51:36,244] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:51:36,245] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:51:36,245] [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 psychrophila	strain=170	GCA_000315075.1	326544	326544	type	True	83.3446	879	1328	95	below_threshold
Paraglaciecola psychrophila	strain=170	GCA_000347635.1	326544	326544	type	True	83.3262	888	1328	95	below_threshold
Paraglaciecola arctica	strain=BSs20135	GCA_000314995.1	1128911	1128911	type	True	81.1964	758	1328	95	below_threshold
Paraglaciecola marina	strain=D3211	GCA_004360155.1	2500157	2500157	type	True	77.6284	218	1328	95	below_threshold
Paraglaciecola aquimarina	strain=GGW-M5	GCA_021532655.1	1235557	1235557	type	True	77.5114	221	1328	95	below_threshold
Paraglaciecola hydrolytica	strain=S66	GCA_001565895.1	1799789	1799789	type	True	76.9633	159	1328	95	below_threshold
Paraglaciecola mesophila	strain=KMM 241	GCA_000315015.1	197222	197222	type	True	76.922	112	1328	95	below_threshold
Aliiglaciecola lipolytica	strain=E3	GCA_000314975.1	477689	477689	type	True	76.6583	81	1328	95	below_threshold
Alteromonas profundi	strain=345S023	GCA_010500865.1	2696062	2696062	type	True	76.2999	51	1328	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:51:36,247] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34885/tc_result.tsv
[2023-03-16 08:51:36,249] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:51:36,249] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:51:36,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e33f32b-209c-49dd-b4cc-3c1c47b21911/dqc_reference/checkm_data
[2023-03-16 08:51:36,250] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:51:36,258] [INFO] Task started: CheckM
[2023-03-16 08:51:36,258] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34885/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34885/checkm_input OceanDNA-b34885/checkm_result
[2023-03-16 08:52:32,585] [INFO] Task succeeded: CheckM
[2023-03-16 08:52:32,586] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:52:32,598] [INFO] ===== Completeness check finished =====
[2023-03-16 08:52:32,598] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:52:32,598] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34885/markers.fasta)
[2023-03-16 08:52:32,599] [INFO] Task started: Blastn
[2023-03-16 08:52:32,599] [INFO] Running command: blastn -query OceanDNA-b34885/markers.fasta -db /var/lib/cwl/stg1e33f32b-209c-49dd-b4cc-3c1c47b21911/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34885/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:52:33,593] [INFO] Task succeeded: Blastn
[2023-03-16 08:52:33,603] [INFO] Selected 7 target genomes.
[2023-03-16 08:52:33,603] [INFO] Target genome list was writen to OceanDNA-b34885/target_genomes_gtdb.txt
[2023-03-16 08:52:33,612] [INFO] Task started: fastANI
[2023-03-16 08:52:33,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg5452b6ba-0d79-49ad-a16d-0e131f6caef5/OceanDNA-b34885.fa --refList OceanDNA-b34885/target_genomes_gtdb.txt --output OceanDNA-b34885/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:52:40,825] [INFO] Task succeeded: fastANI
[2023-03-16 08:52:40,830] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 08:52:40,830] [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_905479025.1	s__Paraglaciecola sp905479025	95.9092	620	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002835935.1	s__Paraglaciecola sp002835935	86.4062	982	1328	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	83.3315	887	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	99.98	99.98	1.00	1.00	2	-
GCA_003232445.1	s__Paraglaciecola arctica_A	83.223	438	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000314995.1	s__Paraglaciecola arctica	81.1966	757	1328	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	78.8411	479	1328	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	77.5315	242	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:52:40,834] [INFO] GTDB search result was written to OceanDNA-b34885/result_gtdb.tsv
[2023-03-16 08:52:40,840] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:52:40,845] [INFO] DFAST_QC result json was written to OceanDNA-b34885/dqc_result.json
[2023-03-16 08:52:40,846] [INFO] DFAST_QC completed!
[2023-03-16 08:52:40,846] [INFO] Total running time: 0h1m41s