[2024-01-24 13:18:26,121] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:26,126] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:26,126] [INFO] DQC Reference Directory: /var/lib/cwl/stg04049215-a00a-49e1-b5ab-32ce3768ceec/dqc_reference
[2024-01-24 13:18:27,526] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:27,529] [INFO] Task started: Prodigal
[2024-01-24 13:18:27,530] [INFO] Running command: gunzip -c /var/lib/cwl/stg225a2508-26c9-4135-b150-b91609f24fb0/GCF_020148005.1_ASM2014800v1_genomic.fna.gz | prodigal -d GCF_020148005.1_ASM2014800v1_genomic.fna/cds.fna -a GCF_020148005.1_ASM2014800v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:38,439] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:38,439] [INFO] Task started: HMMsearch
[2024-01-24 13:18:38,439] [INFO] Running command: hmmsearch --tblout GCF_020148005.1_ASM2014800v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04049215-a00a-49e1-b5ab-32ce3768ceec/dqc_reference/reference_markers.hmm GCF_020148005.1_ASM2014800v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:38,702] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:38,703] [INFO] Found 6/6 markers.
[2024-01-24 13:18:38,738] [INFO] Query marker FASTA was written to GCF_020148005.1_ASM2014800v1_genomic.fna/markers.fasta
[2024-01-24 13:18:38,739] [INFO] Task started: Blastn
[2024-01-24 13:18:38,739] [INFO] Running command: blastn -query GCF_020148005.1_ASM2014800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04049215-a00a-49e1-b5ab-32ce3768ceec/dqc_reference/reference_markers.fasta -out GCF_020148005.1_ASM2014800v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:39,954] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:39,957] [INFO] Selected 18 target genomes.
[2024-01-24 13:18:39,957] [INFO] Target genome list was writen to GCF_020148005.1_ASM2014800v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:39,980] [INFO] Task started: fastANI
[2024-01-24 13:18:39,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg225a2508-26c9-4135-b150-b91609f24fb0/GCF_020148005.1_ASM2014800v1_genomic.fna.gz --refList GCF_020148005.1_ASM2014800v1_genomic.fna/target_genomes.txt --output GCF_020148005.1_ASM2014800v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:55,158] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:55,159] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04049215-a00a-49e1-b5ab-32ce3768ceec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:55,159] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04049215-a00a-49e1-b5ab-32ce3768ceec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:55,174] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:18:55,175] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:18:55,175] [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 zincidurans	strain=B6	GCA_000731955.1	1178777	1178777	type	True	83.397	764	1179	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	82.9202	664	1179	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	82.8078	674	1179	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	82.6277	684	1179	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	82.5304	699	1179	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	82.3525	671	1179	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	82.3229	645	1179	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	82.2721	678	1179	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	82.2553	677	1179	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	82.1686	634	1179	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	82.0027	693	1179	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	81.9523	694	1179	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	81.9106	623	1179	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	81.8098	637	1179	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	81.2213	612	1179	95	below_threshold
Halomonas ilicicola	strain=DSM 19980	GCA_900128925.1	480814	480814	type	True	81.1501	658	1179	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	80.7959	557	1179	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	80.6189	538	1179	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:55,177] [INFO] DFAST Taxonomy check result was written to GCF_020148005.1_ASM2014800v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:55,177] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:55,177] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:55,178] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04049215-a00a-49e1-b5ab-32ce3768ceec/dqc_reference/checkm_data
[2024-01-24 13:18:55,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:55,216] [INFO] Task started: CheckM
[2024-01-24 13:18:55,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020148005.1_ASM2014800v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020148005.1_ASM2014800v1_genomic.fna/checkm_input GCF_020148005.1_ASM2014800v1_genomic.fna/checkm_result
[2024-01-24 13:19:33,930] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:33,931] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:33,949] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:33,949] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:33,950] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020148005.1_ASM2014800v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:33,951] [INFO] Task started: Blastn
[2024-01-24 13:19:33,951] [INFO] Running command: blastn -query GCF_020148005.1_ASM2014800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04049215-a00a-49e1-b5ab-32ce3768ceec/dqc_reference/reference_markers_gtdb.fasta -out GCF_020148005.1_ASM2014800v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:36,056] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:36,060] [INFO] Selected 10 target genomes.
[2024-01-24 13:19:36,060] [INFO] Target genome list was writen to GCF_020148005.1_ASM2014800v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:36,068] [INFO] Task started: fastANI
[2024-01-24 13:19:36,069] [INFO] Running command: fastANI --query /var/lib/cwl/stg225a2508-26c9-4135-b150-b91609f24fb0/GCF_020148005.1_ASM2014800v1_genomic.fna.gz --refList GCF_020148005.1_ASM2014800v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020148005.1_ASM2014800v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:45,714] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:45,728] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:45,729] [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_010993675.1	s__Halomonas_C sp010993675	96.8076	1065	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001577635.1	s__Halomonas_C sp001577635	94.2364	1011	1179	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_004117855.1	s__Halomonas_C coralii	85.9561	882	1179	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_900961225.1	s__Halomonas_C sp900961225	83.5972	803	1179	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_000731955.1	s__Halomonas_C zincidurans	83.3892	765	1179	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_000265245.1	s__Halomonas smyrnensis	82.92	663	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_014192275.1	s__Halomonas stenophila	82.6359	682	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193375.1	s__Halomonas campaniensis	82.3759	669	1179	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	82.2965	674	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCF_001886615.1	s__Halomonas aestuarii	82.1946	634	1179	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 13:19:45,730] [INFO] GTDB search result was written to GCF_020148005.1_ASM2014800v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:45,731] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:45,735] [INFO] DFAST_QC result json was written to GCF_020148005.1_ASM2014800v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:45,735] [INFO] DFAST_QC completed!
[2024-01-24 13:19:45,735] [INFO] Total running time: 0h1m20s