[2024-01-24 11:27:19,364] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:19,365] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:19,366] [INFO] DQC Reference Directory: /var/lib/cwl/stgcee81801-76ba-44e1-b73d-756e9ccd1adb/dqc_reference
[2024-01-24 11:27:21,868] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:21,869] [INFO] Task started: Prodigal
[2024-01-24 11:27:21,869] [INFO] Running command: gunzip -c /var/lib/cwl/stg4982c161-048e-4c33-930d-0912eb5f9bf7/GCF_014651795.1_ASM1465179v1_genomic.fna.gz | prodigal -d GCF_014651795.1_ASM1465179v1_genomic.fna/cds.fna -a GCF_014651795.1_ASM1465179v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:33,625] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:33,626] [INFO] Task started: HMMsearch
[2024-01-24 11:27:33,626] [INFO] Running command: hmmsearch --tblout GCF_014651795.1_ASM1465179v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcee81801-76ba-44e1-b73d-756e9ccd1adb/dqc_reference/reference_markers.hmm GCF_014651795.1_ASM1465179v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:33,891] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:33,893] [INFO] Found 6/6 markers.
[2024-01-24 11:27:33,928] [INFO] Query marker FASTA was written to GCF_014651795.1_ASM1465179v1_genomic.fna/markers.fasta
[2024-01-24 11:27:33,929] [INFO] Task started: Blastn
[2024-01-24 11:27:33,929] [INFO] Running command: blastn -query GCF_014651795.1_ASM1465179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcee81801-76ba-44e1-b73d-756e9ccd1adb/dqc_reference/reference_markers.fasta -out GCF_014651795.1_ASM1465179v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:34,798] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:34,801] [INFO] Selected 16 target genomes.
[2024-01-24 11:27:34,801] [INFO] Target genome list was writen to GCF_014651795.1_ASM1465179v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:34,808] [INFO] Task started: fastANI
[2024-01-24 11:27:34,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg4982c161-048e-4c33-930d-0912eb5f9bf7/GCF_014651795.1_ASM1465179v1_genomic.fna.gz --refList GCF_014651795.1_ASM1465179v1_genomic.fna/target_genomes.txt --output GCF_014651795.1_ASM1465179v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:46,973] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:46,974] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcee81801-76ba-44e1-b73d-756e9ccd1adb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:46,975] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcee81801-76ba-44e1-b73d-756e9ccd1adb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:46,991] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:27:46,991] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:27:46,991] [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 johnsoniae	strain=KCTC 22157	GCA_014651795.1	502832	502832	type	True	100.0	1254	1255	95	inconclusive
Halomonas hamiltonii	strain=KCTC 22154	GCA_014651775.1	502829	502829	type	True	97.5088	1104	1255	95	inconclusive
Halomonas stevensii	strain=S18214	GCA_000275725.1	502821	502821	type	True	96.3487	1039	1255	95	inconclusive
Halomonas meridiana	strain=ACAM 246	GCA_900129255.1	29570	29570	type	True	84.2086	730	1255	95	below_threshold
Halomonas aquamarina	strain=558	GCA_900110265.1	77097	77097	type	True	84.1003	703	1255	95	below_threshold
Halomonas meridiana	strain=NBRC 15608	GCA_006540125.1	29570	29570	type	True	84.0379	697	1255	95	below_threshold
Halomonas piezotolerans	strain=NBT06E8	GCA_012427705.1	2609667	2609667	type	True	82.9612	821	1255	95	below_threshold
Halomonas piezotolerans	strain=NBT06E8	GCA_009660035.1	2609667	2609667	type	True	82.9563	806	1255	95	below_threshold
Halomonas lutescens	strain=CGMCC 1.15122	GCA_014640815.1	1602943	1602943	type	True	82.2453	775	1255	95	below_threshold
Halomonas songnenensis	strain=CGMCC 1.12152	GCA_003002925.1	1176243	1176243	type	True	80.5767	640	1255	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	79.0723	452	1255	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.9263	435	1255	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	78.7931	473	1255	95	below_threshold
Halomonas zhuhanensis	strain=ZH2S	GCA_009793355.1	2684210	2684210	type	True	78.7669	337	1255	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	78.5181	464	1255	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	78.276	375	1255	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:46,993] [INFO] DFAST Taxonomy check result was written to GCF_014651795.1_ASM1465179v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:46,993] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:46,994] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:46,994] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcee81801-76ba-44e1-b73d-756e9ccd1adb/dqc_reference/checkm_data
[2024-01-24 11:27:46,995] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:47,031] [INFO] Task started: CheckM
[2024-01-24 11:27:47,031] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651795.1_ASM1465179v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651795.1_ASM1465179v1_genomic.fna/checkm_input GCF_014651795.1_ASM1465179v1_genomic.fna/checkm_result
[2024-01-24 11:28:23,900] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:23,901] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:23,918] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:23,918] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:23,919] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651795.1_ASM1465179v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:23,919] [INFO] Task started: Blastn
[2024-01-24 11:28:23,919] [INFO] Running command: blastn -query GCF_014651795.1_ASM1465179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcee81801-76ba-44e1-b73d-756e9ccd1adb/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651795.1_ASM1465179v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:25,558] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:25,562] [INFO] Selected 10 target genomes.
[2024-01-24 11:28:25,562] [INFO] Target genome list was writen to GCF_014651795.1_ASM1465179v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:25,591] [INFO] Task started: fastANI
[2024-01-24 11:28:25,591] [INFO] Running command: fastANI --query /var/lib/cwl/stg4982c161-048e-4c33-930d-0912eb5f9bf7/GCF_014651795.1_ASM1465179v1_genomic.fna.gz --refList GCF_014651795.1_ASM1465179v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651795.1_ASM1465179v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:33,516] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:33,528] [INFO] Found 10 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 11:28:33,528] [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_014651775.1	s__Halomonas hamiltonii	97.5126	1103	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	98.09	97.51	0.90	0.88	5	inconclusive
GCF_000275725.1	s__Halomonas stevensii	96.3487	1039	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	97.33	97.21	0.85	0.83	5	inconclusive
GCF_900110265.1	s__Halomonas aquamarina	84.1105	702	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.65	97.09	0.84	0.80	25	-
GCF_012427705.1	s__Halomonas piezotolerans	82.9724	820	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	98.70	0.97	0.94	3	-
GCF_009846525.1	s__Halomonas sp002696125	82.8254	770	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.53	98.53	0.95	0.95	2	-
GCF_014640815.1	s__Halomonas lutescens	82.2381	776	1255	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	80.586	639	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686925.1	s__Halomonas sp000686925	79.928	565	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003990195.1	s__Halomonas sp003990195	79.5731	527	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.00	98.34	0.94	0.91	3	-
GCF_009793355.1	s__Halomonas sp009793355	78.7428	339	1255	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 11:28:33,530] [INFO] GTDB search result was written to GCF_014651795.1_ASM1465179v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:33,530] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:33,534] [INFO] DFAST_QC result json was written to GCF_014651795.1_ASM1465179v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:33,534] [INFO] DFAST_QC completed!
[2024-01-24 11:28:33,534] [INFO] Total running time: 0h1m14s