[2024-01-24 13:25:58,048] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:58,051] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:58,051] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbf169f8-3fdc-4af1-a457-6e44fbc2524b/dqc_reference
[2024-01-24 13:26:00,375] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:00,376] [INFO] Task started: Prodigal
[2024-01-24 13:26:00,377] [INFO] Running command: gunzip -c /var/lib/cwl/stg2fb6d425-a142-4c1e-bb2d-61458d4fc237/GCF_007991155.1_ASM799115v1_genomic.fna.gz | prodigal -d GCF_007991155.1_ASM799115v1_genomic.fna/cds.fna -a GCF_007991155.1_ASM799115v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:15,458] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:15,458] [INFO] Task started: HMMsearch
[2024-01-24 13:26:15,459] [INFO] Running command: hmmsearch --tblout GCF_007991155.1_ASM799115v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbf169f8-3fdc-4af1-a457-6e44fbc2524b/dqc_reference/reference_markers.hmm GCF_007991155.1_ASM799115v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:15,842] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:15,844] [INFO] Found 6/6 markers.
[2024-01-24 13:26:15,897] [INFO] Query marker FASTA was written to GCF_007991155.1_ASM799115v1_genomic.fna/markers.fasta
[2024-01-24 13:26:15,898] [INFO] Task started: Blastn
[2024-01-24 13:26:15,898] [INFO] Running command: blastn -query GCF_007991155.1_ASM799115v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbf169f8-3fdc-4af1-a457-6e44fbc2524b/dqc_reference/reference_markers.fasta -out GCF_007991155.1_ASM799115v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:16,825] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:16,831] [INFO] Selected 17 target genomes.
[2024-01-24 13:26:16,832] [INFO] Target genome list was writen to GCF_007991155.1_ASM799115v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:16,849] [INFO] Task started: fastANI
[2024-01-24 13:26:16,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fb6d425-a142-4c1e-bb2d-61458d4fc237/GCF_007991155.1_ASM799115v1_genomic.fna.gz --refList GCF_007991155.1_ASM799115v1_genomic.fna/target_genomes.txt --output GCF_007991155.1_ASM799115v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:33,383] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:33,383] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbf169f8-3fdc-4af1-a457-6e44fbc2524b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:33,383] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbf169f8-3fdc-4af1-a457-6e44fbc2524b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:33,395] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:26:33,396] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:33,396] [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 cupida	strain=NBRC 102219	GCA_007991155.1	44933	44933	type	True	100.0	1526	1534	95	conclusive
Halomonas cupida	strain=DSM 4740	GCA_900142755.1	44933	44933	type	True	99.9777	1527	1534	95	conclusive
Halomonas huangheensis	strain=BJGMM-B45	GCA_000470745.1	1178482	1178482	type	True	81.976	1030	1534	95	below_threshold
Halomonas huangheensis	strain=BJGMM-B45	GCA_001431725.1	1178482	1178482	type	True	81.9271	1036	1534	95	below_threshold
Halomonas litopenaei	strain=SYSU ZJ2214	GCA_003045775.1	2109328	2109328	type	True	79.8292	685	1534	95	below_threshold
Halomonas borealis	strain=ATF 5.2	GCA_004798905.1	2508710	2508710	type	True	79.3961	446	1534	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.8511	464	1534	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	78.7949	453	1534	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	78.7364	423	1534	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	78.7298	442	1534	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	78.7071	452	1534	95	below_threshold
Halomonas saliphila	strain=LCB169	GCA_002930105.1	1848458	1848458	type	True	78.5389	424	1534	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	75.5104	56	1534	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	75.5073	57	1534	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:33,397] [INFO] DFAST Taxonomy check result was written to GCF_007991155.1_ASM799115v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:33,398] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:33,398] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:33,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbf169f8-3fdc-4af1-a457-6e44fbc2524b/dqc_reference/checkm_data
[2024-01-24 13:26:33,400] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:33,450] [INFO] Task started: CheckM
[2024-01-24 13:26:33,452] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007991155.1_ASM799115v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007991155.1_ASM799115v1_genomic.fna/checkm_input GCF_007991155.1_ASM799115v1_genomic.fna/checkm_result
[2024-01-24 13:27:20,694] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:20,697] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:20,727] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:20,727] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:20,728] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007991155.1_ASM799115v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:20,729] [INFO] Task started: Blastn
[2024-01-24 13:27:20,729] [INFO] Running command: blastn -query GCF_007991155.1_ASM799115v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbf169f8-3fdc-4af1-a457-6e44fbc2524b/dqc_reference/reference_markers_gtdb.fasta -out GCF_007991155.1_ASM799115v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:22,081] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:22,087] [INFO] Selected 17 target genomes.
[2024-01-24 13:27:22,088] [INFO] Target genome list was writen to GCF_007991155.1_ASM799115v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:22,111] [INFO] Task started: fastANI
[2024-01-24 13:27:22,111] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fb6d425-a142-4c1e-bb2d-61458d4fc237/GCF_007991155.1_ASM799115v1_genomic.fna.gz --refList GCF_007991155.1_ASM799115v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007991155.1_ASM799115v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:36,301] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:36,316] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:36,317] [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_900142755.1	s__Halomonas cupida	99.9777	1527	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_001431725.1	s__Halomonas huangheensis	81.9357	1035	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_008329985.2	s__Halomonas sp008329985	79.8436	622	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003045775.1	s__Halomonas litopenaei	79.8216	686	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.31	97.80	0.93	0.89	11	-
GCF_004798905.1	s__Halomonas borealis	79.3791	447	1534	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	79.2611	558	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017303055.1	s__Halomonas litopenaei_A	79.1359	572	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104135.1	s__Halomonas shengliensis	79.0395	439	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCF_001971685.1	s__Halomonas_B sp001971685	78.9757	436	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010994375.1	s__Halomonas sp010994375	78.9024	423	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254665.1	s__Halomonas lactosivorans	78.8406	480	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000246875.1	s__Halomonas sp000246875	78.7763	439	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013697085.1	s__Halomonas kenyensis	78.7624	387	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000761475.1	s__Chromohalobacter israelensis	78.6887	343	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Chromohalobacter	95.0	98.07	97.76	0.86	0.85	6	-
GCF_002930105.1	s__Halomonas saliphila	78.5204	426	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991175.1	s__Halomonas variabilis	77.358	158	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:36,318] [INFO] GTDB search result was written to GCF_007991155.1_ASM799115v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:36,319] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:36,323] [INFO] DFAST_QC result json was written to GCF_007991155.1_ASM799115v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:36,323] [INFO] DFAST_QC completed!
[2024-01-24 13:27:36,323] [INFO] Total running time: 0h1m38s