[2024-01-25 19:59:20,466] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:59:20,467] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:59:20,467] [INFO] DQC Reference Directory: /var/lib/cwl/stg937f3ffa-ec5a-4eda-a843-171b2189219b/dqc_reference
[2024-01-25 19:59:21,608] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:59:21,609] [INFO] Task started: Prodigal
[2024-01-25 19:59:21,609] [INFO] Running command: gunzip -c /var/lib/cwl/stg5cda63ba-00f9-4ab2-a5aa-faebd222d3b5/GCF_003387375.1_ASM338737v1_genomic.fna.gz | prodigal -d GCF_003387375.1_ASM338737v1_genomic.fna/cds.fna -a GCF_003387375.1_ASM338737v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:59:29,854] [INFO] Task succeeded: Prodigal
[2024-01-25 19:59:29,854] [INFO] Task started: HMMsearch
[2024-01-25 19:59:29,854] [INFO] Running command: hmmsearch --tblout GCF_003387375.1_ASM338737v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg937f3ffa-ec5a-4eda-a843-171b2189219b/dqc_reference/reference_markers.hmm GCF_003387375.1_ASM338737v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:59:30,083] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:59:30,085] [INFO] Found 6/6 markers.
[2024-01-25 19:59:30,122] [INFO] Query marker FASTA was written to GCF_003387375.1_ASM338737v1_genomic.fna/markers.fasta
[2024-01-25 19:59:30,122] [INFO] Task started: Blastn
[2024-01-25 19:59:30,122] [INFO] Running command: blastn -query GCF_003387375.1_ASM338737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg937f3ffa-ec5a-4eda-a843-171b2189219b/dqc_reference/reference_markers.fasta -out GCF_003387375.1_ASM338737v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:30,781] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:30,783] [INFO] Selected 22 target genomes.
[2024-01-25 19:59:30,784] [INFO] Target genome list was writen to GCF_003387375.1_ASM338737v1_genomic.fna/target_genomes.txt
[2024-01-25 19:59:30,814] [INFO] Task started: fastANI
[2024-01-25 19:59:30,814] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cda63ba-00f9-4ab2-a5aa-faebd222d3b5/GCF_003387375.1_ASM338737v1_genomic.fna.gz --refList GCF_003387375.1_ASM338737v1_genomic.fna/target_genomes.txt --output GCF_003387375.1_ASM338737v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:59:45,995] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:45,995] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg937f3ffa-ec5a-4eda-a843-171b2189219b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:59:45,995] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg937f3ffa-ec5a-4eda-a843-171b2189219b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:59:46,006] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:59:46,006] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:59:46,006] [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 pollencensis	strain=CECT 7375	GCA_003387375.1	491954	491954	type	True	100.0	1266	1268	95	conclusive
Marinomonas flavescens	strain=ANRC-JHZ47	GCA_004352835.1	2529379	2529379	type	True	81.1291	625	1268	95	below_threshold
Marinomonas profundimaris	strain=D104	GCA_000508165.1	1208321	1208321	type	True	80.0557	328	1268	95	below_threshold
Marinomonas alcarazii	strain=CECT 7730	GCA_003208215.1	491949	491949	type	True	79.5262	321	1268	95	below_threshold
Marinomonas lutimaris	strain=E165	GCA_019426345.1	2846746	2846746	type	True	79.4053	335	1268	95	below_threshold
Marinomonas rhizomae	strain=IVIA-Po-145	GCA_003721275.1	491948	491948	type	True	79.3744	320	1268	95	below_threshold
Marinomonas colpomeniae	strain=SM2066	GCA_014803385.1	2774408	2774408	type	True	79.0677	272	1268	95	below_threshold
Marinomonas ushuaiensis	strain=DSM 15871	GCA_000521805.1	263818	263818	type	True	79.0331	299	1268	95	below_threshold
Marinomonas shanghaiensis	strain=DSL-35	GCA_003259175.1	2202418	2202418	type	True	79.0271	324	1268	95	below_threshold
Marinomonas spartinae	strain=CECT 8886	GCA_900089775.1	1792290	1792290	type	True	78.9014	325	1268	95	below_threshold
Marinomonas posidonica	strain=IVIA-Po-181	GCA_000214215.1	936476	936476	type	True	78.8741	284	1268	95	below_threshold
Marinomonas arctica	strain=CGMCC 1.6498	GCA_014645175.1	383750	383750	type	True	78.8422	328	1268	95	below_threshold
Marinomonas primoryensis	strain=MPKMM3633	GCA_013372285.1	178399	178399	type	True	78.8206	329	1268	95	below_threshold
Marinomonas arctica	strain=328	GCA_003259225.1	383750	383750	type	True	78.7883	331	1268	95	below_threshold
Marinomonas aquiplantarum	strain=CECT 7732	GCA_003314975.1	491951	491951	type	True	78.6019	301	1268	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:59:46,007] [INFO] DFAST Taxonomy check result was written to GCF_003387375.1_ASM338737v1_genomic.fna/tc_result.tsv
[2024-01-25 19:59:46,008] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:59:46,008] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:59:46,008] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg937f3ffa-ec5a-4eda-a843-171b2189219b/dqc_reference/checkm_data
[2024-01-25 19:59:46,009] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:59:46,047] [INFO] Task started: CheckM
[2024-01-25 19:59:46,048] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003387375.1_ASM338737v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003387375.1_ASM338737v1_genomic.fna/checkm_input GCF_003387375.1_ASM338737v1_genomic.fna/checkm_result
[2024-01-25 20:00:14,016] [INFO] Task succeeded: CheckM
[2024-01-25 20:00:14,018] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:00:14,034] [INFO] ===== Completeness check finished =====
[2024-01-25 20:00:14,035] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:00:14,036] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003387375.1_ASM338737v1_genomic.fna/markers.fasta)
[2024-01-25 20:00:14,036] [INFO] Task started: Blastn
[2024-01-25 20:00:14,036] [INFO] Running command: blastn -query GCF_003387375.1_ASM338737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg937f3ffa-ec5a-4eda-a843-171b2189219b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003387375.1_ASM338737v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:15,107] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:15,112] [INFO] Selected 16 target genomes.
[2024-01-25 20:00:15,113] [INFO] Target genome list was writen to GCF_003387375.1_ASM338737v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:00:15,134] [INFO] Task started: fastANI
[2024-01-25 20:00:15,134] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cda63ba-00f9-4ab2-a5aa-faebd222d3b5/GCF_003387375.1_ASM338737v1_genomic.fna.gz --refList GCF_003387375.1_ASM338737v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003387375.1_ASM338737v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:00:26,973] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:26,983] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:00:26,984] [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_003387375.1	s__Marinomonas pollencensis	100.0	1266	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004352855.1	s__Marinomonas sp004352855	83.5198	906	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352835.1	s__Marinomonas sp004352835	81.1183	626	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000508165.1	s__Marinomonas profundimaris	80.0557	328	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122525.1	s__Marinomonas sp008122525	79.7629	279	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016463975.1	s__Marinomonas sp016463975	79.7589	315	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003208215.1	s__Marinomonas alcarazii	79.5337	320	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.70	98.70	0.93	0.93	2	-
GCF_003315485.1	s__Marinomonas rhizomae	79.5112	333	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014803385.1	s__Marinomonas colpomeniae	79.0662	271	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521805.1	s__Marinomonas ushuaiensis	79.033	299	1268	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	78.9858	327	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900089775.1	s__Marinomonas spartinae	78.884	325	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.99	98.99	0.93	0.93	2	-
GCF_016461715.1	s__Marinomonas spartinae_A	78.851	329	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153025.1	s__Marinomonas sp000153025	78.0266	154	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:00:26,985] [INFO] GTDB search result was written to GCF_003387375.1_ASM338737v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:00:26,986] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:00:26,993] [INFO] DFAST_QC result json was written to GCF_003387375.1_ASM338737v1_genomic.fna/dqc_result.json
[2024-01-25 20:00:26,994] [INFO] DFAST_QC completed!
[2024-01-25 20:00:26,994] [INFO] Total running time: 0h1m7s