[2024-01-24 10:47:23,659] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:23,661] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:23,662] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3fca68e-3a05-4553-bb2b-acca9765a1aa/dqc_reference
[2024-01-24 10:47:26,177] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,183] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,184] [INFO] Running command: gunzip -c /var/lib/cwl/stg86f4cbd3-c773-4df6-8270-d67c2f7fc17e/GCF_030409235.1_ASM3040923v1_genomic.fna.gz | prodigal -d GCF_030409235.1_ASM3040923v1_genomic.fna/cds.fna -a GCF_030409235.1_ASM3040923v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:34,835] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:34,836] [INFO] Task started: HMMsearch
[2024-01-24 10:47:34,836] [INFO] Running command: hmmsearch --tblout GCF_030409235.1_ASM3040923v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3fca68e-3a05-4553-bb2b-acca9765a1aa/dqc_reference/reference_markers.hmm GCF_030409235.1_ASM3040923v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:35,088] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:35,090] [INFO] Found 6/6 markers.
[2024-01-24 10:47:35,126] [INFO] Query marker FASTA was written to GCF_030409235.1_ASM3040923v1_genomic.fna/markers.fasta
[2024-01-24 10:47:35,127] [INFO] Task started: Blastn
[2024-01-24 10:47:35,127] [INFO] Running command: blastn -query GCF_030409235.1_ASM3040923v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3fca68e-3a05-4553-bb2b-acca9765a1aa/dqc_reference/reference_markers.fasta -out GCF_030409235.1_ASM3040923v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:36,077] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:36,083] [INFO] Selected 18 target genomes.
[2024-01-24 10:47:36,083] [INFO] Target genome list was writen to GCF_030409235.1_ASM3040923v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:36,090] [INFO] Task started: fastANI
[2024-01-24 10:47:36,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg86f4cbd3-c773-4df6-8270-d67c2f7fc17e/GCF_030409235.1_ASM3040923v1_genomic.fna.gz --refList GCF_030409235.1_ASM3040923v1_genomic.fna/target_genomes.txt --output GCF_030409235.1_ASM3040923v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:50,016] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:50,016] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3fca68e-3a05-4553-bb2b-acca9765a1aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:50,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3fca68e-3a05-4553-bb2b-acca9765a1aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:50,030] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:47:50,030] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:47:50,031] [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
Halomonas halmophila	strain=NBRC 15537	GCA_006540005.1	252	252	type	True	88.7168	761	927	95	below_threshold
Halomonas elongata	strain=type strain: DSM 2581	GCA_000196875.2	2746	2746	type	True	82.2747	664	927	95	below_threshold
Halomonas caseinilytica	strain=JCM 14802	GCA_001662305.1	438744	438744	type	True	81.8689	659	927	95	below_threshold
Halomonas caseinilytica	strain=CGMCC 1.6773	GCA_900109905.1	438744	438744	type	True	81.838	649	927	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	81.2338	606	927	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	81.2334	600	927	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	81.2024	640	927	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	81.1999	618	927	95	below_threshold
Halomonas borealis	strain=ATF 5.2	GCA_004798905.1	2508710	2508710	type	True	80.9015	559	927	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	80.6605	579	927	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	80.3644	527	927	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	80.2147	551	927	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	80.1376	548	927	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	80.0351	509	927	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	80.0005	532	927	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	79.8405	505	927	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	79.6435	450	927	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	79.3393	456	927	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:50,032] [INFO] DFAST Taxonomy check result was written to GCF_030409235.1_ASM3040923v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:50,032] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:50,033] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:50,033] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3fca68e-3a05-4553-bb2b-acca9765a1aa/dqc_reference/checkm_data
[2024-01-24 10:47:50,034] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:50,061] [INFO] Task started: CheckM
[2024-01-24 10:47:50,062] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409235.1_ASM3040923v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409235.1_ASM3040923v1_genomic.fna/checkm_input GCF_030409235.1_ASM3040923v1_genomic.fna/checkm_result
[2024-01-24 10:48:20,025] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:20,027] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:20,045] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:20,045] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:20,046] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409235.1_ASM3040923v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:20,046] [INFO] Task started: Blastn
[2024-01-24 10:48:20,046] [INFO] Running command: blastn -query GCF_030409235.1_ASM3040923v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3fca68e-3a05-4553-bb2b-acca9765a1aa/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409235.1_ASM3040923v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:21,805] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:21,810] [INFO] Selected 14 target genomes.
[2024-01-24 10:48:21,810] [INFO] Target genome list was writen to GCF_030409235.1_ASM3040923v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:21,865] [INFO] Task started: fastANI
[2024-01-24 10:48:21,866] [INFO] Running command: fastANI --query /var/lib/cwl/stg86f4cbd3-c773-4df6-8270-d67c2f7fc17e/GCF_030409235.1_ASM3040923v1_genomic.fna.gz --refList GCF_030409235.1_ASM3040923v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409235.1_ASM3040923v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:33,150] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:33,176] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:48:33,176] [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_006540005.1	s__Halomonas halmophila	88.7101	762	927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196875.2	s__Halomonas elongata	82.2747	664	927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.75	98.56	0.95	0.92	4	-
GCF_001662305.1	s__Halomonas caseinilytica	81.881	658	927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.18	98.28	0.94	0.89	6	-
GCF_008274785.1	s__Halomonas eurihalina	81.8668	655	927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192275.1	s__Halomonas stenophila	81.2565	603	927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192055.1	s__Halomonas organivorans	81.2397	599	927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966155.1	s__Halomonas nitroreducens	81.2089	639	927	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	81.1966	618	927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_002549795.1	s__Halomonas beimenensis	81.138	620	927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363755.1	s__Halomonas sp009363755	80.88	567	927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004798905.1	s__Halomonas borealis	80.8698	564	927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363555.1	s__Halomonas ventosae	80.6615	578	927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.59	95.59	0.89	0.89	2	-
GCF_900104135.1	s__Halomonas shengliensis	80.3481	528	927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCF_002879645.1	s__Halomonas heilongjiangensis	80.1323	548	927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:33,178] [INFO] GTDB search result was written to GCF_030409235.1_ASM3040923v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:33,179] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:33,183] [INFO] DFAST_QC result json was written to GCF_030409235.1_ASM3040923v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:33,184] [INFO] DFAST_QC completed!
[2024-01-24 10:48:33,184] [INFO] Total running time: 0h1m10s