[2024-01-24 11:26:28,085] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:28,087] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:28,087] [INFO] DQC Reference Directory: /var/lib/cwl/stgde7cc3f5-71f8-4de1-8357-7bf19e0a6cdf/dqc_reference
[2024-01-24 11:26:29,480] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:29,481] [INFO] Task started: Prodigal
[2024-01-24 11:26:29,482] [INFO] Running command: gunzip -c /var/lib/cwl/stge8e53fbf-85a6-4501-8b8f-3a1500575ec1/GCF_019249245.1_ASM1924924v1_genomic.fna.gz | prodigal -d GCF_019249245.1_ASM1924924v1_genomic.fna/cds.fna -a GCF_019249245.1_ASM1924924v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:38,161] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:38,162] [INFO] Task started: HMMsearch
[2024-01-24 11:26:38,162] [INFO] Running command: hmmsearch --tblout GCF_019249245.1_ASM1924924v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde7cc3f5-71f8-4de1-8357-7bf19e0a6cdf/dqc_reference/reference_markers.hmm GCF_019249245.1_ASM1924924v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:38,533] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:38,535] [INFO] Found 6/6 markers.
[2024-01-24 11:26:38,583] [INFO] Query marker FASTA was written to GCF_019249245.1_ASM1924924v1_genomic.fna/markers.fasta
[2024-01-24 11:26:38,584] [INFO] Task started: Blastn
[2024-01-24 11:26:38,584] [INFO] Running command: blastn -query GCF_019249245.1_ASM1924924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde7cc3f5-71f8-4de1-8357-7bf19e0a6cdf/dqc_reference/reference_markers.fasta -out GCF_019249245.1_ASM1924924v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:39,367] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:39,370] [INFO] Selected 27 target genomes.
[2024-01-24 11:26:39,370] [INFO] Target genome list was writen to GCF_019249245.1_ASM1924924v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:39,393] [INFO] Task started: fastANI
[2024-01-24 11:26:39,394] [INFO] Running command: fastANI --query /var/lib/cwl/stge8e53fbf-85a6-4501-8b8f-3a1500575ec1/GCF_019249245.1_ASM1924924v1_genomic.fna.gz --refList GCF_019249245.1_ASM1924924v1_genomic.fna/target_genomes.txt --output GCF_019249245.1_ASM1924924v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:00,381] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:00,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde7cc3f5-71f8-4de1-8357-7bf19e0a6cdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:00,382] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde7cc3f5-71f8-4de1-8357-7bf19e0a6cdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:00,395] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:27:00,396] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:27:00,396] [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
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	78.8681	274	1233	95	below_threshold
Salinimonas profundi	strain=HHU 13199	GCA_014750655.1	2729140	2729140	type	True	78.7152	221	1233	95	below_threshold
Salinimonas iocasae	strain=KX18D6	GCA_006228385.1	2572577	2572577	type	True	78.5894	241	1233	95	below_threshold
Salinimonas chungwhensis	strain=DSM 16280	GCA_000378185.1	265425	265425	type	True	78.5729	214	1233	95	below_threshold
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	78.3975	180	1233	95	below_threshold
Alteromonas profundi	strain=345S023	GCA_010500865.1	2696062	2696062	type	True	78.2625	141	1233	95	below_threshold
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	78.2394	136	1233	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	78.0855	141	1233	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	77.9413	132	1233	95	below_threshold
Ningiella ruwaisensis	strain=B66	GCA_004798935.1	2364274	2364274	type	True	77.9276	61	1233	95	below_threshold
Alteromonas hispanica	strain=LMG 22958	GCA_010500915.1	315421	315421	type	True	77.9066	124	1233	95	below_threshold
Alteromonas pelagimontana	strain=5.12	GCA_002499975.2	1858656	1858656	type	True	77.8094	147	1233	95	below_threshold
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	77.7957	130	1233	95	below_threshold
Alteromonas confluentis	strain=KCTC 42603	GCA_001757105.1	1656094	1656094	type	True	77.7306	149	1233	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	77.7053	142	1233	95	below_threshold
Alteromonas oceani	strain=S35	GCA_003731635.1	2071609	2071609	type	True	77.6865	136	1233	95	below_threshold
Alteromonas lipolytica	strain=JW12	GCA_001758465.1	1856405	1856405	type	True	77.5159	142	1233	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:00,398] [INFO] DFAST Taxonomy check result was written to GCF_019249245.1_ASM1924924v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:00,398] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:00,398] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:00,399] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde7cc3f5-71f8-4de1-8357-7bf19e0a6cdf/dqc_reference/checkm_data
[2024-01-24 11:27:00,400] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:00,439] [INFO] Task started: CheckM
[2024-01-24 11:27:00,440] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019249245.1_ASM1924924v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019249245.1_ASM1924924v1_genomic.fna/checkm_input GCF_019249245.1_ASM1924924v1_genomic.fna/checkm_result
[2024-01-24 11:27:32,861] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:32,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:32,882] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:32,882] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:32,883] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019249245.1_ASM1924924v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:32,883] [INFO] Task started: Blastn
[2024-01-24 11:27:32,883] [INFO] Running command: blastn -query GCF_019249245.1_ASM1924924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde7cc3f5-71f8-4de1-8357-7bf19e0a6cdf/dqc_reference/reference_markers_gtdb.fasta -out GCF_019249245.1_ASM1924924v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:34,059] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:34,064] [INFO] Selected 21 target genomes.
[2024-01-24 11:27:34,064] [INFO] Target genome list was writen to GCF_019249245.1_ASM1924924v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:34,081] [INFO] Task started: fastANI
[2024-01-24 11:27:34,082] [INFO] Running command: fastANI --query /var/lib/cwl/stge8e53fbf-85a6-4501-8b8f-3a1500575ec1/GCF_019249245.1_ASM1924924v1_genomic.fna.gz --refList GCF_019249245.1_ASM1924924v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019249245.1_ASM1924924v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:49,788] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:49,812] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:49,813] [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
GCA_019249245.1	s__Alteromonas lipotrueiana	100.0	1231	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015644725.1	s__Alteromonas sp015644725	80.601	659	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003429285.1	s__Alteromonas sediminis	79.6882	394	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.07	99.07	0.95	0.95	2	-
GCF_005222225.1	s__Alteromonas lutimaris	78.8837	273	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014750655.1	s__Alteromonas profundi_A	78.7152	221	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006228385.1	s__Alteromonas iocasae	78.6058	240	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378185.1	s__Alteromonas chungwhensis	78.5551	215	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019249295.1	s__Alteromonas antoniana	78.4269	178	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651815.1	s__Alteromonas halophila	78.2584	160	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584565.2	s__Alteromonas sp002729795	78.189	154	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.21	97.21	0.92	0.92	2	-
GCF_018860805.1	s__Alteromonas sp018860805	78.0988	126	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506055.1	s__Alteromonas lipotrueae	78.0778	130	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.66	99.49	0.97	0.95	4	-
GCF_010500915.1	s__Alteromonas hispanica	77.9418	122	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.81	97.72	0.82	0.79	5	-
GCA_018222405.1	s__Alteromonas sp018222405	77.7756	125	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001757105.1	s__Alteromonas confluentis	77.7306	149	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005117025.1	s__Alteromonas portus	77.7053	142	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001758465.1	s__Alteromonas lipolytica	77.5159	142	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002339125.1	s__Alteromonas sp002335925	77.5156	108	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.57	96.36	0.89	0.83	19	-
GCA_004353515.1	s__M269 sp004353515	77.3946	51	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__M269	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129565.1	s__Alteromonas aggregata	77.3201	136	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.34	96.39	0.91	0.85	11	-
GCA_002691625.1	s__Alteromonas sp002691625	77.0703	103	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.62	99.31	0.91	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:49,815] [INFO] GTDB search result was written to GCF_019249245.1_ASM1924924v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:49,815] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:49,820] [INFO] DFAST_QC result json was written to GCF_019249245.1_ASM1924924v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:49,820] [INFO] DFAST_QC completed!
[2024-01-24 11:27:49,820] [INFO] Total running time: 0h1m22s