[2024-01-24 14:06:45,007] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:45,009] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:45,009] [INFO] DQC Reference Directory: /var/lib/cwl/stg171c5096-63ec-4b69-a42f-fd0bb833572d/dqc_reference
[2024-01-24 14:06:46,429] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:46,430] [INFO] Task started: Prodigal
[2024-01-24 14:06:46,430] [INFO] Running command: gunzip -c /var/lib/cwl/stgecd35bb0-5e54-42f2-800b-910be99ee6bd/GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna.gz | prodigal -d GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna/cds.fna -a GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:02,004] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:02,004] [INFO] Task started: HMMsearch
[2024-01-24 14:07:02,004] [INFO] Running command: hmmsearch --tblout GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg171c5096-63ec-4b69-a42f-fd0bb833572d/dqc_reference/reference_markers.hmm GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:02,297] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:02,298] [INFO] Found 6/6 markers.
[2024-01-24 14:07:02,346] [INFO] Query marker FASTA was written to GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna/markers.fasta
[2024-01-24 14:07:02,347] [INFO] Task started: Blastn
[2024-01-24 14:07:02,347] [INFO] Running command: blastn -query GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna/markers.fasta -db /var/lib/cwl/stg171c5096-63ec-4b69-a42f-fd0bb833572d/dqc_reference/reference_markers.fasta -out GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:03,190] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:03,194] [INFO] Selected 19 target genomes.
[2024-01-24 14:07:03,195] [INFO] Target genome list was writen to GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna/target_genomes.txt
[2024-01-24 14:07:03,204] [INFO] Task started: fastANI
[2024-01-24 14:07:03,204] [INFO] Running command: fastANI --query /var/lib/cwl/stgecd35bb0-5e54-42f2-800b-910be99ee6bd/GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna.gz --refList GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna/target_genomes.txt --output GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:19,882] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:19,883] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg171c5096-63ec-4b69-a42f-fd0bb833572d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:19,883] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg171c5096-63ec-4b69-a42f-fd0bb833572d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:19,897] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:07:19,897] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:19,897] [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 huangheensis	strain=BJGMM-B45	GCA_000470745.1	1178482	1178482	type	True	100.0	1560	1562	95	conclusive
Halomonas huangheensis	strain=BJGMM-B45	GCA_001431725.1	1178482	1178482	type	True	99.9944	1559	1562	95	conclusive
Halomonas cupida	strain=NBRC 102219	GCA_007991155.1	44933	44933	type	True	82.055	1021	1562	95	below_threshold
Halomonas cupida	strain=DSM 4740	GCA_900142755.1	44933	44933	type	True	82.0107	1091	1562	95	below_threshold
Halomonas litopenaei	strain=SYSU ZJ2214	GCA_003045775.1	2109328	2109328	type	True	79.3263	648	1562	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	78.8202	527	1562	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.7316	415	1562	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	78.6015	406	1562	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	78.5972	398	1562	95	below_threshold
Halomonas antri	strain=Y3S6	GCA_019430905.1	2846777	2846777	type	True	78.494	394	1562	95	below_threshold
Halomonas urumqiensis	strain=BZ-SZ-XJ27	GCA_002879635.1	1684789	1684789	type	True	78.4805	395	1562	95	below_threshold
Halomonas niordiana	strain=ATF 5.4	GCA_004798965.1	2508711	2508711	type	True	78.4209	324	1562	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	78.3757	424	1562	95	below_threshold
Halomonas bachuensis	strain=DX6	GCA_011742165.1	2717286	2717286	type	True	78.3634	409	1562	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	75.6332	50	1562	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:19,899] [INFO] DFAST Taxonomy check result was written to GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna/tc_result.tsv
[2024-01-24 14:07:19,900] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:19,900] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:19,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg171c5096-63ec-4b69-a42f-fd0bb833572d/dqc_reference/checkm_data
[2024-01-24 14:07:19,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:19,951] [INFO] Task started: CheckM
[2024-01-24 14:07:19,952] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna/checkm_input GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna/checkm_result
[2024-01-24 14:08:07,892] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:07,894] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:07,917] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:07,918] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:07,918] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna/markers.fasta)
[2024-01-24 14:08:07,919] [INFO] Task started: Blastn
[2024-01-24 14:08:07,919] [INFO] Running command: blastn -query GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna/markers.fasta -db /var/lib/cwl/stg171c5096-63ec-4b69-a42f-fd0bb833572d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:09,285] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:09,290] [INFO] Selected 21 target genomes.
[2024-01-24 14:08:09,290] [INFO] Target genome list was writen to GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:09,306] [INFO] Task started: fastANI
[2024-01-24 14:08:09,306] [INFO] Running command: fastANI --query /var/lib/cwl/stgecd35bb0-5e54-42f2-800b-910be99ee6bd/GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna.gz --refList GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna/target_genomes_gtdb.txt --output GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:26,591] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:26,608] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:26,608] [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_001431725.1	s__Halomonas huangheensis	99.9944	1559	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_900142755.1	s__Halomonas cupida	82.0044	1090	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003045775.1	s__Halomonas litopenaei	79.3116	650	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.31	97.80	0.93	0.89	11	-
GCF_008329985.2	s__Halomonas sp008329985	79.1341	570	1562	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	78.9579	542	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056305.1	s__Halomonas denitrificans	78.8769	439	1562	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	78.812	528	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971685.1	s__Halomonas_B sp001971685	78.7901	387	1562	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_014840935.1	s__Halomonas_E sp014840935	78.7542	375	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002879645.1	s__Halomonas heilongjiangensis	78.5383	439	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	-
GCF_013349955.1	s__Halomonas_E taeanensis_B	78.5284	337	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193375.1	s__Halomonas campaniensis	78.5103	398	1562	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	78.4718	328	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Chromohalobacter	95.0	98.07	97.76	0.86	0.85	6	-
GCF_003028575.1	s__Halomonas urumqiensis	78.4241	399	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.97	1.00	0.99	3	-
GCF_004798965.1	s__Halomonas_E niordiana	78.4216	324	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011742165.1	s__Halomonas bachuensis	78.3775	406	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102875.1	s__Halomonas_B pantelleriensis	78.2203	381	1562	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_013009075.1	s__Halomonas_B sp013009075	78.0651	318	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	99.96	99.96	1.00	0.99	3	-
GCF_000409775.1	s__Halomonas_A anticariensis	77.9277	327	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_A	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:26,610] [INFO] GTDB search result was written to GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:26,611] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:26,616] [INFO] DFAST_QC result json was written to GCF_000470745.1_version_1_of_the_Halomonas_huanghegensis_genomic.fna/dqc_result.json
[2024-01-24 14:08:26,616] [INFO] DFAST_QC completed!
[2024-01-24 14:08:26,616] [INFO] Total running time: 0h1m42s