[2024-01-25 20:18:05,559] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:18:05,562] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:18:05,562] [INFO] DQC Reference Directory: /var/lib/cwl/stg82a2a7c7-bdc7-43dc-a297-1fe5640130a8/dqc_reference
[2024-01-25 20:18:06,693] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:18:06,693] [INFO] Task started: Prodigal
[2024-01-25 20:18:06,694] [INFO] Running command: gunzip -c /var/lib/cwl/stg36635fa2-0f42-40cf-80bc-a40537eb714e/GCF_000372845.1_ASM37284v1_genomic.fna.gz | prodigal -d GCF_000372845.1_ASM37284v1_genomic.fna/cds.fna -a GCF_000372845.1_ASM37284v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:16,567] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:16,567] [INFO] Task started: HMMsearch
[2024-01-25 20:18:16,567] [INFO] Running command: hmmsearch --tblout GCF_000372845.1_ASM37284v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82a2a7c7-bdc7-43dc-a297-1fe5640130a8/dqc_reference/reference_markers.hmm GCF_000372845.1_ASM37284v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:16,827] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:16,828] [INFO] Found 6/6 markers.
[2024-01-25 20:18:16,858] [INFO] Query marker FASTA was written to GCF_000372845.1_ASM37284v1_genomic.fna/markers.fasta
[2024-01-25 20:18:16,858] [INFO] Task started: Blastn
[2024-01-25 20:18:16,858] [INFO] Running command: blastn -query GCF_000372845.1_ASM37284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82a2a7c7-bdc7-43dc-a297-1fe5640130a8/dqc_reference/reference_markers.fasta -out GCF_000372845.1_ASM37284v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:17,637] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:17,640] [INFO] Selected 19 target genomes.
[2024-01-25 20:18:17,640] [INFO] Target genome list was writen to GCF_000372845.1_ASM37284v1_genomic.fna/target_genomes.txt
[2024-01-25 20:18:17,651] [INFO] Task started: fastANI
[2024-01-25 20:18:17,651] [INFO] Running command: fastANI --query /var/lib/cwl/stg36635fa2-0f42-40cf-80bc-a40537eb714e/GCF_000372845.1_ASM37284v1_genomic.fna.gz --refList GCF_000372845.1_ASM37284v1_genomic.fna/target_genomes.txt --output GCF_000372845.1_ASM37284v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:18:36,011] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:36,011] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82a2a7c7-bdc7-43dc-a297-1fe5640130a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:18:36,011] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82a2a7c7-bdc7-43dc-a297-1fe5640130a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:18:36,023] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:18:36,023] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:18:36,024] [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
Methylocystis rosea	strain=SV97	GCA_000372845.1	173366	173366	type	True	100.0	1303	1303	95	conclusive
Methylocystis silviterrae	strain=FS	GCA_013350005.1	2743612	2743612	type	True	93.002	982	1303	95	below_threshold
Methylocystis hirsuta	strain=CSC1	GCA_003722355.1	369798	369798	type	True	92.3015	1027	1303	95	below_threshold
Methylocystis parvus	strain=OBBP	GCA_000283235.1	134	134	type	True	79.7704	596	1303	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_009811675.1	428	428	type	True	79.1078	451	1303	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_003113265.1	428	428	type	True	79.106	428	1303	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	79.0335	479	1303	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	78.9711	482	1303	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	77.0179	203	1303	95	below_threshold
Bradyrhizobium arachidis	strain=CCBAU 051107	GCA_015291705.1	858423	858423	type	True	76.877	218	1303	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	76.8751	166	1303	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.8379	222	1303	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	76.8042	179	1303	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_016653375.1	34017	34017	type	True	76.7946	180	1303	95	below_threshold
Afifella marina	strain=DSM 2698	GCA_016584015.1	1080	1080	type	True	76.7873	112	1303	95	below_threshold
Methylobacterium oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	76.7771	211	1303	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	76.7624	177	1303	95	below_threshold
Afifella marina	strain=DSM 2698	GCA_900102695.1	1080	1080	type	True	76.7508	111	1303	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	76.5655	169	1303	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:18:36,025] [INFO] DFAST Taxonomy check result was written to GCF_000372845.1_ASM37284v1_genomic.fna/tc_result.tsv
[2024-01-25 20:18:36,025] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:18:36,025] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:18:36,026] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82a2a7c7-bdc7-43dc-a297-1fe5640130a8/dqc_reference/checkm_data
[2024-01-25 20:18:36,027] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:18:36,069] [INFO] Task started: CheckM
[2024-01-25 20:18:36,069] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000372845.1_ASM37284v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000372845.1_ASM37284v1_genomic.fna/checkm_input GCF_000372845.1_ASM37284v1_genomic.fna/checkm_result
[2024-01-25 20:19:07,293] [INFO] Task succeeded: CheckM
[2024-01-25 20:19:07,294] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:19:07,331] [INFO] ===== Completeness check finished =====
[2024-01-25 20:19:07,331] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:19:07,332] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000372845.1_ASM37284v1_genomic.fna/markers.fasta)
[2024-01-25 20:19:07,332] [INFO] Task started: Blastn
[2024-01-25 20:19:07,332] [INFO] Running command: blastn -query GCF_000372845.1_ASM37284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82a2a7c7-bdc7-43dc-a297-1fe5640130a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000372845.1_ASM37284v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:08,713] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:08,716] [INFO] Selected 12 target genomes.
[2024-01-25 20:19:08,716] [INFO] Target genome list was writen to GCF_000372845.1_ASM37284v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:19:08,728] [INFO] Task started: fastANI
[2024-01-25 20:19:08,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg36635fa2-0f42-40cf-80bc-a40537eb714e/GCF_000372845.1_ASM37284v1_genomic.fna.gz --refList GCF_000372845.1_ASM37284v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000372845.1_ASM37284v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:19:19,988] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:19,998] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:19:19,998] [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_000372845.1	s__Methylocystis rosea	100.0	1303	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	95.62	95.24	0.85	0.83	5	conclusive
GCA_009773555.1	s__Methylocystis sp009773555	94.5026	1050	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	99.69	99.47	0.95	0.93	3	-
GCF_015709525.1	s__Methylocystis sp015709525	94.0962	1102	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015709515.1	s__Methylocystis sp015709515	93.9224	1114	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013350005.1	s__Methylocystis sp013350005	93.002	982	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	96.16	96.16	0.88	0.88	2	-
GCF_003722355.1	s__Methylocystis hirsuta	92.2702	1028	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	95.95	95.95	0.95	0.95	2	-
GCF_000304315.1	s__Methylocystis sp000304315	91.7537	1003	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869595.1	s__Methylocystis sp016869595	85.0722	808	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379125.1	s__Methylosinus sp000379125	78.8672	477	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793635.1	s__JAEUMD01 sp016793635	76.9454	106	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__JAEUMD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006442205.1	s__Mesorhizobium sp006442205	76.6785	168	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642695.1	s__Parvibaculum sp017642695	76.5531	97	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.96	99.92	0.99	0.97	4	-
--------------------------------------------------------------------------------
[2024-01-25 20:19:19,999] [INFO] GTDB search result was written to GCF_000372845.1_ASM37284v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:19:20,000] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:19:20,004] [INFO] DFAST_QC result json was written to GCF_000372845.1_ASM37284v1_genomic.fna/dqc_result.json
[2024-01-25 20:19:20,004] [INFO] DFAST_QC completed!
[2024-01-25 20:19:20,004] [INFO] Total running time: 0h1m14s