[2024-01-24 13:57:31,336] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:31,339] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:31,339] [INFO] DQC Reference Directory: /var/lib/cwl/stgab018e1c-0fad-4516-912d-fc41e1b63d12/dqc_reference
[2024-01-24 13:57:32,756] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:32,757] [INFO] Task started: Prodigal
[2024-01-24 13:57:32,758] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d830110-4718-4dfa-8a0a-5d650ef4bde1/GCF_030062355.1_ASM3006235v1_genomic.fna.gz | prodigal -d GCF_030062355.1_ASM3006235v1_genomic.fna/cds.fna -a GCF_030062355.1_ASM3006235v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:47,169] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:47,170] [INFO] Task started: HMMsearch
[2024-01-24 13:57:47,170] [INFO] Running command: hmmsearch --tblout GCF_030062355.1_ASM3006235v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab018e1c-0fad-4516-912d-fc41e1b63d12/dqc_reference/reference_markers.hmm GCF_030062355.1_ASM3006235v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:47,483] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:47,484] [INFO] Found 6/6 markers.
[2024-01-24 13:57:47,531] [INFO] Query marker FASTA was written to GCF_030062355.1_ASM3006235v1_genomic.fna/markers.fasta
[2024-01-24 13:57:47,532] [INFO] Task started: Blastn
[2024-01-24 13:57:47,532] [INFO] Running command: blastn -query GCF_030062355.1_ASM3006235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab018e1c-0fad-4516-912d-fc41e1b63d12/dqc_reference/reference_markers.fasta -out GCF_030062355.1_ASM3006235v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:48,554] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:48,558] [INFO] Selected 12 target genomes.
[2024-01-24 13:57:48,558] [INFO] Target genome list was writen to GCF_030062355.1_ASM3006235v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:48,563] [INFO] Task started: fastANI
[2024-01-24 13:57:48,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d830110-4718-4dfa-8a0a-5d650ef4bde1/GCF_030062355.1_ASM3006235v1_genomic.fna.gz --refList GCF_030062355.1_ASM3006235v1_genomic.fna/target_genomes.txt --output GCF_030062355.1_ASM3006235v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:02,848] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:02,848] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab018e1c-0fad-4516-912d-fc41e1b63d12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:02,848] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab018e1c-0fad-4516-912d-fc41e1b63d12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:02,859] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:02,859] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:02,860] [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
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	99.9866	1720	1726	95	conclusive
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	99.977	1650	1726	95	conclusive
Methylosinus sporium	strain=DSM 17706	GCA_009811675.1	428	428	type	True	83.6074	912	1726	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_003113265.1	428	428	type	True	83.5429	854	1726	95	below_threshold
Methylocystis parvus	strain=OBBP	GCA_000283235.1	134	134	type	True	79.2335	576	1726	95	below_threshold
Methylocystis heyeri	strain=H2	GCA_004802635.2	391905	391905	type	True	79.0554	522	1726	95	below_threshold
Methylocystis silviterrae	strain=FS	GCA_013350005.1	2743612	2743612	type	True	78.9105	519	1726	95	below_threshold
Candidatus Rhodoblastus alkanivorans		GCA_022760755.1	2954117	2954117	type	True	77.8667	398	1726	95	below_threshold
Saliniramus fredricksonii	strain=HL-109	GCA_900094735.1	1653334	1653334	type	True	76.8342	242	1726	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.6613	431	1726	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	76.5929	383	1726	95	below_threshold
Salinarimonas ramus	strain=CGMCC 1.9161	GCA_014645695.1	690164	690164	type	True	76.5742	418	1726	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:02,864] [INFO] DFAST Taxonomy check result was written to GCF_030062355.1_ASM3006235v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:02,865] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:02,865] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:02,865] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab018e1c-0fad-4516-912d-fc41e1b63d12/dqc_reference/checkm_data
[2024-01-24 13:58:02,867] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:02,919] [INFO] Task started: CheckM
[2024-01-24 13:58:02,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030062355.1_ASM3006235v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030062355.1_ASM3006235v1_genomic.fna/checkm_input GCF_030062355.1_ASM3006235v1_genomic.fna/checkm_result
[2024-01-24 13:58:50,139] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:50,140] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:50,157] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:50,158] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:50,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030062355.1_ASM3006235v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:50,158] [INFO] Task started: Blastn
[2024-01-24 13:58:50,158] [INFO] Running command: blastn -query GCF_030062355.1_ASM3006235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab018e1c-0fad-4516-912d-fc41e1b63d12/dqc_reference/reference_markers_gtdb.fasta -out GCF_030062355.1_ASM3006235v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:52,167] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:52,170] [INFO] Selected 9 target genomes.
[2024-01-24 13:58:52,171] [INFO] Target genome list was writen to GCF_030062355.1_ASM3006235v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:52,185] [INFO] Task started: fastANI
[2024-01-24 13:58:52,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d830110-4718-4dfa-8a0a-5d650ef4bde1/GCF_030062355.1_ASM3006235v1_genomic.fna.gz --refList GCF_030062355.1_ASM3006235v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030062355.1_ASM3006235v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:05,262] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:05,271] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:05,272] [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_002752655.1	s__Methylosinus trichosporium	99.9866	1723	1726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	99.98	99.98	1.00	1.00	3	conclusive
GCF_015709455.1	s__Methylosinus sp015709455	83.9309	990	1726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009936375.1	s__Methylosinus sp009936375	83.8633	976	1726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811655.1	s__Methylosinus sp009811655	83.8611	900	1726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685825.1	s__Methylosinus sp000685825	83.6858	931	1726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	99.04	98.49	0.94	0.91	4	-
GCF_000745215.1	s__Methylosinus sp000745215	83.6398	976	1726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003113265.1	s__Methylosinus sporium	83.5059	859	1726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	98.07	97.36	0.91	0.86	5	-
GCF_000379125.1	s__Methylosinus sp000379125	83.4979	981	1726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003105285.1	s__Methylosinus sp003105285	81.6929	664	1726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:05,276] [INFO] GTDB search result was written to GCF_030062355.1_ASM3006235v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:05,277] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:05,281] [INFO] DFAST_QC result json was written to GCF_030062355.1_ASM3006235v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:05,281] [INFO] DFAST_QC completed!
[2024-01-24 13:59:05,281] [INFO] Total running time: 0h1m34s