[2024-01-24 13:46:40,123] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:40,125] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:40,125] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d147d7f-1705-4d3a-a4fd-c3f4a14b1298/dqc_reference
[2024-01-24 13:46:41,464] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:41,465] [INFO] Task started: Prodigal
[2024-01-24 13:46:41,465] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8d01a78-7fcc-4b99-a15f-4e72a1061334/GCF_008808095.1_ASM880809v1_genomic.fna.gz | prodigal -d GCF_008808095.1_ASM880809v1_genomic.fna/cds.fna -a GCF_008808095.1_ASM880809v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:53,021] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:53,021] [INFO] Task started: HMMsearch
[2024-01-24 13:46:53,021] [INFO] Running command: hmmsearch --tblout GCF_008808095.1_ASM880809v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d147d7f-1705-4d3a-a4fd-c3f4a14b1298/dqc_reference/reference_markers.hmm GCF_008808095.1_ASM880809v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:53,398] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:53,399] [INFO] Found 6/6 markers.
[2024-01-24 13:46:53,438] [INFO] Query marker FASTA was written to GCF_008808095.1_ASM880809v1_genomic.fna/markers.fasta
[2024-01-24 13:46:53,438] [INFO] Task started: Blastn
[2024-01-24 13:46:53,438] [INFO] Running command: blastn -query GCF_008808095.1_ASM880809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d147d7f-1705-4d3a-a4fd-c3f4a14b1298/dqc_reference/reference_markers.fasta -out GCF_008808095.1_ASM880809v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:54,304] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:54,307] [INFO] Selected 24 target genomes.
[2024-01-24 13:46:54,308] [INFO] Target genome list was writen to GCF_008808095.1_ASM880809v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:54,328] [INFO] Task started: fastANI
[2024-01-24 13:46:54,328] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8d01a78-7fcc-4b99-a15f-4e72a1061334/GCF_008808095.1_ASM880809v1_genomic.fna.gz --refList GCF_008808095.1_ASM880809v1_genomic.fna/target_genomes.txt --output GCF_008808095.1_ASM880809v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:12,868] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:12,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d147d7f-1705-4d3a-a4fd-c3f4a14b1298/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:12,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d147d7f-1705-4d3a-a4fd-c3f4a14b1298/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:12,886] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:12,886] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:12,886] [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
Pseudoalteromonas ruthenica	strain=LMG 19699	GCA_008808095.1	151081	151081	type	True	100.0	1371	1371	95	conclusive
Pseudoalteromonas piscicida	strain=JCM 20779	GCA_000238315.4	43662	43662	type	True	79.3917	187	1371	95	below_threshold
Pseudoalteromonas spongiae	strain=UST010723-006	GCA_000238255.4	298657	298657	type	True	79.3153	142	1371	95	below_threshold
Pseudoalteromonas citrea	strain=DSM 8771	GCA_000238375.4	43655	43655	type	True	79.1052	153	1371	95	below_threshold
Pseudoalteromonas luteoviolacea	strain=CH130	GCA_014925325.1	43657	43657	suspected-type	True	79.023	133	1371	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KCTC 12958	GCA_001455325.1	152297	152297	suspected-type	True	79.0184	188	1371	95	below_threshold
Pseudoalteromonas espejiana	strain=ATCC 29659	GCA_002221525.1	28107	28107	type	True	78.9116	172	1371	95	below_threshold
Pseudoalteromonas luteoviolacea	strain=DSM 6061	GCA_001625655.1	43657	43657	suspected-type	True	78.6596	123	1371	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KMM 3549	GCA_002310795.1	152297	152297	suspected-type	True	78.6509	184	1371	95	below_threshold
Pseudoalteromonas caenipelagi	strain=JBTF-M23	GCA_013140855.1	2726988	2726988	type	True	78.6452	156	1371	95	below_threshold
Pseudoalteromonas byunsanensis	strain=JCM 12483	GCA_001854475.1	327939	327939	type	True	78.6299	164	1371	95	below_threshold
Pseudoalteromonas arabiensis	strain=JCM 17292	GCA_001550155.1	874454	874454	type	True	78.6053	178	1371	95	below_threshold
Pseudoalteromonas nigrifaciens	strain=KMM 661	GCA_002221505.1	28109	28109	type	True	78.5782	182	1371	95	below_threshold
Pseudoalteromonas flavipulchra	strain=NCIMB 2033	GCA_014858715.1	137779	137779	suspected-type	True	78.5571	173	1371	95	below_threshold
Pseudoalteromonas nigrifaciens	strain=NCTC10691	GCA_900455185.1	28109	28109	type	True	78.5156	175	1371	95	below_threshold
Pseudoalteromonas flavipulchra	strain=LMG 20361	GCA_014596995.1	137779	137779	suspected-type	True	78.506	174	1371	95	below_threshold
Pseudoalteromonas piscicida	strain=ATCC 15057	GCA_000382005.1	43662	43662	type	True	78.3117	177	1371	95	below_threshold
Pseudoalteromonas lipolytica	strain=CGMCC 1.8499	GCA_900116435.1	570156	570156	suspected-type	True	78.2904	169	1371	95	below_threshold
Pseudoalteromonas espejiana	strain=NBRC 102222	GCA_007989585.1	28107	28107	type	True	77.9546	160	1371	95	below_threshold
Motilimonas eburnea	strain=YH6	GCA_021295345.1	1737488	1737488	type	True	76.6513	54	1371	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	76.546	53	1371	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:12,888] [INFO] DFAST Taxonomy check result was written to GCF_008808095.1_ASM880809v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:12,889] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:12,889] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:12,889] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d147d7f-1705-4d3a-a4fd-c3f4a14b1298/dqc_reference/checkm_data
[2024-01-24 13:47:12,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:12,932] [INFO] Task started: CheckM
[2024-01-24 13:47:12,932] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008808095.1_ASM880809v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008808095.1_ASM880809v1_genomic.fna/checkm_input GCF_008808095.1_ASM880809v1_genomic.fna/checkm_result
[2024-01-24 13:47:48,855] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:48,857] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:48,875] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:48,876] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:48,876] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008808095.1_ASM880809v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:48,877] [INFO] Task started: Blastn
[2024-01-24 13:47:48,877] [INFO] Running command: blastn -query GCF_008808095.1_ASM880809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d147d7f-1705-4d3a-a4fd-c3f4a14b1298/dqc_reference/reference_markers_gtdb.fasta -out GCF_008808095.1_ASM880809v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:50,010] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:50,012] [INFO] Selected 16 target genomes.
[2024-01-24 13:47:50,012] [INFO] Target genome list was writen to GCF_008808095.1_ASM880809v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:50,042] [INFO] Task started: fastANI
[2024-01-24 13:47:50,042] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8d01a78-7fcc-4b99-a15f-4e72a1061334/GCF_008808095.1_ASM880809v1_genomic.fna.gz --refList GCF_008808095.1_ASM880809v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008808095.1_ASM880809v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:02,562] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:02,579] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:02,579] [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_008808095.1	s__Pseudoalteromonas ruthenica	100.0	1371	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.93	97.29	0.94	0.91	18	conclusive
GCF_002964785.1	s__Pseudoalteromonas sp002964785	79.7692	425	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482385.1	s__Pseudoalteromonas rubra_B	79.702	158	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	95.23	95.23	0.89	0.89	2	-
GCF_002964765.1	s__Pseudoalteromonas sp002964765	79.6693	421	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.33	98.12	0.95	0.94	4	-
GCF_002964705.1	s__Pseudoalteromonas sp002964705	79.5928	437	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.66	96.66	0.91	0.91	2	-
GCF_017638925.1	s__Pseudoalteromonas xiamenensis	79.0596	144	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391845.1	s__Pseudoalteromonas sp002685175	78.942	197	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.05	98.96	0.91	0.83	5	-
GCF_002221525.1	s__Pseudoalteromonas espejiana	78.9388	171	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001854475.1	s__Pseudoalteromonas byunsanensis	78.633	164	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013140855.1	s__Pseudoalteromonas caenipelagi	78.6194	157	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002744175.1	s__Pseudoalteromonas piscicida_B	78.6113	158	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005886535.1	s__Pseudoalteromonas sp005886535	78.3238	163	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723455.1	s__Pseudoalteromonas sp002723455	78.306	158	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.50	98.50	0.93	0.93	2	-
GCF_005876835.1	s__Pseudoalteromonas phenolica_B	78.2203	152	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001306915.1	s__Pseudoalteromonas lipolytica_A	78.0689	207	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.22	97.66	0.91	0.90	9	-
GCA_000333235.1	s__Pseudoalteromonas luteoviolacea_D	77.8278	125	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:02,581] [INFO] GTDB search result was written to GCF_008808095.1_ASM880809v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:02,582] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:02,587] [INFO] DFAST_QC result json was written to GCF_008808095.1_ASM880809v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:02,587] [INFO] DFAST_QC completed!
[2024-01-24 13:48:02,588] [INFO] Total running time: 0h1m22s