[2024-01-24 13:57:55,428] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:55,430] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:55,430] [INFO] DQC Reference Directory: /var/lib/cwl/stg02e752a0-abb6-4a2d-839e-cd562e9a98df/dqc_reference
[2024-01-24 13:57:56,812] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:56,813] [INFO] Task started: Prodigal
[2024-01-24 13:57:56,813] [INFO] Running command: gunzip -c /var/lib/cwl/stge505547f-793a-4af0-9b41-8ad6d6df72fc/GCF_004117855.1_ASM411785v1_genomic.fna.gz | prodigal -d GCF_004117855.1_ASM411785v1_genomic.fna/cds.fna -a GCF_004117855.1_ASM411785v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:09,767] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:09,768] [INFO] Task started: HMMsearch
[2024-01-24 13:58:09,768] [INFO] Running command: hmmsearch --tblout GCF_004117855.1_ASM411785v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02e752a0-abb6-4a2d-839e-cd562e9a98df/dqc_reference/reference_markers.hmm GCF_004117855.1_ASM411785v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:10,100] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:10,101] [INFO] Found 6/6 markers.
[2024-01-24 13:58:10,143] [INFO] Query marker FASTA was written to GCF_004117855.1_ASM411785v1_genomic.fna/markers.fasta
[2024-01-24 13:58:10,144] [INFO] Task started: Blastn
[2024-01-24 13:58:10,144] [INFO] Running command: blastn -query GCF_004117855.1_ASM411785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02e752a0-abb6-4a2d-839e-cd562e9a98df/dqc_reference/reference_markers.fasta -out GCF_004117855.1_ASM411785v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:11,180] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:11,184] [INFO] Selected 22 target genomes.
[2024-01-24 13:58:11,184] [INFO] Target genome list was writen to GCF_004117855.1_ASM411785v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:11,195] [INFO] Task started: fastANI
[2024-01-24 13:58:11,196] [INFO] Running command: fastANI --query /var/lib/cwl/stge505547f-793a-4af0-9b41-8ad6d6df72fc/GCF_004117855.1_ASM411785v1_genomic.fna.gz --refList GCF_004117855.1_ASM411785v1_genomic.fna/target_genomes.txt --output GCF_004117855.1_ASM411785v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:31,562] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:31,563] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02e752a0-abb6-4a2d-839e-cd562e9a98df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:31,563] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02e752a0-abb6-4a2d-839e-cd562e9a98df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:31,580] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:31,581] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:31,581] [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	83.4759	826	1449	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	82.1808	705	1449	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	82.0389	719	1449	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	82.0128	698	1449	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	81.7989	696	1449	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	81.6946	621	1449	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	81.6301	671	1449	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	81.5713	669	1449	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	81.4564	718	1449	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	81.4532	673	1449	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	81.4303	770	1449	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	81.3935	748	1449	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	81.3223	705	1449	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	81.3	711	1449	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	81.0874	641	1449	95	below_threshold
Halomonas ilicicola	strain=DSM 19980	GCA_900128925.1	480814	480814	type	True	81.0193	669	1449	95	below_threshold
Salinicola endophyticus	strain=CPA92	GCA_003206575.1	1949083	1949083	type	True	80.9422	707	1449	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	80.618	622	1449	95	below_threshold
Halomonas antri	strain=Y3S6	GCA_019430905.1	2846777	2846777	type	True	80.5657	619	1449	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	80.3054	655	1449	95	below_threshold
Halomonas alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	80.2944	604	1449	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	80.2593	576	1449	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:31,583] [INFO] DFAST Taxonomy check result was written to GCF_004117855.1_ASM411785v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:31,583] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:31,584] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:31,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02e752a0-abb6-4a2d-839e-cd562e9a98df/dqc_reference/checkm_data
[2024-01-24 13:58:31,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:31,629] [INFO] Task started: CheckM
[2024-01-24 13:58:31,630] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004117855.1_ASM411785v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004117855.1_ASM411785v1_genomic.fna/checkm_input GCF_004117855.1_ASM411785v1_genomic.fna/checkm_result
[2024-01-24 13:59:11,992] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:11,993] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:12,009] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:12,009] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:12,009] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004117855.1_ASM411785v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:12,010] [INFO] Task started: Blastn
[2024-01-24 13:59:12,010] [INFO] Running command: blastn -query GCF_004117855.1_ASM411785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02e752a0-abb6-4a2d-839e-cd562e9a98df/dqc_reference/reference_markers_gtdb.fasta -out GCF_004117855.1_ASM411785v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:13,596] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:13,599] [INFO] Selected 10 target genomes.
[2024-01-24 13:59:13,600] [INFO] Target genome list was writen to GCF_004117855.1_ASM411785v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:13,607] [INFO] Task started: fastANI
[2024-01-24 13:59:13,608] [INFO] Running command: fastANI --query /var/lib/cwl/stge505547f-793a-4af0-9b41-8ad6d6df72fc/GCF_004117855.1_ASM411785v1_genomic.fna.gz --refList GCF_004117855.1_ASM411785v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004117855.1_ASM411785v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:22,921] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:22,932] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:22,932] [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_004117855.1	s__Halomonas_C coralii	100.0	1445	1449	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
GCF_010993675.1	s__Halomonas_C sp010993675	85.9045	892	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001577635.1	s__Halomonas_C sp001577635	85.8676	894	1449	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	83.7946	969	1449	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	83.4643	826	1449	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_001886615.1	s__Halomonas aestuarii	81.6841	622	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202205.1	s__Halomonas sp003202205	81.4423	693	1449	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	78.6521	443	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422485.1	s__Agreia sp001422485	74.9001	72	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agreia	95.0	96.67	96.67	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:22,934] [INFO] GTDB search result was written to GCF_004117855.1_ASM411785v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:22,935] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:22,940] [INFO] DFAST_QC result json was written to GCF_004117855.1_ASM411785v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:22,941] [INFO] DFAST_QC completed!
[2024-01-24 13:59:22,941] [INFO] Total running time: 0h1m28s