[2023-06-18 14:02:05,314] [INFO] DFAST_QC pipeline started.
[2023-06-18 14:02:05,318] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 14:02:05,318] [INFO] DQC Reference Directory: /var/lib/cwl/stgee19c1a6-155b-4f1a-ad32-8f3c33b24726/dqc_reference
[2023-06-18 14:02:06,952] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 14:02:06,953] [INFO] Task started: Prodigal
[2023-06-18 14:02:06,954] [INFO] Running command: gunzip -c /var/lib/cwl/stgfdb2a1b6-d8de-496c-a252-dbb409b654f8/GCA_018823965.1_ASM1882396v1_genomic.fna.gz | prodigal -d GCA_018823965.1_ASM1882396v1_genomic.fna/cds.fna -a GCA_018823965.1_ASM1882396v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 14:02:13,547] [INFO] Task succeeded: Prodigal
[2023-06-18 14:02:13,547] [INFO] Task started: HMMsearch
[2023-06-18 14:02:13,547] [INFO] Running command: hmmsearch --tblout GCA_018823965.1_ASM1882396v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee19c1a6-155b-4f1a-ad32-8f3c33b24726/dqc_reference/reference_markers.hmm GCA_018823965.1_ASM1882396v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 14:02:13,878] [INFO] Task succeeded: HMMsearch
[2023-06-18 14:02:13,880] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgfdb2a1b6-d8de-496c-a252-dbb409b654f8/GCA_018823965.1_ASM1882396v1_genomic.fna.gz]
[2023-06-18 14:02:13,927] [INFO] Query marker FASTA was written to GCA_018823965.1_ASM1882396v1_genomic.fna/markers.fasta
[2023-06-18 14:02:13,928] [INFO] Task started: Blastn
[2023-06-18 14:02:13,928] [INFO] Running command: blastn -query GCA_018823965.1_ASM1882396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee19c1a6-155b-4f1a-ad32-8f3c33b24726/dqc_reference/reference_markers.fasta -out GCA_018823965.1_ASM1882396v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 14:02:14,533] [INFO] Task succeeded: Blastn
[2023-06-18 14:02:14,536] [INFO] Selected 27 target genomes.
[2023-06-18 14:02:14,537] [INFO] Target genome list was writen to GCA_018823965.1_ASM1882396v1_genomic.fna/target_genomes.txt
[2023-06-18 14:02:14,540] [INFO] Task started: fastANI
[2023-06-18 14:02:14,540] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdb2a1b6-d8de-496c-a252-dbb409b654f8/GCA_018823965.1_ASM1882396v1_genomic.fna.gz --refList GCA_018823965.1_ASM1882396v1_genomic.fna/target_genomes.txt --output GCA_018823965.1_ASM1882396v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 14:02:31,747] [INFO] Task succeeded: fastANI
[2023-06-18 14:02:31,747] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee19c1a6-155b-4f1a-ad32-8f3c33b24726/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 14:02:31,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee19c1a6-155b-4f1a-ad32-8f3c33b24726/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 14:02:31,755] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 14:02:31,755] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 14:02:31,755] [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	79.532	196	660	95	below_threshold
Zhongshania antarctica	strain=DSM 25701	GCA_014202945.1	641702	641702	type	True	78.463	178	660	95	below_threshold
Zhongshania antarctica	strain=ZS5-23	GCA_014898265.1	641702	641702	type	True	78.4328	177	660	95	below_threshold
Spongiibacter pelagi	strain=KMU-158	GCA_014705705.1	2760804	2760804	type	True	76.5207	65	660	95	below_threshold
Spongiibacter taiwanensis	strain=SPT1	GCA_023702635.1	1748242	1748242	type	True	76.2301	57	660	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 14:02:31,757] [INFO] DFAST Taxonomy check result was written to GCA_018823965.1_ASM1882396v1_genomic.fna/tc_result.tsv
[2023-06-18 14:02:31,758] [INFO] ===== Taxonomy check completed =====
[2023-06-18 14:02:31,758] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 14:02:31,758] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee19c1a6-155b-4f1a-ad32-8f3c33b24726/dqc_reference/checkm_data
[2023-06-18 14:02:31,760] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 14:02:31,796] [INFO] Task started: CheckM
[2023-06-18 14:02:31,796] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018823965.1_ASM1882396v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018823965.1_ASM1882396v1_genomic.fna/checkm_input GCA_018823965.1_ASM1882396v1_genomic.fna/checkm_result
[2023-06-18 14:02:57,786] [INFO] Task succeeded: CheckM
[2023-06-18 14:02:57,787] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 14:02:57,809] [INFO] ===== Completeness check finished =====
[2023-06-18 14:02:57,809] [INFO] ===== Start GTDB Search =====
[2023-06-18 14:02:57,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018823965.1_ASM1882396v1_genomic.fna/markers.fasta)
[2023-06-18 14:02:57,810] [INFO] Task started: Blastn
[2023-06-18 14:02:57,810] [INFO] Running command: blastn -query GCA_018823965.1_ASM1882396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee19c1a6-155b-4f1a-ad32-8f3c33b24726/dqc_reference/reference_markers_gtdb.fasta -out GCA_018823965.1_ASM1882396v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 14:02:58,587] [INFO] Task succeeded: Blastn
[2023-06-18 14:02:58,590] [INFO] Selected 11 target genomes.
[2023-06-18 14:02:58,591] [INFO] Target genome list was writen to GCA_018823965.1_ASM1882396v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 14:02:58,597] [INFO] Task started: fastANI
[2023-06-18 14:02:58,597] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdb2a1b6-d8de-496c-a252-dbb409b654f8/GCA_018823965.1_ASM1882396v1_genomic.fna.gz --refList GCA_018823965.1_ASM1882396v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018823965.1_ASM1882396v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 14:03:05,611] [INFO] Task succeeded: fastANI
[2023-06-18 14:03:05,622] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 14:03:05,622] [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	97.4285	504	660	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	88.8076	446	660	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	82.6358	410	660	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	81.8165	348	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902705875.1	s__Marortus aliphaticivorans_A	79.9854	217	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001586255.1	s__Zhongshania aliphaticivorans	79.532	196	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Zhongshania	95.0	99.39	99.39	0.94	0.94	2	-
GCF_001010805.1	s__IMCC21906 sp001010805	78.4756	72	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__IMCC21906	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202945.1	s__Zhongshania antarctica	78.463	178	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Zhongshania	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-18 14:03:05,624] [INFO] GTDB search result was written to GCA_018823965.1_ASM1882396v1_genomic.fna/result_gtdb.tsv
[2023-06-18 14:03:05,625] [INFO] ===== GTDB Search completed =====
[2023-06-18 14:03:05,628] [INFO] DFAST_QC result json was written to GCA_018823965.1_ASM1882396v1_genomic.fna/dqc_result.json
[2023-06-18 14:03:05,628] [INFO] DFAST_QC completed!
[2023-06-18 14:03:05,629] [INFO] Total running time: 0h1m0s