[2024-01-25 19:47:35,880] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:35,881] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:35,881] [INFO] DQC Reference Directory: /var/lib/cwl/stg658cd41e-7e23-4eb4-9065-345aad32ff9a/dqc_reference
[2024-01-25 19:47:37,042] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:37,043] [INFO] Task started: Prodigal
[2024-01-25 19:47:37,044] [INFO] Running command: gunzip -c /var/lib/cwl/stg6054964a-108d-4ef6-94c7-62f7de3ea564/GCF_002915595.1_ASM291559v1_genomic.fna.gz | prodigal -d GCF_002915595.1_ASM291559v1_genomic.fna/cds.fna -a GCF_002915595.1_ASM291559v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:45,958] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:45,958] [INFO] Task started: HMMsearch
[2024-01-25 19:47:45,958] [INFO] Running command: hmmsearch --tblout GCF_002915595.1_ASM291559v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg658cd41e-7e23-4eb4-9065-345aad32ff9a/dqc_reference/reference_markers.hmm GCF_002915595.1_ASM291559v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:46,205] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:46,206] [INFO] Found 6/6 markers.
[2024-01-25 19:47:46,247] [INFO] Query marker FASTA was written to GCF_002915595.1_ASM291559v1_genomic.fna/markers.fasta
[2024-01-25 19:47:46,247] [INFO] Task started: Blastn
[2024-01-25 19:47:46,247] [INFO] Running command: blastn -query GCF_002915595.1_ASM291559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg658cd41e-7e23-4eb4-9065-345aad32ff9a/dqc_reference/reference_markers.fasta -out GCF_002915595.1_ASM291559v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:46,910] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:46,913] [INFO] Selected 25 target genomes.
[2024-01-25 19:47:46,914] [INFO] Target genome list was writen to GCF_002915595.1_ASM291559v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:46,927] [INFO] Task started: fastANI
[2024-01-25 19:47:46,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg6054964a-108d-4ef6-94c7-62f7de3ea564/GCF_002915595.1_ASM291559v1_genomic.fna.gz --refList GCF_002915595.1_ASM291559v1_genomic.fna/target_genomes.txt --output GCF_002915595.1_ASM291559v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:48:01,533] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:01,533] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg658cd41e-7e23-4eb4-9065-345aad32ff9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:48:01,533] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg658cd41e-7e23-4eb4-9065-345aad32ff9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:48:01,541] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:48:01,541] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:48:01,541] [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	79.4277	389	1352	95	below_threshold
Zhongshania antarctica	strain=ZS5-23	GCA_014898265.1	641702	641702	type	True	78.988	357	1352	95	below_threshold
Zhongshania antarctica	strain=DSM 25701	GCA_014202945.1	641702	641702	type	True	78.9619	356	1352	95	below_threshold
Spongiibacter taiwanensis	strain=SPT1	GCA_023702635.1	1748242	1748242	type	True	77.7562	160	1352	95	below_threshold
Spongiibacter pelagi	strain=KMU-158	GCA_014705705.1	2760804	2760804	type	True	77.5139	175	1352	95	below_threshold
Spongiibacter tropicus	strain=DSM 19543	GCA_000420325.1	454602	454602	type	True	77.389	145	1352	95	below_threshold
Oceanicoccus sagamiensis	strain=NBRC 107125	GCA_002117105.1	716816	716816	type	True	77.3204	53	1352	95	below_threshold
Spongiibacter nanhainus	strain=csc3.9	GCA_016132545.1	2794344	2794344	type	True	77.218	136	1352	95	below_threshold
Litorivivens lipolytica	strain=CECT 8654	GCA_014191715.1	1524264	1524264	type	True	76.6883	83	1352	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:48:01,542] [INFO] DFAST Taxonomy check result was written to GCF_002915595.1_ASM291559v1_genomic.fna/tc_result.tsv
[2024-01-25 19:48:01,543] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:48:01,543] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:48:01,543] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg658cd41e-7e23-4eb4-9065-345aad32ff9a/dqc_reference/checkm_data
[2024-01-25 19:48:01,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:48:01,586] [INFO] Task started: CheckM
[2024-01-25 19:48:01,586] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002915595.1_ASM291559v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002915595.1_ASM291559v1_genomic.fna/checkm_input GCF_002915595.1_ASM291559v1_genomic.fna/checkm_result
[2024-01-25 19:48:31,559] [INFO] Task succeeded: CheckM
[2024-01-25 19:48:31,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:48:31,577] [INFO] ===== Completeness check finished =====
[2024-01-25 19:48:31,578] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:48:31,578] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002915595.1_ASM291559v1_genomic.fna/markers.fasta)
[2024-01-25 19:48:31,578] [INFO] Task started: Blastn
[2024-01-25 19:48:31,578] [INFO] Running command: blastn -query GCF_002915595.1_ASM291559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg658cd41e-7e23-4eb4-9065-345aad32ff9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002915595.1_ASM291559v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:32,675] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:32,681] [INFO] Selected 14 target genomes.
[2024-01-25 19:48:32,681] [INFO] Target genome list was writen to GCF_002915595.1_ASM291559v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:48:32,694] [INFO] Task started: fastANI
[2024-01-25 19:48:32,694] [INFO] Running command: fastANI --query /var/lib/cwl/stg6054964a-108d-4ef6-94c7-62f7de3ea564/GCF_002915595.1_ASM291559v1_genomic.fna.gz --refList GCF_002915595.1_ASM291559v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002915595.1_ASM291559v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:43,660] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:43,669] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:48:43,669] [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_002915595.1	s__Marortus luteolus	100.0	1349	1352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	97.55	97.55	0.86	0.86	2	conclusive
GCF_902705855.1	s__Marortus aliphaticivorans_B	87.6155	1043	1352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018066965.1	s__Marortus sp018066965	82.3495	730	1352	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	81.0696	575	1352	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	79.5653	462	1352	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	79.4228	389	1352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Zhongshania	95.0	99.39	99.39	0.94	0.94	2	-
GCF_014202945.1	s__Zhongshania antarctica	78.9619	356	1352	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	78.7211	194	1352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__IMCC21906	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422345.1	s__Spongiibacter marinus_A	77.6388	155	1352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705705.1	s__KMU-158 sp014705705	77.5299	174	1352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__KMU-158	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420325.1	s__Spongiibacter tropicus	77.3713	144	1352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	98.00	97.89	0.92	0.88	9	-
GCF_016132545.1	s__CSC3-9 sp016132545	77.312	138	1352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__CSC3-9	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:48:43,670] [INFO] GTDB search result was written to GCF_002915595.1_ASM291559v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:43,671] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:43,673] [INFO] DFAST_QC result json was written to GCF_002915595.1_ASM291559v1_genomic.fna/dqc_result.json
[2024-01-25 19:48:43,673] [INFO] DFAST_QC completed!
[2024-01-25 19:48:43,673] [INFO] Total running time: 0h1m8s