[2024-01-24 13:21:46,041] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:46,043] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:46,043] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ea76891-1cab-4be3-8bc3-31fae5670f6d/dqc_reference
[2024-01-24 13:21:47,405] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:47,406] [INFO] Task started: Prodigal
[2024-01-24 13:21:47,406] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c906b96-b6ee-44d7-b9ad-bb716fe2e938/GCF_003315485.1_ASM331548v1_genomic.fna.gz | prodigal -d GCF_003315485.1_ASM331548v1_genomic.fna/cds.fna -a GCF_003315485.1_ASM331548v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:58,482] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:58,483] [INFO] Task started: HMMsearch
[2024-01-24 13:21:58,483] [INFO] Running command: hmmsearch --tblout GCF_003315485.1_ASM331548v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ea76891-1cab-4be3-8bc3-31fae5670f6d/dqc_reference/reference_markers.hmm GCF_003315485.1_ASM331548v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:58,819] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:58,820] [INFO] Found 6/6 markers.
[2024-01-24 13:21:58,866] [INFO] Query marker FASTA was written to GCF_003315485.1_ASM331548v1_genomic.fna/markers.fasta
[2024-01-24 13:21:58,866] [INFO] Task started: Blastn
[2024-01-24 13:21:58,867] [INFO] Running command: blastn -query GCF_003315485.1_ASM331548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ea76891-1cab-4be3-8bc3-31fae5670f6d/dqc_reference/reference_markers.fasta -out GCF_003315485.1_ASM331548v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:59,594] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:59,598] [INFO] Selected 12 target genomes.
[2024-01-24 13:21:59,598] [INFO] Target genome list was writen to GCF_003315485.1_ASM331548v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:59,602] [INFO] Task started: fastANI
[2024-01-24 13:21:59,603] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c906b96-b6ee-44d7-b9ad-bb716fe2e938/GCF_003315485.1_ASM331548v1_genomic.fna.gz --refList GCF_003315485.1_ASM331548v1_genomic.fna/target_genomes.txt --output GCF_003315485.1_ASM331548v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:10,381] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:10,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ea76891-1cab-4be3-8bc3-31fae5670f6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:10,381] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ea76891-1cab-4be3-8bc3-31fae5670f6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:10,390] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:10,390] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:10,390] [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
Marinomonas rhizomae	strain=CECT 7377	GCA_003315485.1	491948	491948	type	True	100.0	1457	1459	95	conclusive
Marinomonas rhizomae	strain=IVIA-Po-145	GCA_003721275.1	491948	491948	type	True	99.9879	1433	1459	95	conclusive
Marinomonas polaris	strain=DSM 16579	GCA_900129155.1	293552	293552	type	True	84.8561	1074	1459	95	below_threshold
Marinomonas lutimaris	strain=E165	GCA_019426345.1	2846746	2846746	type	True	84.4184	1011	1459	95	below_threshold
Marinomonas foliarum	strain=CECT 7731	GCA_003337275.1	491950	491950	type	True	82.8354	847	1459	95	below_threshold
Marinomonas arctica	strain=328	GCA_003259225.1	383750	383750	type	True	81.4735	798	1459	95	below_threshold
Marinomonas shanghaiensis	strain=DSL-35	GCA_003259175.1	2202418	2202418	type	True	81.3813	785	1459	95	below_threshold
Marinomonas profundi	strain=M1K-6	GCA_012584435.1	2726122	2726122	type	True	81.2948	690	1459	95	below_threshold
Marinomonas primoryensis	strain=MPKMM3633	GCA_013372285.1	178399	178399	type	True	80.5384	723	1459	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:10,392] [INFO] DFAST Taxonomy check result was written to GCF_003315485.1_ASM331548v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:10,392] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:10,392] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:10,393] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ea76891-1cab-4be3-8bc3-31fae5670f6d/dqc_reference/checkm_data
[2024-01-24 13:22:10,394] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:10,436] [INFO] Task started: CheckM
[2024-01-24 13:22:10,436] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003315485.1_ASM331548v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003315485.1_ASM331548v1_genomic.fna/checkm_input GCF_003315485.1_ASM331548v1_genomic.fna/checkm_result
[2024-01-24 13:22:46,497] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:46,499] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:46,519] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:46,520] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:46,520] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003315485.1_ASM331548v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:46,520] [INFO] Task started: Blastn
[2024-01-24 13:22:46,521] [INFO] Running command: blastn -query GCF_003315485.1_ASM331548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ea76891-1cab-4be3-8bc3-31fae5670f6d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003315485.1_ASM331548v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:47,674] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:47,678] [INFO] Selected 8 target genomes.
[2024-01-24 13:22:47,678] [INFO] Target genome list was writen to GCF_003315485.1_ASM331548v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:47,684] [INFO] Task started: fastANI
[2024-01-24 13:22:47,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c906b96-b6ee-44d7-b9ad-bb716fe2e938/GCF_003315485.1_ASM331548v1_genomic.fna.gz --refList GCF_003315485.1_ASM331548v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003315485.1_ASM331548v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:55,729] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:55,737] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:55,737] [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_003315485.1	s__Marinomonas rhizomae	100.0	1457	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900129155.1	s__Marinomonas polaris	84.8657	1073	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	97.53	97.35	0.90	0.88	9	-
GCF_018336955.1	s__Marinomonas sp018336955	84.4173	1025	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017285.1	s__Marinomonas sp000017285	83.9633	1053	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.39	98.39	0.88	0.88	2	-
GCF_003337275.1	s__Marinomonas foliarum	82.8354	847	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.18	98.18	0.87	0.87	2	-
GCF_003259225.1	s__Marinomonas arctica	81.4815	797	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003259175.1	s__Marinomonas shanghaiensis	81.3932	783	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012584435.1	s__Marinomonas sp012584435	81.2935	690	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:55,739] [INFO] GTDB search result was written to GCF_003315485.1_ASM331548v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:55,740] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:55,742] [INFO] DFAST_QC result json was written to GCF_003315485.1_ASM331548v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:55,743] [INFO] DFAST_QC completed!
[2024-01-24 13:22:55,743] [INFO] Total running time: 0h1m10s