[2024-01-24 11:12:25,126] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:25,129] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:25,129] [INFO] DQC Reference Directory: /var/lib/cwl/stgb43ad2bd-12b7-4480-8e01-f6be22bef1fe/dqc_reference
[2024-01-24 11:12:27,084] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:27,094] [INFO] Task started: Prodigal
[2024-01-24 11:12:27,095] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ce991e3-bc2a-4aba-89ee-f3a639eedfe3/GCF_001418205.1_ASM141820v1_genomic.fna.gz | prodigal -d GCF_001418205.1_ASM141820v1_genomic.fna/cds.fna -a GCF_001418205.1_ASM141820v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:37,830] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:37,831] [INFO] Task started: HMMsearch
[2024-01-24 11:12:37,831] [INFO] Running command: hmmsearch --tblout GCF_001418205.1_ASM141820v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb43ad2bd-12b7-4480-8e01-f6be22bef1fe/dqc_reference/reference_markers.hmm GCF_001418205.1_ASM141820v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:38,194] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:38,195] [INFO] Found 6/6 markers.
[2024-01-24 11:12:38,231] [INFO] Query marker FASTA was written to GCF_001418205.1_ASM141820v1_genomic.fna/markers.fasta
[2024-01-24 11:12:38,232] [INFO] Task started: Blastn
[2024-01-24 11:12:38,232] [INFO] Running command: blastn -query GCF_001418205.1_ASM141820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb43ad2bd-12b7-4480-8e01-f6be22bef1fe/dqc_reference/reference_markers.fasta -out GCF_001418205.1_ASM141820v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:38,977] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:38,980] [INFO] Selected 12 target genomes.
[2024-01-24 11:12:38,981] [INFO] Target genome list was writen to GCF_001418205.1_ASM141820v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:38,987] [INFO] Task started: fastANI
[2024-01-24 11:12:38,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ce991e3-bc2a-4aba-89ee-f3a639eedfe3/GCF_001418205.1_ASM141820v1_genomic.fna.gz --refList GCF_001418205.1_ASM141820v1_genomic.fna/target_genomes.txt --output GCF_001418205.1_ASM141820v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:48,335] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:48,336] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb43ad2bd-12b7-4480-8e01-f6be22bef1fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:48,336] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb43ad2bd-12b7-4480-8e01-f6be22bef1fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:48,343] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:12:48,344] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:12:48,344] [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 fungiae	strain=JCM 18476	GCA_001517305.1	1137284	1137284	type	True	100.0	1377	1378	95	conclusive
Marinomonas fungiae	strain=JCM 18476	GCA_001418205.1	1137284	1137284	type	True	100.0	1377	1378	95	conclusive
Marinomonas aquimarina	strain=11SM4	GCA_001639695.1	295068	295068	type	True	83.4412	761	1378	95	below_threshold
Marinomonas aquimarina	strain=CECT 5080	GCA_900089755.1	295068	295068	type	True	83.3429	782	1378	95	below_threshold
Marinomonas communis	strain=DSM 5604	GCA_004363305.1	28254	28254	type	True	81.7994	586	1378	95	below_threshold
Marinomonas gallaica	strain=Cmf 17.2	GCA_001639745.1	1806667	1806667	type	True	80.8628	600	1378	95	below_threshold
Marinomonas atlantica	strain=Cmf 18.22	GCA_001639725.1	1806668	1806668	type	True	80.4589	533	1378	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:48,345] [INFO] DFAST Taxonomy check result was written to GCF_001418205.1_ASM141820v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:48,346] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:48,346] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:48,346] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb43ad2bd-12b7-4480-8e01-f6be22bef1fe/dqc_reference/checkm_data
[2024-01-24 11:12:48,348] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:48,392] [INFO] Task started: CheckM
[2024-01-24 11:12:48,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001418205.1_ASM141820v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001418205.1_ASM141820v1_genomic.fna/checkm_input GCF_001418205.1_ASM141820v1_genomic.fna/checkm_result
[2024-01-24 11:13:24,117] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:24,118] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:24,137] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:24,138] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:24,138] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001418205.1_ASM141820v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:24,139] [INFO] Task started: Blastn
[2024-01-24 11:13:24,139] [INFO] Running command: blastn -query GCF_001418205.1_ASM141820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb43ad2bd-12b7-4480-8e01-f6be22bef1fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_001418205.1_ASM141820v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:25,232] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:25,236] [INFO] Selected 11 target genomes.
[2024-01-24 11:13:25,237] [INFO] Target genome list was writen to GCF_001418205.1_ASM141820v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:25,253] [INFO] Task started: fastANI
[2024-01-24 11:13:25,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ce991e3-bc2a-4aba-89ee-f3a639eedfe3/GCF_001418205.1_ASM141820v1_genomic.fna.gz --refList GCF_001418205.1_ASM141820v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001418205.1_ASM141820v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:33,858] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:33,878] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:33,879] [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_001418205.1	s__Marinomonas fungiae	100.0	1377	1378	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_900089755.1	s__Marinomonas aquimarina	83.3635	779	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016461785.1	s__Marinomonas ostreistagni_A	81.9956	572	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363305.1	s__Marinomonas communis	81.8047	585	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	97.16	97.04	0.89	0.87	3	-
GCF_001639745.1	s__Marinomonas gallaica	80.8622	597	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	96.95	96.94	0.89	0.89	3	-
GCF_016888445.1	s__Marinomonas ostreistagni	80.5885	478	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001639725.1	s__Marinomonas atlantica	80.4563	533	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337275.1	s__Marinomonas foliarum	78.5421	194	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.18	98.18	0.87	0.87	2	-
GCF_004362145.1	s__Marinomonas balearica	78.2415	151	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016461715.1	s__Marinomonas spartinae_A	78.1229	165	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129155.1	s__Marinomonas polaris	78.0101	196	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	97.53	97.35	0.90	0.88	9	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:33,881] [INFO] GTDB search result was written to GCF_001418205.1_ASM141820v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:33,881] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:33,885] [INFO] DFAST_QC result json was written to GCF_001418205.1_ASM141820v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:33,885] [INFO] DFAST_QC completed!
[2024-01-24 11:13:33,885] [INFO] Total running time: 0h1m9s