[2024-01-24 13:57:13,703] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:13,705] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:13,705] [INFO] DQC Reference Directory: /var/lib/cwl/stga0ea7b33-e1f9-4e48-9e47-effb0aba3a7e/dqc_reference
[2024-01-24 13:57:14,938] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:14,938] [INFO] Task started: Prodigal
[2024-01-24 13:57:14,939] [INFO] Running command: gunzip -c /var/lib/cwl/stg7deebe7c-9676-4cc3-bb81-19c9092ba8df/GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna/cds.fna -a GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:27,768] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:27,768] [INFO] Task started: HMMsearch
[2024-01-24 13:57:27,768] [INFO] Running command: hmmsearch --tblout GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0ea7b33-e1f9-4e48-9e47-effb0aba3a7e/dqc_reference/reference_markers.hmm GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:28,052] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:28,054] [INFO] Found 6/6 markers.
[2024-01-24 13:57:28,095] [INFO] Query marker FASTA was written to GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:57:28,095] [INFO] Task started: Blastn
[2024-01-24 13:57:28,095] [INFO] Running command: blastn -query GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga0ea7b33-e1f9-4e48-9e47-effb0aba3a7e/dqc_reference/reference_markers.fasta -out GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:28,979] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:28,983] [INFO] Selected 19 target genomes.
[2024-01-24 13:57:28,984] [INFO] Target genome list was writen to GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:57:28,991] [INFO] Task started: fastANI
[2024-01-24 13:57:28,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg7deebe7c-9676-4cc3-bb81-19c9092ba8df/GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna.gz --refList GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:45,217] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:45,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0ea7b33-e1f9-4e48-9e47-effb0aba3a7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:45,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0ea7b33-e1f9-4e48-9e47-effb0aba3a7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:45,232] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:45,232] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:45,233] [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
Hyphomicrobium facile	strain=DSM 1565	GCA_900116175.1	51670	51670	type	True	100.0	1473	1473	95	conclusive
Hyphomicrobium denitrificans	strain=ATCC 51888	GCA_000143145.1	53399	53399	type	True	79.697	527	1473	95	below_threshold
Hyphomicrobium album	strain=XQ2	GCA_009708035.1	2665159	2665159	type	True	77.7552	259	1473	95	below_threshold
Hyphomicrobium nitrativorans	strain=NL23	GCA_000503895.1	1427356	1427356	type	True	77.7471	218	1473	95	below_threshold
Hyphomicrobium zavarzinii	strain=ZV-622	GCA_000383415.1	48292	48292	type	True	77.4738	256	1473	95	below_threshold
Hyphomicrobium sulfonivorans	strain=S1	GCA_016125985.1	121290	121290	type	True	77.1385	201	1473	95	below_threshold
Hyphomicrobium sulfonivorans	strain=S1	GCA_013306565.1	121290	121290	type	True	77.0979	200	1473	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	76.9435	136	1473	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	76.8789	114	1473	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	76.8562	132	1473	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	76.8165	132	1473	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	76.7542	120	1473	95	below_threshold
Rhizobium indicum	strain=JKLM 12A2	GCA_005862305.2	2583231	2583231	type	True	76.708	124	1473	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	76.6574	110	1473	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	76.6325	143	1473	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	76.6013	145	1473	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	76.5926	122	1473	95	below_threshold
Rhodopseudomonas faecalis	strain=JCM 11668	GCA_003217325.1	99655	99655	type	True	76.5053	124	1473	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.3907	149	1473	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:45,234] [INFO] DFAST Taxonomy check result was written to GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:57:45,235] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:45,235] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:45,235] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0ea7b33-e1f9-4e48-9e47-effb0aba3a7e/dqc_reference/checkm_data
[2024-01-24 13:57:45,236] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:45,283] [INFO] Task started: CheckM
[2024-01-24 13:57:45,284] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna/checkm_input GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:58:27,410] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:27,412] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:27,436] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:27,436] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:27,437] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:58:27,437] [INFO] Task started: Blastn
[2024-01-24 13:58:27,438] [INFO] Running command: blastn -query GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga0ea7b33-e1f9-4e48-9e47-effb0aba3a7e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:29,246] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:29,250] [INFO] Selected 7 target genomes.
[2024-01-24 13:58:29,250] [INFO] Target genome list was writen to GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:29,256] [INFO] Task started: fastANI
[2024-01-24 13:58:29,257] [INFO] Running command: fastANI --query /var/lib/cwl/stg7deebe7c-9676-4cc3-bb81-19c9092ba8df/GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna.gz --refList GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:37,055] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:37,062] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:37,062] [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_900116175.1	s__Hyphomicrobium facile	100.0	1472	1473	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000384335.2	s__Hyphomicrobium sp000384335	84.9008	1074	1473	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003987725.1	s__Hyphomicrobium sp003987725	84.1893	1028	1473	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	98.09	98.09	0.97	0.97	2	-
GCA_018242295.1	s__Hyphomicrobium sp018242295	83.9801	1007	1473	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	97.15	97.15	0.97	0.97	2	-
GCF_000253295.1	s__Hyphomicrobium sp000253295	80.087	686	1473	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	99.46	99.46	0.96	0.96	2	-
GCA_018242215.1	s__Hyphomicrobium sp018242215	79.9149	620	1473	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003987855.1	s__Hyphomicrobium sp003987855	79.3349	568	1473	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:37,064] [INFO] GTDB search result was written to GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:37,064] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:37,069] [INFO] DFAST_QC result json was written to GCF_900116175.1_IMG-taxon_2636416034_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:58:37,069] [INFO] DFAST_QC completed!
[2024-01-24 13:58:37,069] [INFO] Total running time: 0h1m23s