[2024-01-24 13:13:51,519] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:51,522] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:51,522] [INFO] DQC Reference Directory: /var/lib/cwl/stg06e62e6c-e2c2-4e92-a20b-fb593ca57d07/dqc_reference
[2024-01-24 13:13:52,811] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:52,811] [INFO] Task started: Prodigal
[2024-01-24 13:13:52,812] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc57e27c-d1e4-462c-83e3-98de99ee5290/GCF_014489535.1_ASM1448953v1_genomic.fna.gz | prodigal -d GCF_014489535.1_ASM1448953v1_genomic.fna/cds.fna -a GCF_014489535.1_ASM1448953v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:14:10,351] [INFO] Task succeeded: Prodigal
[2024-01-24 13:14:10,352] [INFO] Task started: HMMsearch
[2024-01-24 13:14:10,352] [INFO] Running command: hmmsearch --tblout GCF_014489535.1_ASM1448953v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06e62e6c-e2c2-4e92-a20b-fb593ca57d07/dqc_reference/reference_markers.hmm GCF_014489535.1_ASM1448953v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:14:10,710] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:14:10,711] [INFO] Found 6/6 markers.
[2024-01-24 13:14:10,752] [INFO] Query marker FASTA was written to GCF_014489535.1_ASM1448953v1_genomic.fna/markers.fasta
[2024-01-24 13:14:10,752] [INFO] Task started: Blastn
[2024-01-24 13:14:10,753] [INFO] Running command: blastn -query GCF_014489535.1_ASM1448953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06e62e6c-e2c2-4e92-a20b-fb593ca57d07/dqc_reference/reference_markers.fasta -out GCF_014489535.1_ASM1448953v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:11,740] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:11,744] [INFO] Selected 18 target genomes.
[2024-01-24 13:14:11,745] [INFO] Target genome list was writen to GCF_014489535.1_ASM1448953v1_genomic.fna/target_genomes.txt
[2024-01-24 13:14:11,754] [INFO] Task started: fastANI
[2024-01-24 13:14:11,754] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc57e27c-d1e4-462c-83e3-98de99ee5290/GCF_014489535.1_ASM1448953v1_genomic.fna.gz --refList GCF_014489535.1_ASM1448953v1_genomic.fna/target_genomes.txt --output GCF_014489535.1_ASM1448953v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:29,653] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:29,654] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06e62e6c-e2c2-4e92-a20b-fb593ca57d07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:29,655] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06e62e6c-e2c2-4e92-a20b-fb593ca57d07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:29,674] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:29,674] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:29,674] [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
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	100.0	1649	1649	95	conclusive
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	84.1438	1093	1649	95	below_threshold
Diaphorobacter ruginosibacter	strain=DSM 27467	GCA_014395975.1	1715720	1715720	type	True	82.8345	981	1649	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	80.1626	605	1649	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	80.044	629	1649	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	79.6726	373	1649	95	below_threshold
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	79.6622	525	1649	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	79.587	618	1649	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_000964545.1	363952	363952	type	True	79.5314	540	1649	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	79.4696	663	1649	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001517325.1	363952	363952	type	True	79.4459	541	1649	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.3999	584	1649	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.1721	496	1649	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	78.95	581	1649	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	78.8662	557	1649	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	78.7938	434	1649	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	78.7424	565	1649	95	below_threshold
Xylophilus rhododendri	strain=KACC 21265	GCA_009906855.1	2697032	2697032	type	True	78.6171	483	1649	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:29,677] [INFO] DFAST Taxonomy check result was written to GCF_014489535.1_ASM1448953v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:29,678] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:29,678] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:29,679] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06e62e6c-e2c2-4e92-a20b-fb593ca57d07/dqc_reference/checkm_data
[2024-01-24 13:14:29,681] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:29,745] [INFO] Task started: CheckM
[2024-01-24 13:14:29,746] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014489535.1_ASM1448953v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014489535.1_ASM1448953v1_genomic.fna/checkm_input GCF_014489535.1_ASM1448953v1_genomic.fna/checkm_result
[2024-01-24 13:15:34,849] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:34,851] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:34,874] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:34,874] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:34,875] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014489535.1_ASM1448953v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:34,875] [INFO] Task started: Blastn
[2024-01-24 13:15:34,875] [INFO] Running command: blastn -query GCF_014489535.1_ASM1448953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06e62e6c-e2c2-4e92-a20b-fb593ca57d07/dqc_reference/reference_markers_gtdb.fasta -out GCF_014489535.1_ASM1448953v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:36,815] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:36,819] [INFO] Selected 9 target genomes.
[2024-01-24 13:15:36,819] [INFO] Target genome list was writen to GCF_014489535.1_ASM1448953v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:36,837] [INFO] Task started: fastANI
[2024-01-24 13:15:36,838] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc57e27c-d1e4-462c-83e3-98de99ee5290/GCF_014489535.1_ASM1448953v1_genomic.fna.gz --refList GCF_014489535.1_ASM1448953v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014489535.1_ASM1448953v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:48,912] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:48,928] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:48,928] [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_014489535.1	s__Diaphorobacter_A aerolatus	100.0	1649	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015354245.1	s__Diaphorobacter_A sp015354245	84.1319	1092	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011305535.1	s__Diaphorobacter_A sp011305535	84.0862	1075	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011305995.1	s__Diaphorobacter_A sp011305995	83.4936	1085	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014395975.1	s__Diaphorobacter_A ruginosibacter	82.8634	980	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002331385.1	s__Diaphorobacter_A sp002331385	81.7289	880	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter_A	95.0	95.84	95.84	0.86	0.86	2	-
GCF_002176815.1	s__Acidovorax sp002176815	80.3528	590	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.23	97.20	0.91	0.82	4	-
GCF_014489595.1	s__Acidovorax_F monticola	80.1692	688	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_F	95.0	97.51	97.51	0.93	0.93	2	-
GCF_001424265.1	s__Acidovorax_A sp001424265	79.7664	644	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:48,930] [INFO] GTDB search result was written to GCF_014489535.1_ASM1448953v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:48,931] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:48,936] [INFO] DFAST_QC result json was written to GCF_014489535.1_ASM1448953v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:48,937] [INFO] DFAST_QC completed!
[2024-01-24 13:15:48,937] [INFO] Total running time: 0h1m57s