[2024-01-24 14:22:33,522] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:33,524] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:33,525] [INFO] DQC Reference Directory: /var/lib/cwl/stg437e3b1d-6326-473a-97e4-653aec7a274a/dqc_reference
[2024-01-24 14:22:34,857] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:34,858] [INFO] Task started: Prodigal
[2024-01-24 14:22:34,858] [INFO] Running command: gunzip -c /var/lib/cwl/stgae376629-4031-4ad1-a4d9-d9adaba4d71e/GCF_005952805.1_ASM595280v1_genomic.fna.gz | prodigal -d GCF_005952805.1_ASM595280v1_genomic.fna/cds.fna -a GCF_005952805.1_ASM595280v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:49,012] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:49,013] [INFO] Task started: HMMsearch
[2024-01-24 14:22:49,013] [INFO] Running command: hmmsearch --tblout GCF_005952805.1_ASM595280v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg437e3b1d-6326-473a-97e4-653aec7a274a/dqc_reference/reference_markers.hmm GCF_005952805.1_ASM595280v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:49,359] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:49,360] [INFO] Found 6/6 markers.
[2024-01-24 14:22:49,456] [INFO] Query marker FASTA was written to GCF_005952805.1_ASM595280v1_genomic.fna/markers.fasta
[2024-01-24 14:22:49,457] [INFO] Task started: Blastn
[2024-01-24 14:22:49,457] [INFO] Running command: blastn -query GCF_005952805.1_ASM595280v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg437e3b1d-6326-473a-97e4-653aec7a274a/dqc_reference/reference_markers.fasta -out GCF_005952805.1_ASM595280v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:50,489] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:50,493] [INFO] Selected 15 target genomes.
[2024-01-24 14:22:50,494] [INFO] Target genome list was writen to GCF_005952805.1_ASM595280v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:50,501] [INFO] Task started: fastANI
[2024-01-24 14:22:50,502] [INFO] Running command: fastANI --query /var/lib/cwl/stgae376629-4031-4ad1-a4d9-d9adaba4d71e/GCF_005952805.1_ASM595280v1_genomic.fna.gz --refList GCF_005952805.1_ASM595280v1_genomic.fna/target_genomes.txt --output GCF_005952805.1_ASM595280v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:04,837] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:04,837] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg437e3b1d-6326-473a-97e4-653aec7a274a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:04,838] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg437e3b1d-6326-473a-97e4-653aec7a274a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:04,861] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:23:04,861] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:04,861] [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
Inhella inkyongensis	strain=IMCC1713	GCA_005952805.1	392593	392593	type	True	100.0	1355	1361	95	conclusive
Inhella inkyongensis	strain=DSM 23958	GCA_014202795.1	392593	392593	type	True	99.9907	1333	1361	95	conclusive
Inhella proteolytica	strain=1Y17	GCA_016093275.1	2795029	2795029	type	True	82.7761	918	1361	95	below_threshold
Inhella crocodyli	strain=CCP-18	GCA_004004565.1	2499851	2499851	type	True	80.9321	643	1361	95	below_threshold
Inhella gelatinilytica	strain=4Y10	GCA_016093295.1	2795030	2795030	type	True	80.7068	548	1361	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	78.9827	525	1361	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	78.9587	469	1361	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	78.9445	493	1361	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	78.7031	484	1361	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	78.6497	404	1361	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	78.5573	480	1361	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	78.5365	408	1361	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.3465	394	1361	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	78.3371	480	1361	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	78.0493	314	1361	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:04,864] [INFO] DFAST Taxonomy check result was written to GCF_005952805.1_ASM595280v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:04,864] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:04,864] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:04,865] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg437e3b1d-6326-473a-97e4-653aec7a274a/dqc_reference/checkm_data
[2024-01-24 14:23:04,866] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:04,910] [INFO] Task started: CheckM
[2024-01-24 14:23:04,910] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005952805.1_ASM595280v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005952805.1_ASM595280v1_genomic.fna/checkm_input GCF_005952805.1_ASM595280v1_genomic.fna/checkm_result
[2024-01-24 14:24:09,182] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:09,185] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:09,226] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:09,226] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:09,227] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005952805.1_ASM595280v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:09,227] [INFO] Task started: Blastn
[2024-01-24 14:24:09,227] [INFO] Running command: blastn -query GCF_005952805.1_ASM595280v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg437e3b1d-6326-473a-97e4-653aec7a274a/dqc_reference/reference_markers_gtdb.fasta -out GCF_005952805.1_ASM595280v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:11,347] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:11,351] [INFO] Selected 15 target genomes.
[2024-01-24 14:24:11,352] [INFO] Target genome list was writen to GCF_005952805.1_ASM595280v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:11,366] [INFO] Task started: fastANI
[2024-01-24 14:24:11,366] [INFO] Running command: fastANI --query /var/lib/cwl/stgae376629-4031-4ad1-a4d9-d9adaba4d71e/GCF_005952805.1_ASM595280v1_genomic.fna.gz --refList GCF_005952805.1_ASM595280v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005952805.1_ASM595280v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:27,845] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:27,868] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:27,869] [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_005952805.1	s__Inhella inkyongensis	100.0	1354	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Inhella	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_016093275.1	s__Inhella proteolytica	82.7492	921	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Inhella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004004565.1	s__Inhella crocodyli	80.9163	645	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Inhella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016093295.1	s__Inhella gelatinilytica	80.7217	546	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Inhella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302655.1	s__Inhella sp017302655	80.5078	623	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Inhella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996515.1	s__Pelomonas sp009996515	79.6341	576	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015624425.1	s__Kinneretia sp015624425	79.5415	649	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Kinneretia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302485.1	s__Ideonella sp017302485	79.271	353	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204525.1	s__Paucibacter_A oligotrophus	79.0726	599	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069755.1	s__Ideonella sp018069755	78.9252	520	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069875.1	s__Ideonella sp018069875	78.9075	554	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	98.74	98.74	0.92	0.92	2	-
GCF_000333615.1	s__Ideonella sp000333615	78.8848	423	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302505.1	s__Rubrivivax sp017302505	78.8305	383	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009760915.1	s__Azohydromonas aeria	78.5958	476	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017795745.1	s__Piscinibacter sp017795745	78.5209	452	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:27,870] [INFO] GTDB search result was written to GCF_005952805.1_ASM595280v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:27,871] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:27,874] [INFO] DFAST_QC result json was written to GCF_005952805.1_ASM595280v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:27,875] [INFO] DFAST_QC completed!
[2024-01-24 14:24:27,875] [INFO] Total running time: 0h1m54s