[2023-03-15 11:10:12,603] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:10:12,603] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:10:12,604] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a4678b2-de8e-4dea-a119-9d293211d0e0/dqc_reference
[2023-03-15 11:10:13,716] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:10:13,716] [INFO] Task started: Prodigal
[2023-03-15 11:10:13,716] [INFO] Running command: cat /var/lib/cwl/stg39e00436-a0a6-48f2-b79b-d12724880363/OceanDNA-b41523.fa | prodigal -d OceanDNA-b41523/cds.fna -a OceanDNA-b41523/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:10:37,319] [INFO] Task succeeded: Prodigal
[2023-03-15 11:10:37,319] [INFO] Task started: HMMsearch
[2023-03-15 11:10:37,319] [INFO] Running command: hmmsearch --tblout OceanDNA-b41523/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a4678b2-de8e-4dea-a119-9d293211d0e0/dqc_reference/reference_markers.hmm OceanDNA-b41523/protein.faa > /dev/null
[2023-03-15 11:10:37,530] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:10:37,530] [INFO] Found 6/6 markers.
[2023-03-15 11:10:37,574] [INFO] Query marker FASTA was written to OceanDNA-b41523/markers.fasta
[2023-03-15 11:10:37,575] [INFO] Task started: Blastn
[2023-03-15 11:10:37,575] [INFO] Running command: blastn -query OceanDNA-b41523/markers.fasta -db /var/lib/cwl/stg4a4678b2-de8e-4dea-a119-9d293211d0e0/dqc_reference/reference_markers.fasta -out OceanDNA-b41523/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:10:38,192] [INFO] Task succeeded: Blastn
[2023-03-15 11:10:38,199] [INFO] Selected 24 target genomes.
[2023-03-15 11:10:38,199] [INFO] Target genome list was writen to OceanDNA-b41523/target_genomes.txt
[2023-03-15 11:10:38,215] [INFO] Task started: fastANI
[2023-03-15 11:10:38,215] [INFO] Running command: fastANI --query /var/lib/cwl/stg39e00436-a0a6-48f2-b79b-d12724880363/OceanDNA-b41523.fa --refList OceanDNA-b41523/target_genomes.txt --output OceanDNA-b41523/fastani_result.tsv --threads 1
[2023-03-15 11:10:52,292] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:52,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a4678b2-de8e-4dea-a119-9d293211d0e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:10:52,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a4678b2-de8e-4dea-a119-9d293211d0e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:10:52,297] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:10:52,297] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:10:52,297] [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
Zhongshania aliphaticivorans	strain=SM-2	GCA_001586255.1	1470434	1470434	type	True	80.3747	422	1357	95	below_threshold
Zhongshania antarctica	strain=DSM 25701	GCA_014202945.1	641702	641702	type	True	79.3022	368	1357	95	below_threshold
Zhongshania antarctica	strain=ZS5-23	GCA_014898265.1	641702	641702	type	True	79.2612	370	1357	95	below_threshold
Spongiibacter pelagi	strain=KMU-158	GCA_014705705.1	2760804	2760804	type	True	77.2174	153	1357	95	below_threshold
Spongiibacter taiwanensis	strain=SPT1	GCA_023702635.1	1748242	1748242	type	True	76.9922	150	1357	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:10:52,300] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41523/tc_result.tsv
[2023-03-15 11:10:52,302] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:10:52,302] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:10:52,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a4678b2-de8e-4dea-a119-9d293211d0e0/dqc_reference/checkm_data
[2023-03-15 11:10:52,303] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:10:52,335] [INFO] Task started: CheckM
[2023-03-15 11:10:52,335] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41523/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41523/checkm_input OceanDNA-b41523/checkm_result
[2023-03-15 11:11:50,888] [INFO] Task succeeded: CheckM
[2023-03-15 11:11:50,888] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:11:50,948] [INFO] ===== Completeness check finished =====
[2023-03-15 11:11:50,948] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:11:50,948] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41523/markers.fasta)
[2023-03-15 11:11:50,949] [INFO] Task started: Blastn
[2023-03-15 11:11:50,949] [INFO] Running command: blastn -query OceanDNA-b41523/markers.fasta -db /var/lib/cwl/stg4a4678b2-de8e-4dea-a119-9d293211d0e0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41523/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:11:51,987] [INFO] Task succeeded: Blastn
[2023-03-15 11:11:51,987] [INFO] Selected 9 target genomes.
[2023-03-15 11:11:51,987] [INFO] Target genome list was writen to OceanDNA-b41523/target_genomes_gtdb.txt
[2023-03-15 11:11:51,996] [INFO] Task started: fastANI
[2023-03-15 11:11:51,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg39e00436-a0a6-48f2-b79b-d12724880363/OceanDNA-b41523.fa --refList OceanDNA-b41523/target_genomes_gtdb.txt --output OceanDNA-b41523/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:11:59,338] [INFO] Task succeeded: fastANI
[2023-03-15 11:11:59,344] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:11:59,344] [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_018066965.1	s__Marortus sp018066965	97.7423	995	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_902705855.1	s__Marortus aliphaticivorans_B	89.092	932	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002915595.1	s__Marortus luteolus	82.9476	869	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	97.55	97.55	0.86	0.86	2	-
GCA_018067195.1	s__Marortus sp018067195	82.4224	665	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001586255.1	s__Zhongshania aliphaticivorans	80.3886	421	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Zhongshania	95.0	99.39	99.39	0.94	0.94	2	-
GCF_902705875.1	s__Marortus aliphaticivorans_A	80.2911	493	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014202945.1	s__Zhongshania antarctica	79.3022	368	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Zhongshania	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001010805.1	s__IMCC21906 sp001010805	78.7017	173	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__IMCC21906	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:11:59,344] [INFO] GTDB search result was written to OceanDNA-b41523/result_gtdb.tsv
[2023-03-15 11:11:59,344] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:11:59,345] [INFO] DFAST_QC result json was written to OceanDNA-b41523/dqc_result.json
[2023-03-15 11:11:59,345] [INFO] DFAST_QC completed!
[2023-03-15 11:11:59,345] [INFO] Total running time: 0h1m47s