[2024-01-24 13:55:15,144] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:15,146] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:15,146] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a4f19f0-6ca7-4b39-a983-a35bed89dccb/dqc_reference
[2024-01-24 13:55:16,519] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:16,520] [INFO] Task started: Prodigal
[2024-01-24 13:55:16,521] [INFO] Running command: gunzip -c /var/lib/cwl/stgd41e93b4-c432-4805-b3e7-45eba67a7150/GCF_014652955.1_ASM1465295v1_genomic.fna.gz | prodigal -d GCF_014652955.1_ASM1465295v1_genomic.fna/cds.fna -a GCF_014652955.1_ASM1465295v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:25,632] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:25,632] [INFO] Task started: HMMsearch
[2024-01-24 13:55:25,633] [INFO] Running command: hmmsearch --tblout GCF_014652955.1_ASM1465295v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a4f19f0-6ca7-4b39-a983-a35bed89dccb/dqc_reference/reference_markers.hmm GCF_014652955.1_ASM1465295v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:25,875] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:25,876] [INFO] Found 6/6 markers.
[2024-01-24 13:55:25,903] [INFO] Query marker FASTA was written to GCF_014652955.1_ASM1465295v1_genomic.fna/markers.fasta
[2024-01-24 13:55:25,903] [INFO] Task started: Blastn
[2024-01-24 13:55:25,904] [INFO] Running command: blastn -query GCF_014652955.1_ASM1465295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a4f19f0-6ca7-4b39-a983-a35bed89dccb/dqc_reference/reference_markers.fasta -out GCF_014652955.1_ASM1465295v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:26,881] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:26,885] [INFO] Selected 16 target genomes.
[2024-01-24 13:55:26,885] [INFO] Target genome list was writen to GCF_014652955.1_ASM1465295v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:26,894] [INFO] Task started: fastANI
[2024-01-24 13:55:26,895] [INFO] Running command: fastANI --query /var/lib/cwl/stgd41e93b4-c432-4805-b3e7-45eba67a7150/GCF_014652955.1_ASM1465295v1_genomic.fna.gz --refList GCF_014652955.1_ASM1465295v1_genomic.fna/target_genomes.txt --output GCF_014652955.1_ASM1465295v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:36,138] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:36,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a4f19f0-6ca7-4b39-a983-a35bed89dccb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:36,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a4f19f0-6ca7-4b39-a983-a35bed89dccb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:36,156] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:55:36,156] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:36,156] [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
Salinibacterium amurskyense	strain=KCTC 9931	GCA_014652955.1	205941	205941	type	True	100.0	923	923	95	conclusive
Salinibacterium amurskyense	strain=JCM 12362	GCA_003668745.1	205941	205941	type	True	99.9993	919	923	95	conclusive
Salinibacterium amurskyense	strain=DSM 16400	GCA_002797685.1	205941	205941	type	True	99.9991	920	923	95	conclusive
Conyzicola nivalis	strain=CGMCC 1.12813	GCA_014639655.1	1477021	1477021	type	True	78.0941	240	923	95	below_threshold
Conyzicola lurida	strain=DSM 105784	GCA_014204935.1	1172621	1172621	type	True	78.0665	265	923	95	below_threshold
Lacisediminihabitans profunda	strain=CHu50b-6-2	GCA_008040105.1	2594790	2594790	type	True	77.7365	197	923	95	below_threshold
Microterricola viridarii	strain=DSM 21772	GCA_900104895.1	412690	412690	type	True	77.7146	189	923	95	below_threshold
Okibacterium fritillariae	strain=VKM Ac-2059	GCA_900167575.1	123320	123320	type	True	77.7053	194	923	95	below_threshold
Marisediminicola senii	strain=SM7_A14	GCA_011057645.1	2711233	2711233	type	True	77.6021	188	923	95	below_threshold
Galbitalea soli	strain=DSM 105515	GCA_013410525.1	1268042	1268042	type	True	77.5987	201	923	95	below_threshold
Galbitalea soli	strain=NBRC 108727	GCA_010686725.1	1268042	1268042	type	True	77.545	204	923	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	77.032	185	923	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	77.0125	187	923	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	76.9314	167	923	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	76.9148	180	923	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	76.6437	146	923	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:36,158] [INFO] DFAST Taxonomy check result was written to GCF_014652955.1_ASM1465295v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:36,159] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:36,159] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:36,159] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a4f19f0-6ca7-4b39-a983-a35bed89dccb/dqc_reference/checkm_data
[2024-01-24 13:55:36,160] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:36,188] [INFO] Task started: CheckM
[2024-01-24 13:55:36,189] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652955.1_ASM1465295v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652955.1_ASM1465295v1_genomic.fna/checkm_input GCF_014652955.1_ASM1465295v1_genomic.fna/checkm_result
[2024-01-24 13:56:08,199] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:08,201] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:08,222] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:08,222] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:08,222] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652955.1_ASM1465295v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:08,223] [INFO] Task started: Blastn
[2024-01-24 13:56:08,223] [INFO] Running command: blastn -query GCF_014652955.1_ASM1465295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a4f19f0-6ca7-4b39-a983-a35bed89dccb/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652955.1_ASM1465295v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:09,751] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:09,754] [INFO] Selected 7 target genomes.
[2024-01-24 13:56:09,755] [INFO] Target genome list was writen to GCF_014652955.1_ASM1465295v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:09,769] [INFO] Task started: fastANI
[2024-01-24 13:56:09,769] [INFO] Running command: fastANI --query /var/lib/cwl/stgd41e93b4-c432-4805-b3e7-45eba67a7150/GCF_014652955.1_ASM1465295v1_genomic.fna.gz --refList GCF_014652955.1_ASM1465295v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652955.1_ASM1465295v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:14,858] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:14,865] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:14,865] [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_002797685.1	s__Rhodoglobus amurskyensis	99.9991	920	923	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_004118935.1	s__Rhodoglobus sp004118935	87.4096	757	923	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	96.46	96.46	0.90	0.90	2	-
GCF_015864575.1	s__Rhodoglobus sp015864575	86.32	769	923	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	96.13	96.11	0.92	0.92	6	-
GCF_015864945.1	s__Rhodoglobus sp015864945	85.8762	754	923	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015864665.1	s__Rhodoglobus sp015864665	85.7368	757	923	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	98.48	98.48	0.93	0.93	2	-
GCF_015864955.1	s__Rhodoglobus sp015864955	85.4654	728	923	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000247645.1	s__Rhodoglobus sp000247645	83.3054	649	923	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:14,867] [INFO] GTDB search result was written to GCF_014652955.1_ASM1465295v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:14,868] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:14,872] [INFO] DFAST_QC result json was written to GCF_014652955.1_ASM1465295v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:14,872] [INFO] DFAST_QC completed!
[2024-01-24 13:56:14,872] [INFO] Total running time: 0h0m60s