[2024-01-24 12:31:33,147] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:33,148] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:33,148] [INFO] DQC Reference Directory: /var/lib/cwl/stg4cce2eae-47e6-4d87-983c-fee9b0c2350b/dqc_reference
[2024-01-24 12:31:34,401] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:34,402] [INFO] Task started: Prodigal
[2024-01-24 12:31:34,402] [INFO] Running command: gunzip -c /var/lib/cwl/stg12917cc4-2b6d-43c0-9eb2-ff72996d169e/GCF_003336665.1_ASM333666v1_genomic.fna.gz | prodigal -d GCF_003336665.1_ASM333666v1_genomic.fna/cds.fna -a GCF_003336665.1_ASM333666v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:46,136] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:46,136] [INFO] Task started: HMMsearch
[2024-01-24 12:31:46,136] [INFO] Running command: hmmsearch --tblout GCF_003336665.1_ASM333666v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4cce2eae-47e6-4d87-983c-fee9b0c2350b/dqc_reference/reference_markers.hmm GCF_003336665.1_ASM333666v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:46,372] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:46,373] [INFO] Found 6/6 markers.
[2024-01-24 12:31:46,411] [INFO] Query marker FASTA was written to GCF_003336665.1_ASM333666v1_genomic.fna/markers.fasta
[2024-01-24 12:31:46,412] [INFO] Task started: Blastn
[2024-01-24 12:31:46,412] [INFO] Running command: blastn -query GCF_003336665.1_ASM333666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4cce2eae-47e6-4d87-983c-fee9b0c2350b/dqc_reference/reference_markers.fasta -out GCF_003336665.1_ASM333666v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:47,095] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:47,098] [INFO] Selected 22 target genomes.
[2024-01-24 12:31:47,098] [INFO] Target genome list was writen to GCF_003336665.1_ASM333666v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:47,102] [INFO] Task started: fastANI
[2024-01-24 12:31:47,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg12917cc4-2b6d-43c0-9eb2-ff72996d169e/GCF_003336665.1_ASM333666v1_genomic.fna.gz --refList GCF_003336665.1_ASM333666v1_genomic.fna/target_genomes.txt --output GCF_003336665.1_ASM333666v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:03,711] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:03,712] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4cce2eae-47e6-4d87-983c-fee9b0c2350b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:03,712] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4cce2eae-47e6-4d87-983c-fee9b0c2350b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:03,725] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:03,725] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:03,725] [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 rituensis	strain=TQ8S	GCA_003336665.1	2282306	2282306	type	True	100.0	1403	1409	95	conclusive
Halomonas zhuhanensis	strain=ZH2S	GCA_009793355.1	2684210	2684210	type	True	92.2718	889	1409	95	below_threshold
Halomonas massiliensis	strain=Marseille-P2426	GCA_900155385.1	1816686	1816686	type	True	78.9016	329	1409	95	below_threshold
Halomonas hamiltonii	strain=KCTC 22154	GCA_014651775.1	502829	502829	type	True	78.8314	367	1409	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	78.8091	383	1409	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	78.809	364	1409	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	78.785	359	1409	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	78.7486	368	1409	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	78.744	343	1409	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	78.7313	405	1409	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	78.7257	360	1409	95	below_threshold
Halomonas fontilapidosi	strain=CECT 7341	GCA_014192285.1	616675	616675	type	True	78.6917	358	1409	95	below_threshold
Halomonas johnsoniae	strain=KCTC 22157	GCA_014651795.1	502832	502832	type	True	78.6888	373	1409	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.6727	348	1409	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	78.6394	255	1409	95	below_threshold
Halomonas stevensii	strain=S18214	GCA_000275725.1	502821	502821	type	True	78.5886	383	1409	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	78.4855	350	1409	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	78.4819	350	1409	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	78.3117	369	1409	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	78.2341	337	1409	95	below_threshold
Halomonas taeanensis	strain=BH539	GCA_900100755.1	284577	284577	type	True	78.0561	290	1409	95	below_threshold
Halomonas xinjiangensis	strain=TRM 0175	GCA_000759345.1	1166948	1166948	type	True	77.9402	256	1409	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:03,726] [INFO] DFAST Taxonomy check result was written to GCF_003336665.1_ASM333666v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:03,727] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:03,727] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:03,727] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4cce2eae-47e6-4d87-983c-fee9b0c2350b/dqc_reference/checkm_data
[2024-01-24 12:32:03,728] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:03,768] [INFO] Task started: CheckM
[2024-01-24 12:32:03,768] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003336665.1_ASM333666v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003336665.1_ASM333666v1_genomic.fna/checkm_input GCF_003336665.1_ASM333666v1_genomic.fna/checkm_result
[2024-01-24 12:32:39,445] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:39,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:39,465] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:39,465] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:39,465] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003336665.1_ASM333666v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:39,466] [INFO] Task started: Blastn
[2024-01-24 12:32:39,466] [INFO] Running command: blastn -query GCF_003336665.1_ASM333666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4cce2eae-47e6-4d87-983c-fee9b0c2350b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003336665.1_ASM333666v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:40,504] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:40,506] [INFO] Selected 21 target genomes.
[2024-01-24 12:32:40,506] [INFO] Target genome list was writen to GCF_003336665.1_ASM333666v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:40,534] [INFO] Task started: fastANI
[2024-01-24 12:32:40,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg12917cc4-2b6d-43c0-9eb2-ff72996d169e/GCF_003336665.1_ASM333666v1_genomic.fna.gz --refList GCF_003336665.1_ASM333666v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003336665.1_ASM333666v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:55,933] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:55,945] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:55,946] [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_003336665.1	s__Halomonas sp003336665	100.0	1403	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009793355.1	s__Halomonas sp009793355	92.2718	889	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155385.1	s__Halomonas massiliensis	78.862	332	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.38	98.38	0.88	0.88	2	-
GCF_014651775.1	s__Halomonas hamiltonii	78.8314	367	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	98.09	97.51	0.90	0.88	5	-
GCF_902500215.1	s__Halomonas sp902500215	78.7602	367	1409	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	78.7141	361	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002925.1	s__Halomonas songnenensis	78.7107	355	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192285.1	s__Halomonas fontilapidosi	78.6803	359	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.17	98.17	0.94	0.94	2	-
GCF_000246875.1	s__Halomonas sp000246875	78.6258	341	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000275725.1	s__Halomonas stevensii	78.6257	379	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	97.33	97.21	0.85	0.83	5	-
GCF_001971685.1	s__Halomonas_B sp001971685	78.6142	370	1409	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_015992245.1	s__Halomonas sp015992245	78.6136	351	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	99.35	0.94	0.94	2	-
GCF_900116405.1	s__Halomonas saccharevitans	78.5052	348	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007989625.1	s__Halomonas_F pacifica	78.5048	326	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_F	95.0	98.81	98.81	0.96	0.96	2	-
GCF_003339685.1	s__Halomonas sp003339685	78.4934	301	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834345.1	s__Halomonas sp009834345	78.4855	350	1409	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	78.311	369	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCF_014192055.1	s__Halomonas organivorans	78.2521	336	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003552795.1	s__Halomonas sp003552795	78.223	287	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100755.1	s__Halomonas_E taeanensis	78.0561	290	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	98.15	98.15	0.92	0.92	2	-
GCF_000759345.1	s__Halomonas_A xinjiangensis	77.9359	257	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:55,950] [INFO] GTDB search result was written to GCF_003336665.1_ASM333666v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:55,951] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:55,954] [INFO] DFAST_QC result json was written to GCF_003336665.1_ASM333666v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:55,954] [INFO] DFAST_QC completed!
[2024-01-24 12:32:55,954] [INFO] Total running time: 0h1m23s