[2024-01-24 12:36:24,253] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:24,255] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:24,255] [INFO] DQC Reference Directory: /var/lib/cwl/stg522b0c6c-2ca4-43e7-8038-7b9821571b6e/dqc_reference
[2024-01-24 12:36:25,598] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:25,599] [INFO] Task started: Prodigal
[2024-01-24 12:36:25,599] [INFO] Running command: gunzip -c /var/lib/cwl/stg5bd3d90a-6e7c-488e-b90a-831a1fbef6ff/GCF_000757795.1_ASM75779v1_genomic.fna.gz | prodigal -d GCF_000757795.1_ASM75779v1_genomic.fna/cds.fna -a GCF_000757795.1_ASM75779v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:42,787] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:42,788] [INFO] Task started: HMMsearch
[2024-01-24 12:36:42,788] [INFO] Running command: hmmsearch --tblout GCF_000757795.1_ASM75779v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg522b0c6c-2ca4-43e7-8038-7b9821571b6e/dqc_reference/reference_markers.hmm GCF_000757795.1_ASM75779v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:43,095] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:43,097] [INFO] Found 6/6 markers.
[2024-01-24 12:36:43,147] [INFO] Query marker FASTA was written to GCF_000757795.1_ASM75779v1_genomic.fna/markers.fasta
[2024-01-24 12:36:43,147] [INFO] Task started: Blastn
[2024-01-24 12:36:43,147] [INFO] Running command: blastn -query GCF_000757795.1_ASM75779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg522b0c6c-2ca4-43e7-8038-7b9821571b6e/dqc_reference/reference_markers.fasta -out GCF_000757795.1_ASM75779v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:44,235] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:44,238] [INFO] Selected 10 target genomes.
[2024-01-24 12:36:44,238] [INFO] Target genome list was writen to GCF_000757795.1_ASM75779v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:44,242] [INFO] Task started: fastANI
[2024-01-24 12:36:44,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bd3d90a-6e7c-488e-b90a-831a1fbef6ff/GCF_000757795.1_ASM75779v1_genomic.fna.gz --refList GCF_000757795.1_ASM75779v1_genomic.fna/target_genomes.txt --output GCF_000757795.1_ASM75779v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:00,551] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:00,552] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg522b0c6c-2ca4-43e7-8038-7b9821571b6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:00,552] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg522b0c6c-2ca4-43e7-8038-7b9821571b6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:00,564] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:37:00,564] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:00,564] [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
Methylobacterium phyllosphaerae	strain=CBMB27	GCA_900113465.1	418223	418223	suspected-type	True	98.7859	1870	2095	95	conclusive
Methylobacterium phyllosphaerae	strain=CBMB27	GCA_001936175.1	418223	418223	suspected-type	True	98.7734	1933	2095	95	conclusive
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	91.0463	1694	2095	95	below_threshold
Methylobacterium radiotolerans	strain=NBRC 15690	GCA_007991055.1	31998	31998	type	True	90.9057	1627	2095	95	below_threshold
Methylobacterium tardum	strain=DSM 19566	GCA_023546765.1	374432	374432	type	True	88.0199	1484	2095	95	below_threshold
Methylobacterium tardum	strain=NBRC 103632	GCA_022179585.1	374432	374432	type	True	88.0121	1454	2095	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	87.249	1422	2095	95	below_threshold
Methylobacterium phyllostachyos	strain=BL47	GCA_900103445.1	582672	582672	type	True	86.7813	1389	2095	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	85.7402	1369	2095	95	below_threshold
Methylobacterium aerolatum	strain=DSM 19013	GCA_022179085.1	418708	418708	type	True	82.837	1073	2095	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:00,568] [INFO] DFAST Taxonomy check result was written to GCF_000757795.1_ASM75779v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:00,569] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:00,569] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:00,569] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg522b0c6c-2ca4-43e7-8038-7b9821571b6e/dqc_reference/checkm_data
[2024-01-24 12:37:00,570] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:00,633] [INFO] Task started: CheckM
[2024-01-24 12:37:00,633] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000757795.1_ASM75779v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000757795.1_ASM75779v1_genomic.fna/checkm_input GCF_000757795.1_ASM75779v1_genomic.fna/checkm_result
[2024-01-24 12:37:58,771] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:58,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:58,796] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:58,797] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:58,797] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000757795.1_ASM75779v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:58,797] [INFO] Task started: Blastn
[2024-01-24 12:37:58,797] [INFO] Running command: blastn -query GCF_000757795.1_ASM75779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg522b0c6c-2ca4-43e7-8038-7b9821571b6e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000757795.1_ASM75779v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:00,929] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:00,934] [INFO] Selected 9 target genomes.
[2024-01-24 12:38:00,934] [INFO] Target genome list was writen to GCF_000757795.1_ASM75779v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:00,942] [INFO] Task started: fastANI
[2024-01-24 12:38:00,943] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bd3d90a-6e7c-488e-b90a-831a1fbef6ff/GCF_000757795.1_ASM75779v1_genomic.fna.gz --refList GCF_000757795.1_ASM75779v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000757795.1_ASM75779v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:15,750] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:15,763] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:15,763] [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_014138435.1	s__Methylobacterium fujisawaense	98.8394	1842	2095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.82	98.73	0.93	0.90	12	conclusive
GCF_900112625.1	s__Methylobacterium sp900112625	90.863	1661	2095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.34	98.23	0.93	0.92	9	-
GCA_003096615.1	s__Methylobacterium organophilum	90.7935	1624	2095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.99	98.85	0.91	0.88	18	-
GCF_900103195.1	s__Methylobacterium sp900103195	90.1567	1597	2095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	96.81	96.81	0.87	0.87	2	-
GCF_014873335.1	s__Methylobacterium sp014873335	87.8158	1464	2095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017833295.1	s__Methylobacterium sp017833295	87.5808	1483	2095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000364445.2	s__Methylobacterium mesophilicum	87.3352	1480	2095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009806555.1	s__Methylobacterium sp009806555	87.1243	1420	2095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103445.1	s__Methylobacterium phyllostachyos	86.7591	1392	2095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:15,766] [INFO] GTDB search result was written to GCF_000757795.1_ASM75779v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:15,766] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:15,769] [INFO] DFAST_QC result json was written to GCF_000757795.1_ASM75779v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:15,769] [INFO] DFAST_QC completed!
[2024-01-24 12:38:15,769] [INFO] Total running time: 0h1m52s