[2024-01-24 14:14:20,545] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:20,547] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:20,547] [INFO] DQC Reference Directory: /var/lib/cwl/stgde51a0ab-e32a-4fff-9771-4fb0170d7e1b/dqc_reference
[2024-01-24 14:14:21,808] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:21,809] [INFO] Task started: Prodigal
[2024-01-24 14:14:21,809] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4404ce1-56cf-4054-919d-201271a50526/GCF_014651875.1_ASM1465187v1_genomic.fna.gz | prodigal -d GCF_014651875.1_ASM1465187v1_genomic.fna/cds.fna -a GCF_014651875.1_ASM1465187v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:37,370] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:37,371] [INFO] Task started: HMMsearch
[2024-01-24 14:14:37,371] [INFO] Running command: hmmsearch --tblout GCF_014651875.1_ASM1465187v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde51a0ab-e32a-4fff-9771-4fb0170d7e1b/dqc_reference/reference_markers.hmm GCF_014651875.1_ASM1465187v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:37,647] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:37,649] [INFO] Found 6/6 markers.
[2024-01-24 14:14:37,689] [INFO] Query marker FASTA was written to GCF_014651875.1_ASM1465187v1_genomic.fna/markers.fasta
[2024-01-24 14:14:37,690] [INFO] Task started: Blastn
[2024-01-24 14:14:37,690] [INFO] Running command: blastn -query GCF_014651875.1_ASM1465187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde51a0ab-e32a-4fff-9771-4fb0170d7e1b/dqc_reference/reference_markers.fasta -out GCF_014651875.1_ASM1465187v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:38,690] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:38,694] [INFO] Selected 18 target genomes.
[2024-01-24 14:14:38,694] [INFO] Target genome list was writen to GCF_014651875.1_ASM1465187v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:38,708] [INFO] Task started: fastANI
[2024-01-24 14:14:38,709] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4404ce1-56cf-4054-919d-201271a50526/GCF_014651875.1_ASM1465187v1_genomic.fna.gz --refList GCF_014651875.1_ASM1465187v1_genomic.fna/target_genomes.txt --output GCF_014651875.1_ASM1465187v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:56,054] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:56,055] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde51a0ab-e32a-4fff-9771-4fb0170d7e1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:56,055] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde51a0ab-e32a-4fff-9771-4fb0170d7e1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:56,071] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:14:56,071] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:56,071] [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 qijiaojingensis	strain=KCTC 22228	GCA_014651875.1	980347	980347	type	True	100.0	1546	1547	95	conclusive
Halomonas anticariensis	strain=DSM 16096	GCA_000428505.1	258591	258591	type	True	84.1233	1100	1547	95	below_threshold
Halomonas anticariensis	strain=FP35	GCA_000409775.1	258591	258591	type	True	84.1188	1120	1547	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	80.837	807	1547	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	80.8126	787	1547	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	80.6922	692	1547	95	below_threshold
Halomonas salipaludis	strain=WRN001	GCA_002286975.1	2032625	2032625	type	True	80.45	715	1547	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	80.3487	648	1547	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	80.2015	652	1547	95	below_threshold
Halomonas pantelleriensis	strain=AAP	GCA_900102875.1	48727	48727	type	True	80.1907	645	1547	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	80.083	664	1547	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	80.0735	617	1547	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	79.9679	626	1547	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	79.9364	656	1547	95	below_threshold
Halomonas bachuensis	strain=DX6	GCA_011742165.1	2717286	2717286	type	True	79.8496	624	1547	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	79.6645	542	1547	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	79.6074	567	1547	95	below_threshold
Halomonas xinjiangensis	strain=TRM 0175	GCA_000759345.1	1166948	1166948	type	True	79.4996	556	1547	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:56,073] [INFO] DFAST Taxonomy check result was written to GCF_014651875.1_ASM1465187v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:56,074] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:56,074] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:56,075] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde51a0ab-e32a-4fff-9771-4fb0170d7e1b/dqc_reference/checkm_data
[2024-01-24 14:14:56,076] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:56,122] [INFO] Task started: CheckM
[2024-01-24 14:14:56,122] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651875.1_ASM1465187v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651875.1_ASM1465187v1_genomic.fna/checkm_input GCF_014651875.1_ASM1465187v1_genomic.fna/checkm_result
[2024-01-24 14:15:40,475] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:40,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:40,500] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:40,500] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:40,500] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651875.1_ASM1465187v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:40,501] [INFO] Task started: Blastn
[2024-01-24 14:15:40,501] [INFO] Running command: blastn -query GCF_014651875.1_ASM1465187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde51a0ab-e32a-4fff-9771-4fb0170d7e1b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651875.1_ASM1465187v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:42,121] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:42,125] [INFO] Selected 17 target genomes.
[2024-01-24 14:15:42,126] [INFO] Target genome list was writen to GCF_014651875.1_ASM1465187v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:42,143] [INFO] Task started: fastANI
[2024-01-24 14:15:42,144] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4404ce1-56cf-4054-919d-201271a50526/GCF_014651875.1_ASM1465187v1_genomic.fna.gz --refList GCF_014651875.1_ASM1465187v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651875.1_ASM1465187v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:57,327] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:57,340] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:57,341] [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_014651875.1	s__Halomonas_A qijiaojingensis	100.0	1546	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000409775.1	s__Halomonas_A anticariensis	84.1213	1121	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003202205.1	s__Halomonas sp003202205	81.5601	807	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002879645.1	s__Halomonas heilongjiangensis	80.8442	782	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014192275.1	s__Halomonas stenophila	80.6765	693	1547	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	80.5102	687	1547	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_002286975.1	s__Halomonas_B sp002286975	80.4623	715	1547	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_003056305.1	s__Halomonas denitrificans	80.2654	593	1547	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	80.2201	649	1547	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	80.1696	664	1547	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	80.0902	663	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001577635.1	s__Halomonas_C sp001577635	80.0491	520	1547	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_009363755.1	s__Halomonas sp009363755	80.0039	581	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011742165.1	s__Halomonas bachuensis	79.842	625	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014931605.1	s__Halomonas sp014931605	79.7031	592	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013009075.1	s__Halomonas_B sp013009075	79.5375	535	1547	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_000759345.1	s__Halomonas_A xinjiangensis	79.5173	554	1547	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 14:15:57,342] [INFO] GTDB search result was written to GCF_014651875.1_ASM1465187v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:57,343] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:57,347] [INFO] DFAST_QC result json was written to GCF_014651875.1_ASM1465187v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:57,347] [INFO] DFAST_QC completed!
[2024-01-24 14:15:57,347] [INFO] Total running time: 0h1m37s