[2023-03-17 03:24:50,898] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:24:50,898] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:24:50,898] [INFO] DQC Reference Directory: /var/lib/cwl/stg0db24aa3-1b17-4c9c-85e2-cc2ca559603b/dqc_reference
[2023-03-17 03:24:51,987] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:24:51,987] [INFO] Task started: Prodigal
[2023-03-17 03:24:51,987] [INFO] Running command: cat /var/lib/cwl/stg86e339fe-981e-492c-b62a-4a450cad82a4/OceanDNA-b34665.fa | prodigal -d OceanDNA-b34665/cds.fna -a OceanDNA-b34665/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:24:57,184] [INFO] Task succeeded: Prodigal
[2023-03-17 03:24:57,184] [INFO] Task started: HMMsearch
[2023-03-17 03:24:57,184] [INFO] Running command: hmmsearch --tblout OceanDNA-b34665/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0db24aa3-1b17-4c9c-85e2-cc2ca559603b/dqc_reference/reference_markers.hmm OceanDNA-b34665/protein.faa > /dev/null
[2023-03-17 03:24:57,348] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:24:57,349] [INFO] Found 6/6 markers.
[2023-03-17 03:24:57,364] [INFO] Query marker FASTA was written to OceanDNA-b34665/markers.fasta
[2023-03-17 03:24:57,364] [INFO] Task started: Blastn
[2023-03-17 03:24:57,364] [INFO] Running command: blastn -query OceanDNA-b34665/markers.fasta -db /var/lib/cwl/stg0db24aa3-1b17-4c9c-85e2-cc2ca559603b/dqc_reference/reference_markers.fasta -out OceanDNA-b34665/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:24:57,877] [INFO] Task succeeded: Blastn
[2023-03-17 03:24:57,880] [INFO] Selected 20 target genomes.
[2023-03-17 03:24:57,880] [INFO] Target genome list was writen to OceanDNA-b34665/target_genomes.txt
[2023-03-17 03:24:57,893] [INFO] Task started: fastANI
[2023-03-17 03:24:57,893] [INFO] Running command: fastANI --query /var/lib/cwl/stg86e339fe-981e-492c-b62a-4a450cad82a4/OceanDNA-b34665.fa --refList OceanDNA-b34665/target_genomes.txt --output OceanDNA-b34665/fastani_result.tsv --threads 1
[2023-03-17 03:25:10,387] [INFO] Task succeeded: fastANI
[2023-03-17 03:25:10,388] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0db24aa3-1b17-4c9c-85e2-cc2ca559603b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:25:10,388] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0db24aa3-1b17-4c9c-85e2-cc2ca559603b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:25:10,394] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:25:10,394] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:25:10,394] [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
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	78.9645	88	231	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	78.2146	83	231	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	78.0517	68	231	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	77.7844	62	231	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	77.6837	71	231	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:25:10,394] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34665/tc_result.tsv
[2023-03-17 03:25:10,394] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:25:10,394] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:25:10,394] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0db24aa3-1b17-4c9c-85e2-cc2ca559603b/dqc_reference/checkm_data
[2023-03-17 03:25:10,395] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:25:10,399] [INFO] Task started: CheckM
[2023-03-17 03:25:10,400] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34665/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34665/checkm_input OceanDNA-b34665/checkm_result
[2023-03-17 03:25:29,584] [INFO] Task succeeded: CheckM
[2023-03-17 03:25:29,584] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 42.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:25:29,628] [INFO] ===== Completeness check finished =====
[2023-03-17 03:25:29,628] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:25:29,628] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34665/markers.fasta)
[2023-03-17 03:25:29,630] [INFO] Task started: Blastn
[2023-03-17 03:25:29,630] [INFO] Running command: blastn -query OceanDNA-b34665/markers.fasta -db /var/lib/cwl/stg0db24aa3-1b17-4c9c-85e2-cc2ca559603b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34665/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:25:30,317] [INFO] Task succeeded: Blastn
[2023-03-17 03:25:30,319] [INFO] Selected 12 target genomes.
[2023-03-17 03:25:30,319] [INFO] Target genome list was writen to OceanDNA-b34665/target_genomes_gtdb.txt
[2023-03-17 03:25:30,340] [INFO] Task started: fastANI
[2023-03-17 03:25:30,340] [INFO] Running command: fastANI --query /var/lib/cwl/stg86e339fe-981e-492c-b62a-4a450cad82a4/OceanDNA-b34665.fa --refList OceanDNA-b34665/target_genomes_gtdb.txt --output OceanDNA-b34665/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:25:37,928] [INFO] Task succeeded: fastANI
[2023-03-17 03:25:37,936] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:25:37,936] [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_003521815.1	s__Colwellia sp003521815	93.8298	207	231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003333305.1	s__Colwellia aromaticivorans	86.037	197	231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733765.1	s__Colwellia sp002733765	84.5637	202	231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.46	99.46	0.95	0.95	2	-
GCA_013215465.1	s__Colwellia sp013215465	84.0902	195	231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	96.15	96.15	0.84	0.84	2	-
GCA_002163005.1	s__Colwellia psychrerythraea_C	78.9944	72	231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836255.1	s__Colwellia sp002836255	78.6317	81	231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832865.1	s__Colwellia sp009832865	78.5228	105	231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764185.1	s__Colwellia psychrerythraea_B	78.354	67	231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836775.1	s__Colwellia sp002836775	78.2248	83	231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885605.1	s__Colwellia ponticola	78.2146	83	231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860585.1	s__Colwellia sp018860585	78.1022	71	231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765685.1	s__Colwellia sp016765685	78.0371	73	231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:25:37,940] [INFO] GTDB search result was written to OceanDNA-b34665/result_gtdb.tsv
[2023-03-17 03:25:37,943] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:25:37,947] [INFO] DFAST_QC result json was written to OceanDNA-b34665/dqc_result.json
[2023-03-17 03:25:37,948] [INFO] DFAST_QC completed!
[2023-03-17 03:25:37,948] [INFO] Total running time: 0h0m47s