[2024-01-24 11:35:10,354] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:10,355] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:10,356] [INFO] DQC Reference Directory: /var/lib/cwl/stg85aa3963-ba05-4495-9779-bfaf34873de8/dqc_reference
[2024-01-24 11:35:11,674] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:11,674] [INFO] Task started: Prodigal
[2024-01-24 11:35:11,675] [INFO] Running command: gunzip -c /var/lib/cwl/stgf59c2c1f-bacb-42b9-8c24-0246330fb188/GCF_002211445.1_ASM221144v1_genomic.fna.gz | prodigal -d GCF_002211445.1_ASM221144v1_genomic.fna/cds.fna -a GCF_002211445.1_ASM221144v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:31,128] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:31,129] [INFO] Task started: HMMsearch
[2024-01-24 11:35:31,129] [INFO] Running command: hmmsearch --tblout GCF_002211445.1_ASM221144v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85aa3963-ba05-4495-9779-bfaf34873de8/dqc_reference/reference_markers.hmm GCF_002211445.1_ASM221144v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:31,510] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:31,511] [INFO] Found 6/6 markers.
[2024-01-24 11:35:31,570] [INFO] Query marker FASTA was written to GCF_002211445.1_ASM221144v1_genomic.fna/markers.fasta
[2024-01-24 11:35:31,570] [INFO] Task started: Blastn
[2024-01-24 11:35:31,570] [INFO] Running command: blastn -query GCF_002211445.1_ASM221144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85aa3963-ba05-4495-9779-bfaf34873de8/dqc_reference/reference_markers.fasta -out GCF_002211445.1_ASM221144v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:32,510] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:32,513] [INFO] Selected 17 target genomes.
[2024-01-24 11:35:32,514] [INFO] Target genome list was writen to GCF_002211445.1_ASM221144v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:32,520] [INFO] Task started: fastANI
[2024-01-24 11:35:32,520] [INFO] Running command: fastANI --query /var/lib/cwl/stgf59c2c1f-bacb-42b9-8c24-0246330fb188/GCF_002211445.1_ASM221144v1_genomic.fna.gz --refList GCF_002211445.1_ASM221144v1_genomic.fna/target_genomes.txt --output GCF_002211445.1_ASM221144v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:51,402] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:51,403] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85aa3963-ba05-4495-9779-bfaf34873de8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:51,403] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85aa3963-ba05-4495-9779-bfaf34873de8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:51,416] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:51,416] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:51,417] [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 denitrificans	strain=TSA40	GCA_002211445.1	1968433	1968433	type	True	100.0	1898	1906	95	conclusive
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	81.1517	732	1906	95	below_threshold
Noviherbaspirillum malthae	strain=CC-AFH3	GCA_015352985.1	1260987	1260987	type	True	80.9939	808	1906	95	below_threshold
Noviherbaspirillum galbum	strain=17J57-3	GCA_010974945.1	2709383	2709383	type	True	80.6629	710	1906	95	below_threshold
Noviherbaspirillum aerium	strain=122213-3	GCA_008929045.1	2588497	2588497	type	True	80.653	731	1906	95	below_threshold
Noviherbaspirillum autotrophicum	strain=TSA66	GCA_000818395.1	709839	709839	type	True	80.6384	736	1906	95	below_threshold
Noviherbaspirillum humi	strain=U15	GCA_900188095.1	1688639	1688639	type	True	80.451	610	1906	95	below_threshold
Noviherbaspirillum cavernae	strain=K2R10-39	GCA_003590875.1	2320862	2320862	type	True	79.8619	604	1906	95	below_threshold
Noviherbaspirillum saxi	strain=K1R23-30	GCA_003591035.1	2320863	2320863	type	True	79.8304	660	1906	95	below_threshold
Oxalicibacterium flavum	strain=CCM 7086	GCA_014635065.1	179467	179467	type	True	79.7309	450	1906	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	79.684	404	1906	95	below_threshold
Herbaspirillum robiniae	strain=HZ10	GCA_002213415.1	2014887	2014887	type	True	79.6654	559	1906	95	below_threshold
Oxalicibacterium solurbis	strain=CCM 7664	GCA_014635845.1	69280	69280	type	True	79.3336	403	1906	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	79.2902	482	1906	95	below_threshold
Herbaspirillum rhizosphaerae	strain=UMS-37	GCA_001189965.1	346179	346179	type	True	79.08	464	1906	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	79.0296	548	1906	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	78.8106	418	1906	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:51,418] [INFO] DFAST Taxonomy check result was written to GCF_002211445.1_ASM221144v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:51,419] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:51,419] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:51,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85aa3963-ba05-4495-9779-bfaf34873de8/dqc_reference/checkm_data
[2024-01-24 11:35:51,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:51,475] [INFO] Task started: CheckM
[2024-01-24 11:35:51,476] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002211445.1_ASM221144v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002211445.1_ASM221144v1_genomic.fna/checkm_input GCF_002211445.1_ASM221144v1_genomic.fna/checkm_result
[2024-01-24 11:36:49,295] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:49,297] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:49,322] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:49,322] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:49,323] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002211445.1_ASM221144v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:49,323] [INFO] Task started: Blastn
[2024-01-24 11:36:49,323] [INFO] Running command: blastn -query GCF_002211445.1_ASM221144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85aa3963-ba05-4495-9779-bfaf34873de8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002211445.1_ASM221144v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:51,061] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:51,064] [INFO] Selected 14 target genomes.
[2024-01-24 11:36:51,065] [INFO] Target genome list was writen to GCF_002211445.1_ASM221144v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:51,077] [INFO] Task started: fastANI
[2024-01-24 11:36:51,077] [INFO] Running command: fastANI --query /var/lib/cwl/stgf59c2c1f-bacb-42b9-8c24-0246330fb188/GCF_002211445.1_ASM221144v1_genomic.fna.gz --refList GCF_002211445.1_ASM221144v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002211445.1_ASM221144v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:08,074] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:08,088] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:08,089] [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_002211445.1	s__Noviherbaspirillum denitrificans	100.0	1899	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007874125.1	s__Noviherbaspirillum sp007874125	81.0186	779	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015352985.1	s__Noviherbaspirillum malthae	81.0031	807	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004570315.1	s__Noviherbaspirillum sp004570315	80.7815	596	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010974945.1	s__Noviherbaspirillum galbum	80.6488	711	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000818395.1	s__Noviherbaspirillum autotrophicum	80.6448	734	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008929045.1	s__Noviherbaspirillum aerium	80.633	732	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188095.1	s__Noviherbaspirillum humi	80.4188	614	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004804275.1	s__Noviherbaspirillum sp004804275	80.3343	771	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744395.1	s__Herbaspirillum sp017744395	80.1197	508	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002213415.1	s__Herbaspirillum robiniae	79.6289	564	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.55	98.54	0.93	0.92	3	-
GCF_004563925.1	s__Herbaspirillum sp004563925	79.2913	472	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	100.00	99.99	0.98	0.95	4	-
GCF_001189965.1	s__Herbaspirillum rhizosphaerae	79.0704	465	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001584185.1	s__Collimonas pratensis	78.8106	418	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	98.16	98.11	0.88	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:08,090] [INFO] GTDB search result was written to GCF_002211445.1_ASM221144v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:08,091] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:08,094] [INFO] DFAST_QC result json was written to GCF_002211445.1_ASM221144v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:08,095] [INFO] DFAST_QC completed!
[2024-01-24 11:37:08,095] [INFO] Total running time: 0h1m58s