[2023-03-16 20:17:00,296] [INFO] DFAST_QC pipeline started.
[2023-03-16 20:17:00,301] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 20:17:00,301] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3c84e5b-7566-4cbe-8855-91e72bb8de95/dqc_reference
[2023-03-16 20:17:01,946] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 20:17:01,946] [INFO] Task started: Prodigal
[2023-03-16 20:17:01,946] [INFO] Running command: cat /var/lib/cwl/stgb6d3ba0c-fa27-4de7-b97e-e71fea6371e1/OceanDNA-b38601.fa | prodigal -d OceanDNA-b38601/cds.fna -a OceanDNA-b38601/protein.faa -g 11 -q > /dev/null
[2023-03-16 20:17:17,129] [INFO] Task succeeded: Prodigal
[2023-03-16 20:17:17,129] [INFO] Task started: HMMsearch
[2023-03-16 20:17:17,129] [INFO] Running command: hmmsearch --tblout OceanDNA-b38601/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3c84e5b-7566-4cbe-8855-91e72bb8de95/dqc_reference/reference_markers.hmm OceanDNA-b38601/protein.faa > /dev/null
[2023-03-16 20:17:17,337] [INFO] Task succeeded: HMMsearch
[2023-03-16 20:17:17,338] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb6d3ba0c-fa27-4de7-b97e-e71fea6371e1/OceanDNA-b38601.fa]
[2023-03-16 20:17:17,353] [INFO] Query marker FASTA was written to OceanDNA-b38601/markers.fasta
[2023-03-16 20:17:17,357] [INFO] Task started: Blastn
[2023-03-16 20:17:17,357] [INFO] Running command: blastn -query OceanDNA-b38601/markers.fasta -db /var/lib/cwl/stgf3c84e5b-7566-4cbe-8855-91e72bb8de95/dqc_reference/reference_markers.fasta -out OceanDNA-b38601/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:17:17,858] [INFO] Task succeeded: Blastn
[2023-03-16 20:17:17,859] [INFO] Selected 13 target genomes.
[2023-03-16 20:17:17,859] [INFO] Target genome list was writen to OceanDNA-b38601/target_genomes.txt
[2023-03-16 20:17:17,867] [INFO] Task started: fastANI
[2023-03-16 20:17:17,867] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6d3ba0c-fa27-4de7-b97e-e71fea6371e1/OceanDNA-b38601.fa --refList OceanDNA-b38601/target_genomes.txt --output OceanDNA-b38601/fastani_result.tsv --threads 1
[2023-03-16 20:17:26,253] [INFO] Task succeeded: fastANI
[2023-03-16 20:17:26,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3c84e5b-7566-4cbe-8855-91e72bb8de95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 20:17:26,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3c84e5b-7566-4cbe-8855-91e72bb8de95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 20:17:26,262] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 20:17:26,262] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 20:17:26,262] [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
Psychrobacter pacificensis	strain=DSM 23406	GCA_900101915.1	112002	112002	type	True	83.5063	650	894	95	below_threshold
Psychrobacter fozii	strain=CECT 5889	GCA_003217155.1	198480	198480	type	True	82.2301	670	894	95	below_threshold
Psychrobacter glaciei	strain=KCTC 42280	GCA_014652895.1	619771	619771	type	True	81.9258	637	894	95	below_threshold
Psychrobacter aquimaris	strain=DSM 16329	GCA_016107525.1	292733	292733	type	True	81.16	602	894	95	below_threshold
Psychrobacter cibarius	strain=DSM 16327	GCA_016107535.1	282669	282669	type	True	80.9252	587	894	95	below_threshold
Psychrobacter immobilis	strain=DSM 7229	GCA_003148585.1	498	498	suspected-type	True	80.9161	586	894	95	below_threshold
Psychrobacter namhaensis	strain=DSM 16330	GCA_016107545.1	292734	292734	type	True	80.5435	559	894	95	below_threshold
Psychrobacter aquaticus	strain=CMS 56	GCA_000471625.1	248452	248452	type	True	80.4291	558	894	95	below_threshold
Psychrobacter celer	strain=DSM 23510	GCA_016107555.1	306572	306572	type	True	79.7403	479	894	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	79.5547	471	894	95	below_threshold
Psychrobacter communis	strain=Sa4CVA2	GCA_014836505.1	2762238	2762238	type	True	79.333	462	894	95	below_threshold
Psychrobacter coccoides	strain=F1192	GCA_017498085.1	2818440	2818440	type	True	77.9683	331	894	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 20:17:26,262] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38601/tc_result.tsv
[2023-03-16 20:17:26,262] [INFO] ===== Taxonomy check completed =====
[2023-03-16 20:17:26,262] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 20:17:26,262] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3c84e5b-7566-4cbe-8855-91e72bb8de95/dqc_reference/checkm_data
[2023-03-16 20:17:26,263] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 20:17:26,286] [INFO] Task started: CheckM
[2023-03-16 20:17:26,286] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38601/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38601/checkm_input OceanDNA-b38601/checkm_result
[2023-03-16 20:18:19,696] [INFO] Task succeeded: CheckM
[2023-03-16 20:18:19,697] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.84%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 20:18:19,699] [INFO] ===== Completeness check finished =====
[2023-03-16 20:18:19,699] [INFO] ===== Start GTDB Search =====
[2023-03-16 20:18:19,700] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38601/markers.fasta)
[2023-03-16 20:18:19,701] [INFO] Task started: Blastn
[2023-03-16 20:18:19,701] [INFO] Running command: blastn -query OceanDNA-b38601/markers.fasta -db /var/lib/cwl/stgf3c84e5b-7566-4cbe-8855-91e72bb8de95/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38601/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:18:21,203] [INFO] Task succeeded: Blastn
[2023-03-16 20:18:21,207] [INFO] Selected 11 target genomes.
[2023-03-16 20:18:21,207] [INFO] Target genome list was writen to OceanDNA-b38601/target_genomes_gtdb.txt
[2023-03-16 20:18:21,218] [INFO] Task started: fastANI
[2023-03-16 20:18:21,218] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6d3ba0c-fa27-4de7-b97e-e71fea6371e1/OceanDNA-b38601.fa --refList OceanDNA-b38601/target_genomes_gtdb.txt --output OceanDNA-b38601/fastani_result_gtdb.tsv --threads 1
[2023-03-16 20:18:33,366] [INFO] Task succeeded: fastANI
[2023-03-16 20:18:33,373] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 20:18:33,373] [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_002377945.1	s__Psychrobacter sp002377945	94.79	841	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435845.1	s__Psychrobacter sp001435845	94.5261	831	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014770435.1	s__Psychrobacter sp014770435	94.4712	825	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846625.1	s__Psychrobacter sp000586415	94.4126	832	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	99.91	99.91	1.00	1.00	2	-
GCF_002836505.1	s__Psychrobacter sp002836505	94.2242	792	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.96	95.05	0.93	0.86	11	-
GCF_002836735.1	s__Psychrobacter sp002836735	94.168	786	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	95.08	95.08	0.86	0.86	2	-
GCF_013414195.1	s__Psychrobacter sp013414195	94.148	792	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846705.1	s__Psychrobacter sp904846705	94.1294	792	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846645.1	s__Psychrobacter sp904846645	94.0685	805	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000586435.1	s__Psychrobacter sp000586435	94.0479	799	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846235.1	s__Psychrobacter immobilis_C	93.9928	791	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 20:18:33,374] [INFO] GTDB search result was written to OceanDNA-b38601/result_gtdb.tsv
[2023-03-16 20:18:33,375] [INFO] ===== GTDB Search completed =====
[2023-03-16 20:18:33,377] [INFO] DFAST_QC result json was written to OceanDNA-b38601/dqc_result.json
[2023-03-16 20:18:33,377] [INFO] DFAST_QC completed!
[2023-03-16 20:18:33,377] [INFO] Total running time: 0h1m33s