[2024-01-25 17:50:35,626] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:50:35,627] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:50:35,627] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ec9779b-3940-42fb-bcc1-6d23a466059b/dqc_reference
[2024-01-25 17:50:36,753] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:50:36,753] [INFO] Task started: Prodigal
[2024-01-25 17:50:36,753] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b91e3ef-e7fa-41d3-a9d8-45c8fda0ffe0/GCF_003113265.1_ASM311326v1_genomic.fna.gz | prodigal -d GCF_003113265.1_ASM311326v1_genomic.fna/cds.fna -a GCF_003113265.1_ASM311326v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:50:46,839] [INFO] Task succeeded: Prodigal
[2024-01-25 17:50:46,840] [INFO] Task started: HMMsearch
[2024-01-25 17:50:46,840] [INFO] Running command: hmmsearch --tblout GCF_003113265.1_ASM311326v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ec9779b-3940-42fb-bcc1-6d23a466059b/dqc_reference/reference_markers.hmm GCF_003113265.1_ASM311326v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:50:47,049] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:50:47,050] [INFO] Found 6/6 markers.
[2024-01-25 17:50:47,078] [INFO] Query marker FASTA was written to GCF_003113265.1_ASM311326v1_genomic.fna/markers.fasta
[2024-01-25 17:50:47,078] [INFO] Task started: Blastn
[2024-01-25 17:50:47,078] [INFO] Running command: blastn -query GCF_003113265.1_ASM311326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ec9779b-3940-42fb-bcc1-6d23a466059b/dqc_reference/reference_markers.fasta -out GCF_003113265.1_ASM311326v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:47,976] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:47,979] [INFO] Selected 13 target genomes.
[2024-01-25 17:50:47,980] [INFO] Target genome list was writen to GCF_003113265.1_ASM311326v1_genomic.fna/target_genomes.txt
[2024-01-25 17:50:48,002] [INFO] Task started: fastANI
[2024-01-25 17:50:48,002] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b91e3ef-e7fa-41d3-a9d8-45c8fda0ffe0/GCF_003113265.1_ASM311326v1_genomic.fna.gz --refList GCF_003113265.1_ASM311326v1_genomic.fna/target_genomes.txt --output GCF_003113265.1_ASM311326v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:51:00,352] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:00,352] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ec9779b-3940-42fb-bcc1-6d23a466059b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:51:00,352] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ec9779b-3940-42fb-bcc1-6d23a466059b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:51:00,361] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:51:00,361] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:51:00,361] [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 sporium	strain=DSM 17706	GCA_003113265.1	428	428	type	True	100.0	1229	1234	95	conclusive
Methylosinus sporium	strain=DSM 17706	GCA_009811675.1	428	428	type	True	99.9935	1215	1234	95	conclusive
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	83.6775	850	1234	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	83.6697	850	1234	95	below_threshold
Methylocystis parvus	strain=OBBP	GCA_000283235.1	134	134	type	True	79.219	540	1234	95	below_threshold
Methylocystis silviterrae	strain=FS	GCA_013350005.1	2743612	2743612	type	True	79.0043	444	1234	95	below_threshold
Methylocystis rosea	strain=SV97	GCA_000372845.1	173366	173366	type	True	78.9615	438	1234	95	below_threshold
Methylocystis heyeri	strain=H2	GCA_004802635.2	391905	391905	type	True	78.7565	480	1234	95	below_threshold
Candidatus Rhodoblastus alkanivorans		GCA_022760755.1	2954117	2954117	type	True	77.7237	330	1234	95	below_threshold
Methylocella silvestris	strain=BL2	GCA_000021745.1	199596	199596	type	True	77.5786	313	1234	95	below_threshold
Methylobacterium jeotgali	strain=LMG 23639	GCA_022179345.1	381630	381630	type	True	76.8872	240	1234	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.8021	301	1234	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	76.4068	291	1234	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:51:00,363] [INFO] DFAST Taxonomy check result was written to GCF_003113265.1_ASM311326v1_genomic.fna/tc_result.tsv
[2024-01-25 17:51:00,363] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:51:00,363] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:51:00,363] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ec9779b-3940-42fb-bcc1-6d23a466059b/dqc_reference/checkm_data
[2024-01-25 17:51:00,364] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:51:00,402] [INFO] Task started: CheckM
[2024-01-25 17:51:00,402] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003113265.1_ASM311326v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003113265.1_ASM311326v1_genomic.fna/checkm_input GCF_003113265.1_ASM311326v1_genomic.fna/checkm_result
[2024-01-25 17:51:31,069] [INFO] Task succeeded: CheckM
[2024-01-25 17:51:31,070] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:51:31,088] [INFO] ===== Completeness check finished =====
[2024-01-25 17:51:31,088] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:51:31,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003113265.1_ASM311326v1_genomic.fna/markers.fasta)
[2024-01-25 17:51:31,089] [INFO] Task started: Blastn
[2024-01-25 17:51:31,089] [INFO] Running command: blastn -query GCF_003113265.1_ASM311326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ec9779b-3940-42fb-bcc1-6d23a466059b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003113265.1_ASM311326v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:32,868] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:32,871] [INFO] Selected 7 target genomes.
[2024-01-25 17:51:32,871] [INFO] Target genome list was writen to GCF_003113265.1_ASM311326v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:51:32,876] [INFO] Task started: fastANI
[2024-01-25 17:51:32,876] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b91e3ef-e7fa-41d3-a9d8-45c8fda0ffe0/GCF_003113265.1_ASM311326v1_genomic.fna.gz --refList GCF_003113265.1_ASM311326v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003113265.1_ASM311326v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:51:40,998] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:41,003] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:51:41,003] [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_003113265.1	s__Methylosinus sporium	100.0	1229	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	98.07	97.36	0.91	0.86	5	conclusive
GCF_000685825.1	s__Methylosinus sp000685825	91.5061	1038	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	99.04	98.49	0.94	0.91	4	-
GCF_009936375.1	s__Methylosinus sp009936375	91.4683	1035	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745215.1	s__Methylosinus sp000745215	91.3095	1006	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379125.1	s__Methylosinus sp000379125	91.094	1013	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015709455.1	s__Methylosinus sp015709455	89.4507	1031	1234	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	88.2002	899	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:51:41,004] [INFO] GTDB search result was written to GCF_003113265.1_ASM311326v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:51:41,005] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:51:41,007] [INFO] DFAST_QC result json was written to GCF_003113265.1_ASM311326v1_genomic.fna/dqc_result.json
[2024-01-25 17:51:41,007] [INFO] DFAST_QC completed!
[2024-01-25 17:51:41,008] [INFO] Total running time: 0h1m5s