[2023-03-19 00:15:41,729] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:15:41,730] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:15:41,730] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa3edbdc-1b06-49d9-a5d8-89396bc1a417/dqc_reference
[2023-03-19 00:15:43,440] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:15:43,440] [INFO] Task started: Prodigal
[2023-03-19 00:15:43,440] [INFO] Running command: cat /var/lib/cwl/stgc14f05b7-c918-424c-a6f3-8b7b09bba553/OceanDNA-b26391.fa | prodigal -d OceanDNA-b26391/cds.fna -a OceanDNA-b26391/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:15:54,069] [INFO] Task succeeded: Prodigal
[2023-03-19 00:15:54,070] [INFO] Task started: HMMsearch
[2023-03-19 00:15:54,070] [INFO] Running command: hmmsearch --tblout OceanDNA-b26391/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa3edbdc-1b06-49d9-a5d8-89396bc1a417/dqc_reference/reference_markers.hmm OceanDNA-b26391/protein.faa > /dev/null
[2023-03-19 00:15:54,266] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:15:54,267] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc14f05b7-c918-424c-a6f3-8b7b09bba553/OceanDNA-b26391.fa]
[2023-03-19 00:15:54,288] [INFO] Query marker FASTA was written to OceanDNA-b26391/markers.fasta
[2023-03-19 00:15:54,290] [INFO] Task started: Blastn
[2023-03-19 00:15:54,290] [INFO] Running command: blastn -query OceanDNA-b26391/markers.fasta -db /var/lib/cwl/stgaa3edbdc-1b06-49d9-a5d8-89396bc1a417/dqc_reference/reference_markers.fasta -out OceanDNA-b26391/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:15:54,917] [INFO] Task succeeded: Blastn
[2023-03-19 00:15:54,918] [INFO] Selected 24 target genomes.
[2023-03-19 00:15:54,918] [INFO] Target genome list was writen to OceanDNA-b26391/target_genomes.txt
[2023-03-19 00:15:54,933] [INFO] Task started: fastANI
[2023-03-19 00:15:54,933] [INFO] Running command: fastANI --query /var/lib/cwl/stgc14f05b7-c918-424c-a6f3-8b7b09bba553/OceanDNA-b26391.fa --refList OceanDNA-b26391/target_genomes.txt --output OceanDNA-b26391/fastani_result.tsv --threads 1
[2023-03-19 00:16:13,613] [INFO] Task succeeded: fastANI
[2023-03-19 00:16:13,613] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa3edbdc-1b06-49d9-a5d8-89396bc1a417/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:16:13,614] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa3edbdc-1b06-49d9-a5d8-89396bc1a417/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:16:13,620] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:16:13,620] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:16:13,621] [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
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.0619	64	563	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.017	72	563	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.9632	57	563	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	75.7737	71	563	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.7702	68	563	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	75.449	57	563	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.2191	62	563	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	75.2121	56	563	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	74.9241	52	563	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:16:13,643] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26391/tc_result.tsv
[2023-03-19 00:16:13,643] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:16:13,644] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:16:13,644] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa3edbdc-1b06-49d9-a5d8-89396bc1a417/dqc_reference/checkm_data
[2023-03-19 00:16:13,645] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:16:13,648] [INFO] Task started: CheckM
[2023-03-19 00:16:13,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26391/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26391/checkm_input OceanDNA-b26391/checkm_result
[2023-03-19 00:16:44,345] [INFO] Task succeeded: CheckM
[2023-03-19 00:16:44,345] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 38.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:16:44,347] [INFO] ===== Completeness check finished =====
[2023-03-19 00:16:44,348] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:16:44,348] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26391/markers.fasta)
[2023-03-19 00:16:44,349] [INFO] Task started: Blastn
[2023-03-19 00:16:44,349] [INFO] Running command: blastn -query OceanDNA-b26391/markers.fasta -db /var/lib/cwl/stgaa3edbdc-1b06-49d9-a5d8-89396bc1a417/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26391/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:16:45,387] [INFO] Task succeeded: Blastn
[2023-03-19 00:16:45,388] [INFO] Selected 16 target genomes.
[2023-03-19 00:16:45,388] [INFO] Target genome list was writen to OceanDNA-b26391/target_genomes_gtdb.txt
[2023-03-19 00:16:45,448] [INFO] Task started: fastANI
[2023-03-19 00:16:45,448] [INFO] Running command: fastANI --query /var/lib/cwl/stgc14f05b7-c918-424c-a6f3-8b7b09bba553/OceanDNA-b26391.fa --refList OceanDNA-b26391/target_genomes_gtdb.txt --output OceanDNA-b26391/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:16:52,747] [INFO] Task succeeded: fastANI
[2023-03-19 00:16:52,753] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:16:52,753] [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_011522725.1	s__UBA8309 sp001627655	82.638	397	563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.91	98.58	0.92	0.89	8	-
GCA_002457745.1	s__UBA8309 sp002457745	81.3461	287	563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018624035.1	s__UBA8309 sp018624035	80.0037	339	563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009920665.1	s__UBA8309 sp009920665	79.7843	358	563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686685.1	s__UBA8309 sp002686685	77.9517	156	563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	97.96	97.78	0.70	0.66	5	-
GCA_002683535.1	s__UBA8309 sp002683535	77.673	105	563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780765.1	s__UBA8309 sp016780765	77.4271	166	563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.39	97.46	0.74	0.59	14	-
GCA_002731315.1	s__UBA8309 sp002731315	77.1948	76	563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004212735.1	s__MED-G116 sp004212735	76.5748	81	563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__MED-G116	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:16:52,754] [INFO] GTDB search result was written to OceanDNA-b26391/result_gtdb.tsv
[2023-03-19 00:16:52,754] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:16:52,756] [INFO] DFAST_QC result json was written to OceanDNA-b26391/dqc_result.json
[2023-03-19 00:16:52,756] [INFO] DFAST_QC completed!
[2023-03-19 00:16:52,756] [INFO] Total running time: 0h1m11s