[2024-01-24 14:31:14,780] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:14,782] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:14,783] [INFO] DQC Reference Directory: /var/lib/cwl/stg1bfbbcb8-2a99-481d-a1f3-f552ae1e689d/dqc_reference
[2024-01-24 14:31:16,128] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:16,128] [INFO] Task started: Prodigal
[2024-01-24 14:31:16,129] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd0d0bd4-4f5c-433e-ad50-0bfed6c8f6d9/GCF_003590835.1_ASM359083v1_genomic.fna.gz | prodigal -d GCF_003590835.1_ASM359083v1_genomic.fna/cds.fna -a GCF_003590835.1_ASM359083v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:34,281] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:34,282] [INFO] Task started: HMMsearch
[2024-01-24 14:31:34,282] [INFO] Running command: hmmsearch --tblout GCF_003590835.1_ASM359083v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1bfbbcb8-2a99-481d-a1f3-f552ae1e689d/dqc_reference/reference_markers.hmm GCF_003590835.1_ASM359083v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:34,619] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:34,621] [INFO] Found 6/6 markers.
[2024-01-24 14:31:34,670] [INFO] Query marker FASTA was written to GCF_003590835.1_ASM359083v1_genomic.fna/markers.fasta
[2024-01-24 14:31:34,670] [INFO] Task started: Blastn
[2024-01-24 14:31:34,670] [INFO] Running command: blastn -query GCF_003590835.1_ASM359083v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bfbbcb8-2a99-481d-a1f3-f552ae1e689d/dqc_reference/reference_markers.fasta -out GCF_003590835.1_ASM359083v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:35,781] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:35,787] [INFO] Selected 25 target genomes.
[2024-01-24 14:31:35,787] [INFO] Target genome list was writen to GCF_003590835.1_ASM359083v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:35,796] [INFO] Task started: fastANI
[2024-01-24 14:31:35,797] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd0d0bd4-4f5c-433e-ad50-0bfed6c8f6d9/GCF_003590835.1_ASM359083v1_genomic.fna.gz --refList GCF_003590835.1_ASM359083v1_genomic.fna/target_genomes.txt --output GCF_003590835.1_ASM359083v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:59,726] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:59,727] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1bfbbcb8-2a99-481d-a1f3-f552ae1e689d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:59,727] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1bfbbcb8-2a99-481d-a1f3-f552ae1e689d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:59,747] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:31:59,747] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:31:59,748] [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
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	80.0853	484	1678	95	below_threshold
Herbaspirillum robiniae	strain=HZ10	GCA_002213415.1	2014887	2014887	type	True	79.8732	493	1678	95	below_threshold
Herbaspirillum chlorophenolicum	strain=CPW301	GCA_001189955.1	211589	211589	type	True	79.8667	447	1678	95	below_threshold
Herbaspirillum chlorophenolicum	strain=NBRC 102525	GCA_001571165.1	211589	211589	type	True	79.8455	444	1678	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_001040945.1	964	964	type	True	79.807	438	1678	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	79.7428	408	1678	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	79.7237	445	1678	95	below_threshold
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	79.679	454	1678	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_013180375.1	964	964	type	True	79.5711	440	1678	95	below_threshold
Noviherbaspirillum cavernae	strain=K2R10-39	GCA_003590875.1	2320862	2320862	type	True	79.5393	439	1678	95	below_threshold
Oxalicibacterium solurbis	strain=CCM 7664	GCA_014635845.1	69280	69280	type	True	79.5004	398	1678	95	below_threshold
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	79.4933	458	1678	95	below_threshold
Noviherbaspirillum saxi	strain=K1R23-30	GCA_003591035.1	2320863	2320863	type	True	79.4733	470	1678	95	below_threshold
Herbaspirillum huttiense subsp. putei	strain=IAM 15032	GCA_000478365.1	230311	863372	type	True	79.4705	448	1678	95	below_threshold
Herbaspirillum aquaticum	strain=IEH 4430	GCA_002213425.1	568783	568783	type	True	79.3974	436	1678	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	79.3531	465	1678	95	below_threshold
Noviherbaspirillum aerium	strain=122213-3	GCA_008929045.1	2588497	2588497	type	True	79.3334	470	1678	95	below_threshold
Herbaspirillum rubrisubalbicans	strain=DSM 11543	GCA_003719195.1	80842	80842	type	True	79.2392	441	1678	95	below_threshold
Massilia atriviolacea	strain=SOD	GCA_003953935.1	2495579	2495579	type	True	79.2154	502	1678	95	below_threshold
Massilia mucilaginosa	strain=CCM 8733	GCA_011682145.1	2609282	2609282	type	True	79.1838	459	1678	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	79.1191	448	1678	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	79.0606	432	1678	95	below_threshold
Herbaspirillum rubrisubalbicans	strain=NBRC 102523	GCA_001591225.1	80842	80842	type	True	79.0306	429	1678	95	below_threshold
Collimonas arenae	strain=Ter10	GCA_001584165.1	279058	279058	type	True	78.995	370	1678	95	below_threshold
Collimonas silvisoli	strain=RXD178	GCA_018305005.1	2825884	2825884	type	True	78.912	383	1678	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:59,749] [INFO] DFAST Taxonomy check result was written to GCF_003590835.1_ASM359083v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:59,750] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:59,750] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:59,750] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1bfbbcb8-2a99-481d-a1f3-f552ae1e689d/dqc_reference/checkm_data
[2024-01-24 14:31:59,751] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:59,799] [INFO] Task started: CheckM
[2024-01-24 14:31:59,800] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003590835.1_ASM359083v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003590835.1_ASM359083v1_genomic.fna/checkm_input GCF_003590835.1_ASM359083v1_genomic.fna/checkm_result
[2024-01-24 14:32:50,146] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:50,147] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:50,171] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:50,171] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:50,172] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003590835.1_ASM359083v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:50,172] [INFO] Task started: Blastn
[2024-01-24 14:32:50,172] [INFO] Running command: blastn -query GCF_003590835.1_ASM359083v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bfbbcb8-2a99-481d-a1f3-f552ae1e689d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003590835.1_ASM359083v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:52,050] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:52,061] [INFO] Selected 14 target genomes.
[2024-01-24 14:32:52,061] [INFO] Target genome list was writen to GCF_003590835.1_ASM359083v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:52,072] [INFO] Task started: fastANI
[2024-01-24 14:32:52,072] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd0d0bd4-4f5c-433e-ad50-0bfed6c8f6d9/GCF_003590835.1_ASM359083v1_genomic.fna.gz --refList GCF_003590835.1_ASM359083v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003590835.1_ASM359083v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:07,063] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:07,080] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:07,080] [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_003590835.1	s__Paucimonas sp003590835	100.0	1676	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004114795.1	s__Paucimonas sp004114795	85.0728	895	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003537575.1	s__Paucimonas sp003537575	84.3931	832	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342585.1	s__Paucimonas lemoignei	82.0628	746	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744395.1	s__Herbaspirillum sp017744395	80.2973	478	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009914615.1	s__Herbaspirillum frisingense_B	79.9381	441	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007874125.1	s__Noviherbaspirillum sp007874125	79.8804	529	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001040945.1	s__Herbaspirillum seropedicae	79.7289	438	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.53	96.09	0.94	0.89	6	-
GCF_018304945.1	s__Collimonas sp018304945	79.6884	454	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	98.22	98.22	0.87	0.87	2	-
GCF_000221045.1	s__Collimonas fungivorans_A	79.6423	471	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	95.12	95.12	0.85	0.85	2	-
GCF_900112135.1	s__Collimonas sp900112135	79.5496	450	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	96.00	96.00	0.87	0.87	2	-
GCF_008929045.1	s__Noviherbaspirillum aerium	79.2873	474	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003719195.1	s__Herbaspirillum rubrisubalbicans	79.2807	439	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.49	96.58	0.87	0.83	8	-
GCF_900114705.1	s__Rugamonas rubra	79.2554	530	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	96.24	96.24	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:07,082] [INFO] GTDB search result was written to GCF_003590835.1_ASM359083v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:07,083] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:07,087] [INFO] DFAST_QC result json was written to GCF_003590835.1_ASM359083v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:07,087] [INFO] DFAST_QC completed!
[2024-01-24 14:33:07,087] [INFO] Total running time: 0h1m52s