[2024-01-25 20:14:35,568] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:14:35,569] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:14:35,570] [INFO] DQC Reference Directory: /var/lib/cwl/stg31a40ba5-11a5-4452-a667-b854a90fb0e2/dqc_reference
[2024-01-25 20:14:36,815] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:14:36,816] [INFO] Task started: Prodigal
[2024-01-25 20:14:36,817] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd954acb-ee2a-4eb8-86dd-f0247196641b/GCF_014645555.1_ASM1464555v1_genomic.fna.gz | prodigal -d GCF_014645555.1_ASM1464555v1_genomic.fna/cds.fna -a GCF_014645555.1_ASM1464555v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:14:50,914] [INFO] Task succeeded: Prodigal
[2024-01-25 20:14:50,914] [INFO] Task started: HMMsearch
[2024-01-25 20:14:50,914] [INFO] Running command: hmmsearch --tblout GCF_014645555.1_ASM1464555v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31a40ba5-11a5-4452-a667-b854a90fb0e2/dqc_reference/reference_markers.hmm GCF_014645555.1_ASM1464555v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:14:51,179] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:14:51,180] [INFO] Found 6/6 markers.
[2024-01-25 20:14:51,224] [INFO] Query marker FASTA was written to GCF_014645555.1_ASM1464555v1_genomic.fna/markers.fasta
[2024-01-25 20:14:51,225] [INFO] Task started: Blastn
[2024-01-25 20:14:51,225] [INFO] Running command: blastn -query GCF_014645555.1_ASM1464555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31a40ba5-11a5-4452-a667-b854a90fb0e2/dqc_reference/reference_markers.fasta -out GCF_014645555.1_ASM1464555v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:51,941] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:51,943] [INFO] Selected 16 target genomes.
[2024-01-25 20:14:51,944] [INFO] Target genome list was writen to GCF_014645555.1_ASM1464555v1_genomic.fna/target_genomes.txt
[2024-01-25 20:14:51,952] [INFO] Task started: fastANI
[2024-01-25 20:14:51,952] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd954acb-ee2a-4eb8-86dd-f0247196641b/GCF_014645555.1_ASM1464555v1_genomic.fna.gz --refList GCF_014645555.1_ASM1464555v1_genomic.fna/target_genomes.txt --output GCF_014645555.1_ASM1464555v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:15:04,952] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:04,952] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31a40ba5-11a5-4452-a667-b854a90fb0e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:15:04,952] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31a40ba5-11a5-4452-a667-b854a90fb0e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:15:04,960] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:15:04,961] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:15:04,961] [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
Silvimonas amylolytica	strain=CGMCC 1.8860	GCA_014645555.1	449663	449663	type	True	100.0	1509	1512	95	conclusive
Silvimonas iriomotensis	strain=CGMCC 1.8859	GCA_014645535.1	449662	449662	type	True	86.4867	1284	1512	95	below_threshold
Silvimonas terrae	strain=DSM 18233	GCA_014202765.1	300266	300266	type	True	84.1997	1202	1512	95	below_threshold
Andreprevotia lacus	strain=DSM 23236	GCA_900176275.1	1121000	1121000	type	True	78.2863	301	1512	95	below_threshold
Andreprevotia chitinilytica	strain=DSM 18519	GCA_000711875.1	396808	396808	type	True	78.0791	302	1512	95	below_threshold
Jeongeupia naejangsanensis	strain=DSM 24253	GCA_016865585.1	613195	613195	type	True	77.8767	240	1512	95	below_threshold
Jeongeupia chitinilytica	strain=KCTC 23701	GCA_014652315.1	1041641	1041641	type	True	77.7677	234	1512	95	below_threshold
Chitinilyticum litopenaei	strain=DSM 21440	GCA_000428145.1	1121276	1121276	type	True	77.6157	203	1512	95	below_threshold
Chitinilyticum aquatile	strain=DSM 21506	GCA_000430805.1	362520	362520	type	True	77.5191	212	1512	95	below_threshold
Chitinilyticum piscinae	strain=4Y14	GCA_015223195.1	2866724	2866724	type	True	77.4377	203	1512	95	below_threshold
Formivibrio citricus	strain=DSM 6150	GCA_900115065.1	83765	83765	type	True	77.1992	157	1512	95	below_threshold
Chitinibacter fontanus	strain=STM-7	GCA_013423785.1	1737446	1737446	type	True	76.2327	89	1512	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:15:04,962] [INFO] DFAST Taxonomy check result was written to GCF_014645555.1_ASM1464555v1_genomic.fna/tc_result.tsv
[2024-01-25 20:15:04,963] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:15:04,963] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:15:04,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31a40ba5-11a5-4452-a667-b854a90fb0e2/dqc_reference/checkm_data
[2024-01-25 20:15:04,964] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:15:05,005] [INFO] Task started: CheckM
[2024-01-25 20:15:05,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645555.1_ASM1464555v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645555.1_ASM1464555v1_genomic.fna/checkm_input GCF_014645555.1_ASM1464555v1_genomic.fna/checkm_result
[2024-01-25 20:15:48,262] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:48,263] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:48,289] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:48,290] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:48,290] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645555.1_ASM1464555v1_genomic.fna/markers.fasta)
[2024-01-25 20:15:48,290] [INFO] Task started: Blastn
[2024-01-25 20:15:48,290] [INFO] Running command: blastn -query GCF_014645555.1_ASM1464555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31a40ba5-11a5-4452-a667-b854a90fb0e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645555.1_ASM1464555v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:49,574] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:49,584] [INFO] Selected 11 target genomes.
[2024-01-25 20:15:49,584] [INFO] Target genome list was writen to GCF_014645555.1_ASM1464555v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:49,590] [INFO] Task started: fastANI
[2024-01-25 20:15:49,590] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd954acb-ee2a-4eb8-86dd-f0247196641b/GCF_014645555.1_ASM1464555v1_genomic.fna.gz --refList GCF_014645555.1_ASM1464555v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645555.1_ASM1464555v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:59,619] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:59,627] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:15:59,628] [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_014645555.1	s__Silvimonas amylolytica	100.0	1508	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Silvimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014645535.1	s__Silvimonas iriomotensis	86.4939	1283	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Silvimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202765.1	s__Silvimonas terrae	84.1997	1202	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Silvimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001313065.1	s__Amantichitinum sp001313065	78.9375	424	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Amantichitinum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001294205.1	s__Amantichitinum ursilacus	78.9156	521	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Amantichitinum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176275.1	s__Andreprevotia lacus	78.2863	301	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009848685.1	s__Andreprevotia sp009848685	77.7947	299	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652315.1	s__Jeongeupia chitinilytica	77.7677	234	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430805.1	s__Chitinilyticum aquatile	77.5323	211	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018261735.1	s__Formivibrio sp018261735	77.2655	172	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Formivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115065.1	s__Formivibrio citricus	77.1992	157	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Formivibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:59,629] [INFO] GTDB search result was written to GCF_014645555.1_ASM1464555v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:59,630] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:59,633] [INFO] DFAST_QC result json was written to GCF_014645555.1_ASM1464555v1_genomic.fna/dqc_result.json
[2024-01-25 20:15:59,633] [INFO] DFAST_QC completed!
[2024-01-25 20:15:59,633] [INFO] Total running time: 0h1m24s