[2024-01-24 13:52:12,797] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:52:12,799] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:52:12,799] [INFO] DQC Reference Directory: /var/lib/cwl/stg04492f6c-360d-4ac5-8892-b030c7382171/dqc_reference
[2024-01-24 13:52:14,026] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:52:14,026] [INFO] Task started: Prodigal
[2024-01-24 13:52:14,027] [INFO] Running command: gunzip -c /var/lib/cwl/stg03413938-aa23-4103-9eb9-c69175c131de/GCF_004768465.1_ASM476846v1_genomic.fna.gz | prodigal -d GCF_004768465.1_ASM476846v1_genomic.fna/cds.fna -a GCF_004768465.1_ASM476846v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:52:27,368] [INFO] Task succeeded: Prodigal
[2024-01-24 13:52:27,369] [INFO] Task started: HMMsearch
[2024-01-24 13:52:27,369] [INFO] Running command: hmmsearch --tblout GCF_004768465.1_ASM476846v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04492f6c-360d-4ac5-8892-b030c7382171/dqc_reference/reference_markers.hmm GCF_004768465.1_ASM476846v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:52:27,638] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:52:27,639] [INFO] Found 6/6 markers.
[2024-01-24 13:52:27,678] [INFO] Query marker FASTA was written to GCF_004768465.1_ASM476846v1_genomic.fna/markers.fasta
[2024-01-24 13:52:27,679] [INFO] Task started: Blastn
[2024-01-24 13:52:27,679] [INFO] Running command: blastn -query GCF_004768465.1_ASM476846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04492f6c-360d-4ac5-8892-b030c7382171/dqc_reference/reference_markers.fasta -out GCF_004768465.1_ASM476846v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:28,516] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:28,519] [INFO] Selected 28 target genomes.
[2024-01-24 13:52:28,519] [INFO] Target genome list was writen to GCF_004768465.1_ASM476846v1_genomic.fna/target_genomes.txt
[2024-01-24 13:52:28,536] [INFO] Task started: fastANI
[2024-01-24 13:52:28,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg03413938-aa23-4103-9eb9-c69175c131de/GCF_004768465.1_ASM476846v1_genomic.fna.gz --refList GCF_004768465.1_ASM476846v1_genomic.fna/target_genomes.txt --output GCF_004768465.1_ASM476846v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:52:46,312] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:46,313] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04492f6c-360d-4ac5-8892-b030c7382171/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:52:46,313] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04492f6c-360d-4ac5-8892-b030c7382171/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:52:46,333] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:52:46,334] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:52:46,334] [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
Natronospirillum operosum	strain=G-116	GCA_004768465.1	2759953	2759953	type	True	100.0	1429	1429	95	conclusive
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	76.739	153	1429	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	76.6629	159	1429	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	76.6086	158	1429	95	below_threshold
Halomonas caseinilytica	strain=JCM 14802	GCA_001662305.1	438744	438744	type	True	76.6086	121	1429	95	below_threshold
Halomonas caseinilytica	strain=CGMCC 1.6773	GCA_900109905.1	438744	438744	type	True	76.5827	123	1429	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	76.5229	166	1429	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	76.5027	100	1429	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	76.4995	144	1429	95	below_threshold
Marinobacter persicus	strain=KCTC 23561	GCA_014652295.1	930118	930118	type	True	76.4554	107	1429	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.4315	175	1429	95	below_threshold
Salinicola endophyticus	strain=CPA92	GCA_003206575.1	1949083	1949083	type	True	76.4035	126	1429	95	below_threshold
Halomonas alimentaria	strain=DSM 15356	GCA_009902005.1	147248	147248	type	True	76.3516	125	1429	95	below_threshold
Halomonas ilicicola	strain=DSM 19980	GCA_900128925.1	480814	480814	type	True	76.3498	122	1429	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	76.342	113	1429	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	76.3418	161	1429	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	76.3113	107	1429	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	76.2143	79	1429	95	below_threshold
Pseudomonas nitroreducens	strain=DSM 14399	GCA_012986245.1	46680	46680	suspected-type	True	76.1632	158	1429	95	below_threshold
Pseudomonas nitroreducens	strain=NBRC 12694	GCA_002091755.1	46680	46680	suspected-type	True	76.0934	153	1429	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	76.0617	114	1429	95	below_threshold
Pseudomonas flavescens	strain=NBRC 103044	GCA_002091575.1	29435	29435	type	True	76.0104	127	1429	95	below_threshold
Xanthomonas cassavae	strain=NCPPB 101	GCA_020783895.1	56450	56450	type	True	75.9966	60	1429	95	below_threshold
Xanthomonas cassavae	strain=CFBP 4642	GCA_000454545.1	56450	56450	type	True	75.9557	62	1429	95	below_threshold
Pseudomonas flavescens	strain=LMG 18387	GCA_900100535.1	29435	29435	type	True	75.9371	125	1429	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	75.8932	74	1429	95	below_threshold
Leeia aquatica	strain=IMCC25680	GCA_012641365.1	2725557	2725557	type	True	75.8829	56	1429	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	75.8366	129	1429	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:52:46,336] [INFO] DFAST Taxonomy check result was written to GCF_004768465.1_ASM476846v1_genomic.fna/tc_result.tsv
[2024-01-24 13:52:46,337] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:52:46,337] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:52:46,337] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04492f6c-360d-4ac5-8892-b030c7382171/dqc_reference/checkm_data
[2024-01-24 13:52:46,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:52:46,379] [INFO] Task started: CheckM
[2024-01-24 13:52:46,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004768465.1_ASM476846v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004768465.1_ASM476846v1_genomic.fna/checkm_input GCF_004768465.1_ASM476846v1_genomic.fna/checkm_result
[2024-01-24 13:53:28,938] [INFO] Task succeeded: CheckM
[2024-01-24 13:53:28,940] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:53:28,972] [INFO] ===== Completeness check finished =====
[2024-01-24 13:53:28,973] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:53:28,973] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004768465.1_ASM476846v1_genomic.fna/markers.fasta)
[2024-01-24 13:53:28,974] [INFO] Task started: Blastn
[2024-01-24 13:53:28,974] [INFO] Running command: blastn -query GCF_004768465.1_ASM476846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04492f6c-360d-4ac5-8892-b030c7382171/dqc_reference/reference_markers_gtdb.fasta -out GCF_004768465.1_ASM476846v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:53:30,357] [INFO] Task succeeded: Blastn
[2024-01-24 13:53:30,362] [INFO] Selected 29 target genomes.
[2024-01-24 13:53:30,362] [INFO] Target genome list was writen to GCF_004768465.1_ASM476846v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:53:30,411] [INFO] Task started: fastANI
[2024-01-24 13:53:30,411] [INFO] Running command: fastANI --query /var/lib/cwl/stg03413938-aa23-4103-9eb9-c69175c131de/GCF_004768465.1_ASM476846v1_genomic.fna.gz --refList GCF_004768465.1_ASM476846v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004768465.1_ASM476846v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:53:50,231] [INFO] Task succeeded: fastANI
[2024-01-24 13:53:50,260] [INFO] Found 29 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:53:50,260] [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_004768465.1	s__Natronospirillum operosum	100.0	1429	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Natronospirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001545155.1	s__Halomonas chromatireducens	76.8569	131	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265245.1	s__Halomonas smyrnensis	76.7386	153	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_003205495.1	s__Pseudomonas_E alcaligenes_B	76.632	149	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401555.1	s__Halomonas sp018401555	76.5959	127	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016565.1	s__Pseudomonas_E mendocina_A	76.5328	169	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	97.37	0.90	0.88	7	-
GCF_900104135.1	s__Halomonas shengliensis	76.4723	146	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCF_004327355.1	s__Pseudomonas_E dryadis	76.4076	149	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.58	99.16	0.96	0.92	3	-
GCF_003206575.1	s__Salinicola endophyticus	76.4035	126	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.06	99.06	0.96	0.96	2	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	76.3943	143	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCF_015645095.1	s__Halomonas_F sp015645095	76.3876	167	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109175.1	s__Pseudomonas_K linyingensis	76.3831	158	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943415.1	s__Perlucidibaca sp002943415	76.3807	73	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Perlucidibaca	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128925.1	s__Halomonas_C ilicicola	76.3498	122	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009902005.1	s__Halomonas alimentaria	76.336	126	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934325.1	s__Marinobacter persicus_A	76.3003	101	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	0.99	0.99	3	-
GCA_002796985.1	s__Pseudomonas sp002796985	76.2979	140	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019061305.1	s__Marinobacterium sp019061305	76.2821	101	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000689415.1	s__Pseudomonas knackmussii	76.2229	149	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	98.27	98.27	0.91	0.91	2	-
GCF_000349845.1	s__Pseudomonas sp000349845	76.16	154	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204515.1	s__Pseudomonas nitritireducens_A	76.1212	165	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017589465.1	s__Pseudomonas sp017589465	76.0218	158	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013523165.1	s__Pseudomonas_E entomophila_A	76.003	114	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000454545.1	s__Xanthomonas cassavae	75.9557	62	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100535.1	s__Pseudomonas_E flavescens	75.9256	126	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006265115.1	s__Arenimonas terrae	75.9135	73	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641365.1	s__Leeia aquatica	75.9097	55	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Leeiaceae;g__Leeia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016658545.1	s__Pseudomonas_E sp016658545	75.8429	113	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004025535.1	s__Pseudomonas_E alkylphenolica_A	75.5732	103	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:53:50,263] [INFO] GTDB search result was written to GCF_004768465.1_ASM476846v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:53:50,264] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:53:50,269] [INFO] DFAST_QC result json was written to GCF_004768465.1_ASM476846v1_genomic.fna/dqc_result.json
[2024-01-24 13:53:50,269] [INFO] DFAST_QC completed!
[2024-01-24 13:53:50,269] [INFO] Total running time: 0h1m37s