[2024-01-25 19:37:05,608] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:37:05,609] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:37:05,609] [INFO] DQC Reference Directory: /var/lib/cwl/stge7d593f8-d68c-4731-837b-6138551dacd6/dqc_reference
[2024-01-25 19:37:06,699] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:37:06,699] [INFO] Task started: Prodigal
[2024-01-25 19:37:06,699] [INFO] Running command: gunzip -c /var/lib/cwl/stg410bd4a2-70b7-448d-bed6-6092557c6e4a/GCF_017354945.1_ASM1735494v1_genomic.fna.gz | prodigal -d GCF_017354945.1_ASM1735494v1_genomic.fna/cds.fna -a GCF_017354945.1_ASM1735494v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:37:17,031] [INFO] Task succeeded: Prodigal
[2024-01-25 19:37:17,032] [INFO] Task started: HMMsearch
[2024-01-25 19:37:17,032] [INFO] Running command: hmmsearch --tblout GCF_017354945.1_ASM1735494v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7d593f8-d68c-4731-837b-6138551dacd6/dqc_reference/reference_markers.hmm GCF_017354945.1_ASM1735494v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:37:17,272] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:37:17,273] [INFO] Found 6/6 markers.
[2024-01-25 19:37:17,307] [INFO] Query marker FASTA was written to GCF_017354945.1_ASM1735494v1_genomic.fna/markers.fasta
[2024-01-25 19:37:17,308] [INFO] Task started: Blastn
[2024-01-25 19:37:17,308] [INFO] Running command: blastn -query GCF_017354945.1_ASM1735494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7d593f8-d68c-4731-837b-6138551dacd6/dqc_reference/reference_markers.fasta -out GCF_017354945.1_ASM1735494v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:18,048] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:18,055] [INFO] Selected 23 target genomes.
[2024-01-25 19:37:18,056] [INFO] Target genome list was writen to GCF_017354945.1_ASM1735494v1_genomic.fna/target_genomes.txt
[2024-01-25 19:37:18,062] [INFO] Task started: fastANI
[2024-01-25 19:37:18,063] [INFO] Running command: fastANI --query /var/lib/cwl/stg410bd4a2-70b7-448d-bed6-6092557c6e4a/GCF_017354945.1_ASM1735494v1_genomic.fna.gz --refList GCF_017354945.1_ASM1735494v1_genomic.fna/target_genomes.txt --output GCF_017354945.1_ASM1735494v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:37:35,327] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:35,328] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7d593f8-d68c-4731-837b-6138551dacd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:37:35,328] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7d593f8-d68c-4731-837b-6138551dacd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:37:35,345] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:37:35,345] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:37:35,345] [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
Shewanella avicenniae	strain=FJAT-51800	GCA_017354945.1	2814294	2814294	type	True	100.0	1396	1400	95	conclusive
Shewanella mangrovi	strain=YQH10	GCA_000753795.1	1515746	1515746	type	True	82.5627	906	1400	95	below_threshold
Shewanella litorisediminis	strain=SMK1-12	GCA_016834455.1	1173586	1173586	type	True	79.2613	171	1400	95	below_threshold
Shewanella algae	strain=CECT 5071	GCA_009183365.2	38313	38313	type	True	79.1059	229	1400	95	below_threshold
Shewanella baltica	strain=NCTC10735	GCA_900456975.1	62322	62322	type	True	79.0133	210	1400	95	below_threshold
Shewanella denitrificans	strain=OS217	GCA_000013765.1	192073	192073	type	True	78.9907	123	1400	95	below_threshold
Shewanella dokdonensis	strain=DSM 23626	GCA_018394335.1	712036	712036	type	True	78.5746	307	1400	95	below_threshold
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	78.5163	147	1400	95	below_threshold
Shewanella corallii	strain=DSM 21332	GCA_023349125.1	560080	560080	type	True	78.5048	156	1400	95	below_threshold
Shewanella litorisediminis	strain=CCUG 62411	GCA_023349165.1	1173586	1173586	type	True	78.4102	162	1400	95	below_threshold
Shewanella chilikensis	strain=CCUG 57101	GCA_023283475.1	558541	558541	type	True	78.3161	206	1400	95	below_threshold
Shewanella algae	strain=ATCC 51192	GCA_012396675.1	38313	38313	type	True	78.3088	224	1400	95	below_threshold
Shewanella xiamenensis	strain=JCM 16212	GCA_014647135.1	332186	332186	type	True	78.2112	205	1400	95	below_threshold
Shewanella decolorationis	strain=S12	GCA_000485795.1	256839	256839	type	True	78.1045	223	1400	95	below_threshold
Shewanella algae	strain=NBRC 103173	GCA_001598875.1	38313	38313	type	True	78.0606	214	1400	95	below_threshold
Parashewanella hymeniacidonis	strain=202IG2-18	GCA_016900895.1	2807618	2807618	type	True	77.9399	92	1400	95	below_threshold
Shewanella seohaensis	strain=CCUG 60900	GCA_023283775.1	755175	755175	type	True	77.8175	219	1400	95	below_threshold
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	77.7341	179	1400	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	77.6678	139	1400	95	below_threshold
Shewanella marisflavi	strain=JCM 12192	GCA_023283925.1	260364	260364	type	True	77.5064	152	1400	95	below_threshold
Shewanella schlegeliana	strain=LMG 21406	GCA_023283605.1	190308	190308	type	True	77.4391	128	1400	95	below_threshold
Shewanella morhuae	strain=ATCC BAA-1205	GCA_900156405.1	365591	365591	type	True	77.4213	168	1400	95	below_threshold
Shewanella algicola	strain=JCM 31091	GCA_014648035.1	640633	640633	type	True	77.3206	143	1400	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:37:35,346] [INFO] DFAST Taxonomy check result was written to GCF_017354945.1_ASM1735494v1_genomic.fna/tc_result.tsv
[2024-01-25 19:37:35,347] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:37:35,347] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:37:35,347] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7d593f8-d68c-4731-837b-6138551dacd6/dqc_reference/checkm_data
[2024-01-25 19:37:35,348] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:37:35,390] [INFO] Task started: CheckM
[2024-01-25 19:37:35,390] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017354945.1_ASM1735494v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017354945.1_ASM1735494v1_genomic.fna/checkm_input GCF_017354945.1_ASM1735494v1_genomic.fna/checkm_result
[2024-01-25 19:38:08,436] [INFO] Task succeeded: CheckM
[2024-01-25 19:38:08,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:38:08,458] [INFO] ===== Completeness check finished =====
[2024-01-25 19:38:08,459] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:38:08,460] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017354945.1_ASM1735494v1_genomic.fna/markers.fasta)
[2024-01-25 19:38:08,460] [INFO] Task started: Blastn
[2024-01-25 19:38:08,460] [INFO] Running command: blastn -query GCF_017354945.1_ASM1735494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7d593f8-d68c-4731-837b-6138551dacd6/dqc_reference/reference_markers_gtdb.fasta -out GCF_017354945.1_ASM1735494v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:09,632] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:09,635] [INFO] Selected 19 target genomes.
[2024-01-25 19:38:09,635] [INFO] Target genome list was writen to GCF_017354945.1_ASM1735494v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:38:09,653] [INFO] Task started: fastANI
[2024-01-25 19:38:09,653] [INFO] Running command: fastANI --query /var/lib/cwl/stg410bd4a2-70b7-448d-bed6-6092557c6e4a/GCF_017354945.1_ASM1735494v1_genomic.fna.gz --refList GCF_017354945.1_ASM1735494v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017354945.1_ASM1735494v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:38:25,354] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:25,366] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:38:25,366] [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_017354945.1	s__Shewanella sp017354945	100.0	1396	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000753795.1	s__Shewanella mangrovi	82.5585	907	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016834455.1	s__Shewanella litorisediminis	79.1451	168	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009183365.2	s__Shewanella algae	79.0487	228	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.21	97.66	0.95	0.92	87	-
GCF_018223345.1	s__Shewanella sp018223345	79.0303	298	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900456975.1	s__Shewanella baltica	78.9946	211	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.88	96.32	0.89	0.85	16	-
GCF_011765625.1	s__Shewanella aestuarii_A	78.9372	141	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013765.1	s__Shewanella denitrificans	78.8623	125	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203935.1	s__Shewanella sp000203935	78.8171	241	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.76	95.76	0.86	0.86	2	-
GCF_002216875.1	s__Shewanella bicestrii	78.7997	233	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.51	96.32	0.89	0.87	4	-
GCF_000018285.1	s__Shewanella pealeana	78.7876	149	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018394335.1	s__Shewanella dokdonensis	78.6125	308	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836975.1	s__Shewanella indica	78.2484	224	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	98.42	98.01	0.95	0.93	6	-
GCF_002836945.1	s__Shewanella chilikensis	78.2392	205	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	99.40	98.79	0.97	0.93	5	-
GCF_000485795.1	s__Shewanella decolorationis	78.1045	223	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.60	97.51	0.93	0.92	3	-
GCF_014163735.1	s__Shewanella sp014163735	77.8693	127	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518705.1	s__Shewanella colwelliana	77.6324	141	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.91	98.91	0.92	0.92	2	-
GCF_900156405.1	s__Shewanella morhuae	77.4022	171	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.45	98.44	0.93	0.93	3	-
GCF_014648035.1	s__Shewanella algicola	77.3007	144	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:38:25,368] [INFO] GTDB search result was written to GCF_017354945.1_ASM1735494v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:38:25,368] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:38:25,372] [INFO] DFAST_QC result json was written to GCF_017354945.1_ASM1735494v1_genomic.fna/dqc_result.json
[2024-01-25 19:38:25,372] [INFO] DFAST_QC completed!
[2024-01-25 19:38:25,372] [INFO] Total running time: 0h1m20s