[2023-03-15 12:33:51,592] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:33:51,592] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:33:51,593] [INFO] DQC Reference Directory: /var/lib/cwl/stg449636ec-d228-49e1-a2d7-680b0c369f99/dqc_reference
[2023-03-15 12:33:52,742] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:33:52,743] [INFO] Task started: Prodigal
[2023-03-15 12:33:52,743] [INFO] Running command: cat /var/lib/cwl/stg2ae41de6-1edc-4291-abd1-cc3a80c23626/OceanDNA-b41544.fa | prodigal -d OceanDNA-b41544/cds.fna -a OceanDNA-b41544/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:34:15,495] [INFO] Task succeeded: Prodigal
[2023-03-15 12:34:15,495] [INFO] Task started: HMMsearch
[2023-03-15 12:34:15,495] [INFO] Running command: hmmsearch --tblout OceanDNA-b41544/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg449636ec-d228-49e1-a2d7-680b0c369f99/dqc_reference/reference_markers.hmm OceanDNA-b41544/protein.faa > /dev/null
[2023-03-15 12:34:15,703] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:34:15,704] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2ae41de6-1edc-4291-abd1-cc3a80c23626/OceanDNA-b41544.fa]
[2023-03-15 12:34:15,732] [INFO] Query marker FASTA was written to OceanDNA-b41544/markers.fasta
[2023-03-15 12:34:15,733] [INFO] Task started: Blastn
[2023-03-15 12:34:15,734] [INFO] Running command: blastn -query OceanDNA-b41544/markers.fasta -db /var/lib/cwl/stg449636ec-d228-49e1-a2d7-680b0c369f99/dqc_reference/reference_markers.fasta -out OceanDNA-b41544/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:34:16,296] [INFO] Task succeeded: Blastn
[2023-03-15 12:34:16,298] [INFO] Selected 12 target genomes.
[2023-03-15 12:34:16,298] [INFO] Target genome list was writen to OceanDNA-b41544/target_genomes.txt
[2023-03-15 12:34:16,318] [INFO] Task started: fastANI
[2023-03-15 12:34:16,318] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ae41de6-1edc-4291-abd1-cc3a80c23626/OceanDNA-b41544.fa --refList OceanDNA-b41544/target_genomes.txt --output OceanDNA-b41544/fastani_result.tsv --threads 1
[2023-03-15 12:34:24,059] [INFO] Task succeeded: fastANI
[2023-03-15 12:34:24,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg449636ec-d228-49e1-a2d7-680b0c369f99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:34:24,059] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg449636ec-d228-49e1-a2d7-680b0c369f99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:34:24,065] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:34:24,065] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 12:34:24,066] [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 antarctica	strain=DSM 25701	GCA_014202945.1	641702	641702	type	True	82.0946	707	1295	95	below_threshold
Zhongshania antarctica	strain=ZS5-23	GCA_014898265.1	641702	641702	type	True	82.0202	711	1295	95	below_threshold
Zhongshania aliphaticivorans	strain=SM-2	GCA_001586255.1	1470434	1470434	type	True	81.1286	703	1295	95	below_threshold
Spongiibacter thalassae	strain=KMU-166	GCA_012272835.1	2721624	2721624	type	True	77.0861	123	1295	95	below_threshold
Spongiibacter pelagi	strain=KMU-158	GCA_014705705.1	2760804	2760804	type	True	76.8114	130	1295	95	below_threshold
Spongiibacter tropicus	strain=DSM 19543	GCA_000420325.1	454602	454602	type	True	76.306	117	1295	95	below_threshold
Litorivivens lipolytica	strain=CECT 8654	GCA_014191715.1	1524264	1524264	type	True	75.9503	55	1295	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:34:24,067] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41544/tc_result.tsv
[2023-03-15 12:34:24,069] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:34:24,069] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:34:24,069] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg449636ec-d228-49e1-a2d7-680b0c369f99/dqc_reference/checkm_data
[2023-03-15 12:34:24,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:34:24,078] [INFO] Task started: CheckM
[2023-03-15 12:34:24,078] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41544/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41544/checkm_input OceanDNA-b41544/checkm_result
[2023-03-15 12:35:20,438] [INFO] Task succeeded: CheckM
[2023-03-15 12:35:20,438] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.82%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:35:20,464] [INFO] ===== Completeness check finished =====
[2023-03-15 12:35:20,465] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:35:20,465] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41544/markers.fasta)
[2023-03-15 12:35:20,466] [INFO] Task started: Blastn
[2023-03-15 12:35:20,466] [INFO] Running command: blastn -query OceanDNA-b41544/markers.fasta -db /var/lib/cwl/stg449636ec-d228-49e1-a2d7-680b0c369f99/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41544/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:35:21,314] [INFO] Task succeeded: Blastn
[2023-03-15 12:35:21,319] [INFO] Selected 13 target genomes.
[2023-03-15 12:35:21,319] [INFO] Target genome list was writen to OceanDNA-b41544/target_genomes_gtdb.txt
[2023-03-15 12:35:21,481] [INFO] Task started: fastANI
[2023-03-15 12:35:21,481] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ae41de6-1edc-4291-abd1-cc3a80c23626/OceanDNA-b41544.fa --refList OceanDNA-b41544/target_genomes_gtdb.txt --output OceanDNA-b41544/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:35:30,296] [INFO] Task succeeded: fastANI
[2023-03-15 12:35:30,301] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:35:30,302] [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
GCF_014202945.1	s__Zhongshania antarctica	82.0918	707	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Zhongshania	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001586255.1	s__Zhongshania aliphaticivorans	81.1227	704	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Zhongshania	95.0	99.39	99.39	0.94	0.94	2	-
GCA_018066965.1	s__Marortus sp018066965	78.2179	292	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902705855.1	s__Marortus aliphaticivorans_B	78.1729	324	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067195.1	s__Marortus sp018067195	77.9941	274	1295	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	77.9457	323	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	97.55	97.55	0.86	0.86	2	-
GCF_902705875.1	s__Marortus aliphaticivorans_A	77.5926	237	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014705705.1	s__KMU-158 sp014705705	76.8114	130	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__KMU-158	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:35:30,303] [INFO] GTDB search result was written to OceanDNA-b41544/result_gtdb.tsv
[2023-03-15 12:35:30,308] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:35:30,311] [INFO] DFAST_QC result json was written to OceanDNA-b41544/dqc_result.json
[2023-03-15 12:35:30,311] [INFO] DFAST_QC completed!
[2023-03-15 12:35:30,311] [INFO] Total running time: 0h1m39s