[2024-01-25 18:43:50,561] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:43:50,563] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:43:50,563] [INFO] DQC Reference Directory: /var/lib/cwl/stg30f0d86d-8875-4cfa-9e0a-0f03762e942b/dqc_reference
[2024-01-25 18:43:51,658] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:43:51,659] [INFO] Task started: Prodigal
[2024-01-25 18:43:51,659] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b06052e-c79a-45e5-8b32-8398cf06f0f3/GCF_002282895.1_ASM228289v1_genomic.fna.gz | prodigal -d GCF_002282895.1_ASM228289v1_genomic.fna/cds.fna -a GCF_002282895.1_ASM228289v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:43:58,881] [INFO] Task succeeded: Prodigal
[2024-01-25 18:43:58,882] [INFO] Task started: HMMsearch
[2024-01-25 18:43:58,882] [INFO] Running command: hmmsearch --tblout GCF_002282895.1_ASM228289v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30f0d86d-8875-4cfa-9e0a-0f03762e942b/dqc_reference/reference_markers.hmm GCF_002282895.1_ASM228289v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:43:59,119] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:43:59,120] [INFO] Found 6/6 markers.
[2024-01-25 18:43:59,145] [INFO] Query marker FASTA was written to GCF_002282895.1_ASM228289v1_genomic.fna/markers.fasta
[2024-01-25 18:43:59,146] [INFO] Task started: Blastn
[2024-01-25 18:43:59,146] [INFO] Running command: blastn -query GCF_002282895.1_ASM228289v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30f0d86d-8875-4cfa-9e0a-0f03762e942b/dqc_reference/reference_markers.fasta -out GCF_002282895.1_ASM228289v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:59,845] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:59,848] [INFO] Selected 28 target genomes.
[2024-01-25 18:43:59,848] [INFO] Target genome list was writen to GCF_002282895.1_ASM228289v1_genomic.fna/target_genomes.txt
[2024-01-25 18:43:59,856] [INFO] Task started: fastANI
[2024-01-25 18:43:59,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b06052e-c79a-45e5-8b32-8398cf06f0f3/GCF_002282895.1_ASM228289v1_genomic.fna.gz --refList GCF_002282895.1_ASM228289v1_genomic.fna/target_genomes.txt --output GCF_002282895.1_ASM228289v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:44:18,222] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:18,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30f0d86d-8875-4cfa-9e0a-0f03762e942b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:44:18,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30f0d86d-8875-4cfa-9e0a-0f03762e942b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:44:18,233] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:44:18,233] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:44:18,234] [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
Paraferrimonas haliotis	strain=AFRC7-2-1	GCA_002282895.1	2013866	2013866	type	True	100.0	1054	1054	95	conclusive
Shewanella decolorationis	strain=S12	GCA_000485795.1	256839	256839	type	True	80.7561	84	1054	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	79.9106	83	1054	95	below_threshold
Paraferrimonas sedimenticola	strain=NBRC 101628	GCA_002282855.1	375674	375674	type	True	78.4708	219	1054	95	below_threshold
Shewanella aquimarina	strain=JCM 12193	GCA_023349185.1	260365	260365	type	True	77.6325	53	1054	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	77.4954	54	1054	95	below_threshold
Shewanella corallii	strain=DSM 21332	GCA_023349125.1	560080	560080	type	True	77.1919	53	1054	95	below_threshold
Shewanella maritima	strain=D4-2	GCA_004295345.1	2520507	2520507	type	True	77.0629	87	1054	95	below_threshold
Parashewanella hymeniacidonis	strain=202IG2-18	GCA_016900895.1	2807618	2807618	type	True	77.0614	53	1054	95	below_threshold
Shewanella algae	strain=ATCC 51192	GCA_012396675.1	38313	38313	type	True	76.8968	53	1054	95	below_threshold
Shewanella algae	strain=CECT 5071	GCA_009183365.2	38313	38313	type	True	76.8851	56	1054	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_009828585.1	2282700	2282700	type	True	76.8643	72	1054	95	below_threshold
Shewanella saliphila	strain=JCM 32304	GCA_014648295.1	2282698	2282698	type	True	76.8602	66	1054	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	76.8262	68	1054	95	below_threshold
Shewanella nanhaiensis	strain=NR704-98	GCA_019457885.1	2864872	2864872	type	True	76.8142	62	1054	95	below_threshold
Shewanella olleyana	strain=LMG 21437	GCA_023283825.1	135626	135626	type	True	76.7894	59	1054	95	below_threshold
Shewanella algae	strain=NBRC 103173	GCA_001598875.1	38313	38313	type	True	76.6793	53	1054	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.5686	56	1054	95	below_threshold
Shewanella abyssi	strain=DSM 17171	GCA_023284025.1	311789	311789	type	True	76.5446	52	1054	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:44:18,237] [INFO] DFAST Taxonomy check result was written to GCF_002282895.1_ASM228289v1_genomic.fna/tc_result.tsv
[2024-01-25 18:44:18,237] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:44:18,238] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:44:18,238] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30f0d86d-8875-4cfa-9e0a-0f03762e942b/dqc_reference/checkm_data
[2024-01-25 18:44:18,239] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:44:18,273] [INFO] Task started: CheckM
[2024-01-25 18:44:18,273] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002282895.1_ASM228289v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002282895.1_ASM228289v1_genomic.fna/checkm_input GCF_002282895.1_ASM228289v1_genomic.fna/checkm_result
[2024-01-25 18:44:43,952] [INFO] Task succeeded: CheckM
[2024-01-25 18:44:43,964] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:44:43,982] [INFO] ===== Completeness check finished =====
[2024-01-25 18:44:43,982] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:44:43,982] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002282895.1_ASM228289v1_genomic.fna/markers.fasta)
[2024-01-25 18:44:43,983] [INFO] Task started: Blastn
[2024-01-25 18:44:43,983] [INFO] Running command: blastn -query GCF_002282895.1_ASM228289v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30f0d86d-8875-4cfa-9e0a-0f03762e942b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002282895.1_ASM228289v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:45,080] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:45,083] [INFO] Selected 25 target genomes.
[2024-01-25 18:44:45,083] [INFO] Target genome list was writen to GCF_002282895.1_ASM228289v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:44:45,105] [INFO] Task started: fastANI
[2024-01-25 18:44:45,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b06052e-c79a-45e5-8b32-8398cf06f0f3/GCF_002282895.1_ASM228289v1_genomic.fna.gz --refList GCF_002282895.1_ASM228289v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002282895.1_ASM228289v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:45:01,679] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:01,691] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:45:01,691] [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_002282895.1	s__Paraferrimonas haliotis	100.0	1054	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Paraferrimonas	95.0	99.27	99.27	0.96	0.96	2	conclusive
GCF_003596335.1	s__Motilimonas pumila	83.8876	57	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Motilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000485795.1	s__Shewanella decolorationis	80.7831	83	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.60	97.51	0.93	0.92	3	-
GCF_010993985.1	s__SM1919 sp010993985	78.482	57	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__SM1919	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002282855.1	s__Paraferrimonas sedimenticola	78.4708	219	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Paraferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203935.1	s__Shewanella sp000203935	77.7644	73	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.76	95.76	0.86	0.86	2	-
GCF_011765625.1	s__Shewanella aestuarii_A	77.6727	65	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000832025.1	s__Shewanella sp000832025	77.4273	53	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004295345.1	s__Shewanella maritima	77.0629	87	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.24	98.24	0.95	0.95	2	-
GCF_018221465.1	s__Shewanella intestini	76.959	56	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004358445.1	s__Parashewanella tropica	76.9489	61	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009183365.2	s__Shewanella algae	76.8909	55	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.21	97.66	0.95	0.92	87	-
GCF_009828585.1	s__Shewanella litoralis	76.8643	72	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002836975.1	s__Shewanella indica	76.8524	55	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	98.42	98.01	0.95	0.93	6	-
GCF_004168585.1	s__Parashewanella sp004168585	76.8429	54	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648295.1	s__Shewanella saliphila	76.8238	66	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_000019185.1	s__Shewanella halifaxensis	76.7994	62	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757755.1	s__Shewanella sp016757755	76.6424	67	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018596335.1	s__Shewanella sp018596335	76.5686	56	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013369385.1	s__Vibrio sp013369385	76.2896	52	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:45:01,693] [INFO] GTDB search result was written to GCF_002282895.1_ASM228289v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:45:01,694] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:45:01,697] [INFO] DFAST_QC result json was written to GCF_002282895.1_ASM228289v1_genomic.fna/dqc_result.json
[2024-01-25 18:45:01,697] [INFO] DFAST_QC completed!
[2024-01-25 18:45:01,697] [INFO] Total running time: 0h1m11s