[2024-01-24 12:07:06,602] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:06,605] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:06,608] [INFO] DQC Reference Directory: /var/lib/cwl/stg959e313c-a20b-4e97-9c38-56279e9afc26/dqc_reference
[2024-01-24 12:07:07,863] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:07,864] [INFO] Task started: Prodigal
[2024-01-24 12:07:07,864] [INFO] Running command: gunzip -c /var/lib/cwl/stg02fcfc72-67bf-47da-a643-baa502f6331e/GCF_018448785.1_ASM1844878v1_genomic.fna.gz | prodigal -d GCF_018448785.1_ASM1844878v1_genomic.fna/cds.fna -a GCF_018448785.1_ASM1844878v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:20,097] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:20,098] [INFO] Task started: HMMsearch
[2024-01-24 12:07:20,098] [INFO] Running command: hmmsearch --tblout GCF_018448785.1_ASM1844878v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg959e313c-a20b-4e97-9c38-56279e9afc26/dqc_reference/reference_markers.hmm GCF_018448785.1_ASM1844878v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:20,428] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:20,430] [INFO] Found 6/6 markers.
[2024-01-24 12:07:20,470] [INFO] Query marker FASTA was written to GCF_018448785.1_ASM1844878v1_genomic.fna/markers.fasta
[2024-01-24 12:07:20,471] [INFO] Task started: Blastn
[2024-01-24 12:07:20,471] [INFO] Running command: blastn -query GCF_018448785.1_ASM1844878v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg959e313c-a20b-4e97-9c38-56279e9afc26/dqc_reference/reference_markers.fasta -out GCF_018448785.1_ASM1844878v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:21,336] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:21,340] [INFO] Selected 18 target genomes.
[2024-01-24 12:07:21,340] [INFO] Target genome list was writen to GCF_018448785.1_ASM1844878v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:21,348] [INFO] Task started: fastANI
[2024-01-24 12:07:21,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg02fcfc72-67bf-47da-a643-baa502f6331e/GCF_018448785.1_ASM1844878v1_genomic.fna.gz --refList GCF_018448785.1_ASM1844878v1_genomic.fna/target_genomes.txt --output GCF_018448785.1_ASM1844878v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:35,953] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:35,954] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg959e313c-a20b-4e97-9c38-56279e9afc26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:35,954] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg959e313c-a20b-4e97-9c38-56279e9afc26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:35,969] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:07:35,970] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:07:35,970] [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 korlensis	strain=CGMCC 1.6981	GCA_900116705.1	463301	463301	type	True	88.2502	1016	1347	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	81.7997	748	1347	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	81.604	729	1347	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	81.5573	724	1347	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	81.3777	676	1347	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	81.3399	690	1347	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	81.266	688	1347	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	81.1976	707	1347	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	81.1443	631	1347	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	81.1187	699	1347	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	81.1116	640	1347	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	80.7766	643	1347	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	80.6375	624	1347	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	80.5352	643	1347	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	80.1093	592	1347	95	below_threshold
Halomonas montanilacus	strain=PYC7W	GCA_003336675.1	2282305	2282305	type	True	79.9343	584	1347	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	79.8307	535	1347	95	below_threshold
Halomonas antri	strain=Y3S6	GCA_019430905.1	2846777	2846777	type	True	79.8001	587	1347	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:35,971] [INFO] DFAST Taxonomy check result was written to GCF_018448785.1_ASM1844878v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:35,972] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:35,972] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:35,972] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg959e313c-a20b-4e97-9c38-56279e9afc26/dqc_reference/checkm_data
[2024-01-24 12:07:35,973] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:36,016] [INFO] Task started: CheckM
[2024-01-24 12:07:36,016] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018448785.1_ASM1844878v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018448785.1_ASM1844878v1_genomic.fna/checkm_input GCF_018448785.1_ASM1844878v1_genomic.fna/checkm_result
[2024-01-24 12:08:14,768] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:14,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:14,791] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:14,792] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:14,792] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018448785.1_ASM1844878v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:14,793] [INFO] Task started: Blastn
[2024-01-24 12:08:14,793] [INFO] Running command: blastn -query GCF_018448785.1_ASM1844878v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg959e313c-a20b-4e97-9c38-56279e9afc26/dqc_reference/reference_markers_gtdb.fasta -out GCF_018448785.1_ASM1844878v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:16,309] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:16,313] [INFO] Selected 13 target genomes.
[2024-01-24 12:08:16,313] [INFO] Target genome list was writen to GCF_018448785.1_ASM1844878v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:16,321] [INFO] Task started: fastANI
[2024-01-24 12:08:16,321] [INFO] Running command: fastANI --query /var/lib/cwl/stg02fcfc72-67bf-47da-a643-baa502f6331e/GCF_018448785.1_ASM1844878v1_genomic.fna.gz --refList GCF_018448785.1_ASM1844878v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018448785.1_ASM1844878v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:26,944] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:26,962] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:26,962] [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_018448785.1	s__Halomonas sp018448785	100.0	1346	1347	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_900116705.1	s__Halomonas korlensis	88.2447	1015	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363555.1	s__Halomonas ventosae	81.7944	748	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.59	95.59	0.89	0.89	2	-
GCF_002879645.1	s__Halomonas heilongjiangensis	81.5822	724	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003202205.1	s__Halomonas sp003202205	81.5586	744	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886615.1	s__Halomonas aestuarii	81.3767	687	1347	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	81.3675	677	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363755.1	s__Halomonas sp009363755	81.3188	648	1347	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	81.2955	685	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116405.1	s__Halomonas saccharevitans	81.1101	641	1347	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	80.5696	639	1347	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	80.4428	447	1347	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	80.3057	620	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:26,964] [INFO] GTDB search result was written to GCF_018448785.1_ASM1844878v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:26,965] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:26,968] [INFO] DFAST_QC result json was written to GCF_018448785.1_ASM1844878v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:26,969] [INFO] DFAST_QC completed!
[2024-01-24 12:08:26,969] [INFO] Total running time: 0h1m20s