[2024-01-24 12:25:20,575] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:25:20,577] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:25:20,578] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8b10577-49d9-4d2c-9010-1a7a7a3d1954/dqc_reference
[2024-01-24 12:25:21,801] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:25:21,802] [INFO] Task started: Prodigal
[2024-01-24 12:25:21,802] [INFO] Running command: gunzip -c /var/lib/cwl/stg38c53e1e-8e07-4e6e-b076-458300229f72/GCF_007474605.1_ASM747460v1_genomic.fna.gz | prodigal -d GCF_007474605.1_ASM747460v1_genomic.fna/cds.fna -a GCF_007474605.1_ASM747460v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:25:38,888] [INFO] Task succeeded: Prodigal
[2024-01-24 12:25:38,889] [INFO] Task started: HMMsearch
[2024-01-24 12:25:38,889] [INFO] Running command: hmmsearch --tblout GCF_007474605.1_ASM747460v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8b10577-49d9-4d2c-9010-1a7a7a3d1954/dqc_reference/reference_markers.hmm GCF_007474605.1_ASM747460v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:25:39,209] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:25:39,210] [INFO] Found 6/6 markers.
[2024-01-24 12:25:39,259] [INFO] Query marker FASTA was written to GCF_007474605.1_ASM747460v1_genomic.fna/markers.fasta
[2024-01-24 12:25:39,260] [INFO] Task started: Blastn
[2024-01-24 12:25:39,260] [INFO] Running command: blastn -query GCF_007474605.1_ASM747460v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8b10577-49d9-4d2c-9010-1a7a7a3d1954/dqc_reference/reference_markers.fasta -out GCF_007474605.1_ASM747460v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:40,045] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:40,049] [INFO] Selected 23 target genomes.
[2024-01-24 12:25:40,050] [INFO] Target genome list was writen to GCF_007474605.1_ASM747460v1_genomic.fna/target_genomes.txt
[2024-01-24 12:25:40,058] [INFO] Task started: fastANI
[2024-01-24 12:25:40,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg38c53e1e-8e07-4e6e-b076-458300229f72/GCF_007474605.1_ASM747460v1_genomic.fna.gz --refList GCF_007474605.1_ASM747460v1_genomic.fna/target_genomes.txt --output GCF_007474605.1_ASM747460v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:26:01,349] [INFO] Task succeeded: fastANI
[2024-01-24 12:26:01,350] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8b10577-49d9-4d2c-9010-1a7a7a3d1954/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:26:01,350] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8b10577-49d9-4d2c-9010-1a7a7a3d1954/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:26:01,371] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:26:01,371] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:26:01,372] [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
Rhodoligotrophos appendicifer	strain=120-1	GCA_007474605.1	987056	987056	type	True	100.0	1845	1848	95	conclusive
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	77.7761	415	1848	95	below_threshold
Kaustia mangrovi	strain=R1DC25	GCA_015482775.1	2593653	2593653	type	True	77.2368	234	1848	95	below_threshold
Methyloceanibacter superfactus	strain=R-67175	GCA_001723305.1	1774969	1774969	type	True	76.6373	90	1848	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.577	151	1848	95	below_threshold
Aureimonas endophytica	strain=CGMCC 1.15367	GCA_014642635.1	2027858	2027858	type	True	76.4296	169	1848	95	below_threshold
Aestuariivirga litoralis	strain=KCTC 52945	GCA_003234965.1	2650924	2650924	type	True	76.3347	153	1848	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	76.2523	154	1848	95	below_threshold
Methylobacterium currus	strain=PR1016A	GCA_003058325.1	2051553	2051553	type	True	76.2144	173	1848	95	below_threshold
Xanthobacter autotrophicus	strain=DSM 432	GCA_005871085.1	280	280	type	True	76.2125	131	1848	95	below_threshold
Bosea robiniae	strain=DSM 26672	GCA_900102525.1	1036780	1036780	type	True	76.2101	174	1848	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	76.2039	85	1848	95	below_threshold
Parvibaculum sedimenti	strain=HXT-9	GCA_009184905.1	2608632	2608632	type	True	76.1783	101	1848	95	below_threshold
Bradyrhizobium neotropicale	strain=BR 10247	GCA_001641695.1	1497615	1497615	type	True	76.1583	166	1848	95	below_threshold
Bradyrhizobium rifense	strain=CTAW71	GCA_008123425.1	515499	515499	type	True	76.0856	159	1848	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	76.0844	171	1848	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.0559	178	1848	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	75.9913	154	1848	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	75.9698	193	1848	95	below_threshold
Bradyrhizobium tropiciagri	strain=SEMIA 6148	GCA_001189845.1	312253	312253	type	True	75.9045	167	1848	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	75.7849	99	1848	95	below_threshold
Cohaesibacter haloalkalitolerans	strain=JC131	GCA_003574655.1	1162980	1162980	type	True	75.7487	54	1848	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:26:01,373] [INFO] DFAST Taxonomy check result was written to GCF_007474605.1_ASM747460v1_genomic.fna/tc_result.tsv
[2024-01-24 12:26:01,374] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:26:01,374] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:26:01,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8b10577-49d9-4d2c-9010-1a7a7a3d1954/dqc_reference/checkm_data
[2024-01-24 12:26:01,376] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:26:01,430] [INFO] Task started: CheckM
[2024-01-24 12:26:01,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007474605.1_ASM747460v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007474605.1_ASM747460v1_genomic.fna/checkm_input GCF_007474605.1_ASM747460v1_genomic.fna/checkm_result
[2024-01-24 12:26:54,047] [INFO] Task succeeded: CheckM
[2024-01-24 12:26:54,049] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:26:54,075] [INFO] ===== Completeness check finished =====
[2024-01-24 12:26:54,076] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:26:54,076] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007474605.1_ASM747460v1_genomic.fna/markers.fasta)
[2024-01-24 12:26:54,077] [INFO] Task started: Blastn
[2024-01-24 12:26:54,077] [INFO] Running command: blastn -query GCF_007474605.1_ASM747460v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8b10577-49d9-4d2c-9010-1a7a7a3d1954/dqc_reference/reference_markers_gtdb.fasta -out GCF_007474605.1_ASM747460v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:26:55,494] [INFO] Task succeeded: Blastn
[2024-01-24 12:26:55,498] [INFO] Selected 24 target genomes.
[2024-01-24 12:26:55,499] [INFO] Target genome list was writen to GCF_007474605.1_ASM747460v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:26:55,636] [INFO] Task started: fastANI
[2024-01-24 12:26:55,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg38c53e1e-8e07-4e6e-b076-458300229f72/GCF_007474605.1_ASM747460v1_genomic.fna.gz --refList GCF_007474605.1_ASM747460v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007474605.1_ASM747460v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:27:14,929] [INFO] Task succeeded: fastANI
[2024-01-24 12:27:14,952] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:27:14,953] [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_007474605.1	s__Rhodoligotrophos appendicifer	100.0	1845	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Im1;g__Rhodoligotrophos	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005281615.1	s__Rhodoligotrophos sp005281615	77.7941	412	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Im1;g__Rhodoligotrophos	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015482775.1	s__Kaustia mangrovi	77.2368	234	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Im1;g__Kaustia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799445.1	s__Bradyrhizobium sp004799445	76.7743	87	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576695.1	s__Nordella sp003576695	76.7502	195	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869535.1	s__Methyloceanibacter sp016869535	76.6003	80	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005502925.1	s__Nordella sp005502925	76.536	197	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella	95.0	100.00	100.00	1.00	1.00	3	-
GCA_017849325.1	s__Xanthobacter autotrophicus_B	76.38	88	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003234965.1	s__Aestuariivirga litoralis	76.3347	153	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Aestuariivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185245.1	s__Aestuariivirga sp016185245	76.3179	119	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Aestuariivirga	95.0	99.81	99.81	0.97	0.97	2	-
GCF_016595235.1	s__Nordella sp016595235	76.2336	204	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102525.1	s__Bosea robiniae	76.2101	174	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	97.62	97.45	0.92	0.88	4	-
GCF_001641695.1	s__Bradyrhizobium neotropicale	76.1696	165	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.90	97.90	0.88	0.88	2	-
GCA_002700095.1	s__Jiella sp002700095	76.1457	165	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900298995.1	s__Aestuariivirga sp900298995	76.1167	110	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Aestuariivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745635.1	s__Methylobacterium sp004745635	76.0559	178	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019216885.1	s__Methylobacterium sp019216885	76.0295	163	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006151805.1	s__Methylobacterium sp006151805	75.961	193	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899065.1	s__Devosia_A sp001899065	75.9518	81	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	98.96	98.00	0.93	0.88	3	-
GCA_002841195.1	s__Parvibaculum sp002841195	75.8866	93	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016774605.1	s__Stappia sp016774605	75.8713	100	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930095.1	s__Aestuariivirga sp903930095	75.8209	87	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Aestuariivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963405.1	s__Methylocystis sp003963405	75.7503	85	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014380485.1	s__Methyloceanibacter sp014380485	75.4785	62	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:27:14,954] [INFO] GTDB search result was written to GCF_007474605.1_ASM747460v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:27:14,955] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:27:14,960] [INFO] DFAST_QC result json was written to GCF_007474605.1_ASM747460v1_genomic.fna/dqc_result.json
[2024-01-24 12:27:14,960] [INFO] DFAST_QC completed!
[2024-01-24 12:27:14,960] [INFO] Total running time: 0h1m54s