[2024-01-24 10:57:38,835] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:38,840] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:38,841] [INFO] DQC Reference Directory: /var/lib/cwl/stg307f5e8b-4b48-41c7-ad5c-ff164c3c0cfb/dqc_reference
[2024-01-24 10:57:40,202] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:40,203] [INFO] Task started: Prodigal
[2024-01-24 10:57:40,203] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d9c30d7-05d8-4ad4-87da-6996e5c66504/GCF_003986955.1_ASM398695v1_genomic.fna.gz | prodigal -d GCF_003986955.1_ASM398695v1_genomic.fna/cds.fna -a GCF_003986955.1_ASM398695v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:47,893] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:47,894] [INFO] Task started: HMMsearch
[2024-01-24 10:57:47,894] [INFO] Running command: hmmsearch --tblout GCF_003986955.1_ASM398695v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg307f5e8b-4b48-41c7-ad5c-ff164c3c0cfb/dqc_reference/reference_markers.hmm GCF_003986955.1_ASM398695v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:48,158] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:48,159] [INFO] Found 6/6 markers.
[2024-01-24 10:57:48,193] [INFO] Query marker FASTA was written to GCF_003986955.1_ASM398695v1_genomic.fna/markers.fasta
[2024-01-24 10:57:48,193] [INFO] Task started: Blastn
[2024-01-24 10:57:48,194] [INFO] Running command: blastn -query GCF_003986955.1_ASM398695v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg307f5e8b-4b48-41c7-ad5c-ff164c3c0cfb/dqc_reference/reference_markers.fasta -out GCF_003986955.1_ASM398695v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:48,984] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:48,988] [INFO] Selected 22 target genomes.
[2024-01-24 10:57:48,988] [INFO] Target genome list was writen to GCF_003986955.1_ASM398695v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:49,012] [INFO] Task started: fastANI
[2024-01-24 10:57:49,013] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d9c30d7-05d8-4ad4-87da-6996e5c66504/GCF_003986955.1_ASM398695v1_genomic.fna.gz --refList GCF_003986955.1_ASM398695v1_genomic.fna/target_genomes.txt --output GCF_003986955.1_ASM398695v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:01,967] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:01,968] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg307f5e8b-4b48-41c7-ad5c-ff164c3c0cfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:01,968] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg307f5e8b-4b48-41c7-ad5c-ff164c3c0cfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:01,979] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:58:01,979] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 10:58:01,979] [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
Aliidiomarina sedimenti	strain=GBSy1	GCA_003986955.1	1933879	1933879	type	True	100.0	947	947	95	inconclusive
Aliidiomarina soli	strain=Y4G10-17	GCA_003986975.1	1928574	1928574	type	True	95.0513	899	947	95	inconclusive
Aliidiomarina maris	strain=CF12-14	GCA_003987335.1	531312	531312	type	True	79.0739	206	947	95	below_threshold
Aliidiomarina minuta	strain=MLST1	GCA_003987145.1	880057	880057	type	True	78.61	202	947	95	below_threshold
Pseudidiomarina maritima	strain=CGMCC 1.7285	GCA_900115255.1	519453	519453	type	True	77.8801	51	947	95	below_threshold
Pseudidiomarina piscicola	strain=CECT 9734	GCA_902806985.1	2614830	2614830	type	True	77.7505	55	947	95	below_threshold
Pseudidiomarina marina	strain=PIM1	GCA_003987045.1	502366	502366	type	True	77.7271	62	947	95	below_threshold
Pseudidiomarina planktonica	strain=CGMCC 1.12458	GCA_900177775.1	1323738	1323738	type	True	77.621	80	947	95	below_threshold
Idiomarina aquatica	strain=SN-14	GCA_003987185.1	1327752	1327752	type	True	77.491	79	947	95	below_threshold
Pseudidiomarina planktonica	strain=TS-T11	GCA_003987425.1	1323738	1323738	type	True	77.4777	83	947	95	below_threshold
Idiomarina ramblicola	strain=R22	GCA_003987255.1	263724	263724	type	True	76.9628	70	947	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	76.6279	52	947	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:01,981] [INFO] DFAST Taxonomy check result was written to GCF_003986955.1_ASM398695v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:01,982] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:01,982] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:01,982] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg307f5e8b-4b48-41c7-ad5c-ff164c3c0cfb/dqc_reference/checkm_data
[2024-01-24 10:58:01,984] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:02,017] [INFO] Task started: CheckM
[2024-01-24 10:58:02,017] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003986955.1_ASM398695v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003986955.1_ASM398695v1_genomic.fna/checkm_input GCF_003986955.1_ASM398695v1_genomic.fna/checkm_result
[2024-01-24 10:58:30,379] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:30,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:30,399] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:30,400] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:30,400] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003986955.1_ASM398695v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:30,401] [INFO] Task started: Blastn
[2024-01-24 10:58:30,401] [INFO] Running command: blastn -query GCF_003986955.1_ASM398695v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg307f5e8b-4b48-41c7-ad5c-ff164c3c0cfb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003986955.1_ASM398695v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:31,647] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:31,653] [INFO] Selected 19 target genomes.
[2024-01-24 10:58:31,653] [INFO] Target genome list was writen to GCF_003986955.1_ASM398695v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:31,666] [INFO] Task started: fastANI
[2024-01-24 10:58:31,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d9c30d7-05d8-4ad4-87da-6996e5c66504/GCF_003986955.1_ASM398695v1_genomic.fna.gz --refList GCF_003986955.1_ASM398695v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003986955.1_ASM398695v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:42,461] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:42,474] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:42,474] [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_003986955.1	s__Aliidiomarina sedimenti	100.0	947	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0513	N/A	N/A	N/A	N/A	1	conclusive
GCF_003986975.1	s__Aliidiomarina soli	95.0312	900	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0513	N/A	N/A	N/A	N/A	1	-
GCF_003987335.1	s__Aliidiomarina maris	79.0739	206	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	99.15	98.30	0.97	0.95	3	-
GCF_003987145.1	s__Aliidiomarina minuta	78.5822	204	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902806985.1	s__Pseudidiomarina piscicola	77.7927	55	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001870515.1	s__Idiomarina sp001870515	77.7812	56	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987045.1	s__Pseudidiomarina marina	77.7432	63	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.46	97.46	0.94	0.94	2	-
GCF_900177775.1	s__Pseudidiomarina planktonica	77.6136	81	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003999375.1	s__Pseudidiomarina mangrovi	77.5336	51	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987185.1	s__Idiomarina aquatica	77.475	78	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	99.08	99.08	0.91	0.91	2	-
GCF_003987255.1	s__Idiomarina ramblicola	76.937	69	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:42,476] [INFO] GTDB search result was written to GCF_003986955.1_ASM398695v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:42,476] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:42,480] [INFO] DFAST_QC result json was written to GCF_003986955.1_ASM398695v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:42,480] [INFO] DFAST_QC completed!
[2024-01-24 10:58:42,480] [INFO] Total running time: 0h1m4s