[2024-01-24 12:13:58,370] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:58,376] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:58,376] [INFO] DQC Reference Directory: /var/lib/cwl/stg63289067-7c07-4836-89ff-0d83aafba258/dqc_reference
[2024-01-24 12:13:59,745] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:59,745] [INFO] Task started: Prodigal
[2024-01-24 12:13:59,746] [INFO] Running command: gunzip -c /var/lib/cwl/stg952ad2c9-7774-414d-af28-5806f431888f/GCF_003173755.1_ASM317375v1_genomic.fna.gz | prodigal -d GCF_003173755.1_ASM317375v1_genomic.fna/cds.fna -a GCF_003173755.1_ASM317375v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:15,543] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:15,543] [INFO] Task started: HMMsearch
[2024-01-24 12:14:15,543] [INFO] Running command: hmmsearch --tblout GCF_003173755.1_ASM317375v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63289067-7c07-4836-89ff-0d83aafba258/dqc_reference/reference_markers.hmm GCF_003173755.1_ASM317375v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:15,908] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:15,909] [INFO] Found 6/6 markers.
[2024-01-24 12:14:15,960] [INFO] Query marker FASTA was written to GCF_003173755.1_ASM317375v1_genomic.fna/markers.fasta
[2024-01-24 12:14:15,960] [INFO] Task started: Blastn
[2024-01-24 12:14:15,960] [INFO] Running command: blastn -query GCF_003173755.1_ASM317375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63289067-7c07-4836-89ff-0d83aafba258/dqc_reference/reference_markers.fasta -out GCF_003173755.1_ASM317375v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:17,146] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:17,149] [INFO] Selected 13 target genomes.
[2024-01-24 12:14:17,150] [INFO] Target genome list was writen to GCF_003173755.1_ASM317375v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:17,155] [INFO] Task started: fastANI
[2024-01-24 12:14:17,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg952ad2c9-7774-414d-af28-5806f431888f/GCF_003173755.1_ASM317375v1_genomic.fna.gz --refList GCF_003173755.1_ASM317375v1_genomic.fna/target_genomes.txt --output GCF_003173755.1_ASM317375v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:47,675] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:47,676] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63289067-7c07-4836-89ff-0d83aafba258/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:47,676] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63289067-7c07-4836-89ff-0d83aafba258/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:47,688] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:47,688] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:47,689] [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 terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	100.0	2054	2054	95	conclusive
Methylobacterium platani	strain=PMB02	GCA_001653715.1	427683	427683	type	True	91.9689	1696	2054	95	below_threshold
Methylobacterium platani	strain=JCM 14648	GCA_001043885.1	427683	427683	type	True	91.8995	1488	2054	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	91.4785	1734	2054	95	below_threshold
Methylobacterium tarhaniae	strain=DSM 25844	GCA_001043955.1	1187852	1187852	type	True	90.9117	1502	2054	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	90.8245	1676	2054	95	below_threshold
Methylobacterium currus	strain=PR1016A	GCA_003058325.1	2051553	2051553	type	True	90.7417	1711	2054	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	90.4257	1669	2054	95	below_threshold
Methylobacterium ajmalii	strain=IF7SW-B2	GCA_016613415.1	2738439	2738439	type	True	90.3748	1555	2054	95	below_threshold
Methylobacterium indicum	strain=SE2.11	GCA_001043895.1	1775910	1775910	type	True	90.3595	1464	2054	95	below_threshold
Methylobacterium variabile	strain=DSM 16961	GCA_001043975.1	298794	298794	type	True	90.268	1467	2054	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	85.2568	1435	2054	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	84.9433	1353	2054	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:47,691] [INFO] DFAST Taxonomy check result was written to GCF_003173755.1_ASM317375v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:47,692] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:47,692] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:47,693] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63289067-7c07-4836-89ff-0d83aafba258/dqc_reference/checkm_data
[2024-01-24 12:14:47,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:47,762] [INFO] Task started: CheckM
[2024-01-24 12:14:47,763] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003173755.1_ASM317375v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003173755.1_ASM317375v1_genomic.fna/checkm_input GCF_003173755.1_ASM317375v1_genomic.fna/checkm_result
[2024-01-24 12:15:41,886] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:41,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:41,937] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:41,937] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:41,938] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003173755.1_ASM317375v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:41,938] [INFO] Task started: Blastn
[2024-01-24 12:15:41,938] [INFO] Running command: blastn -query GCF_003173755.1_ASM317375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63289067-7c07-4836-89ff-0d83aafba258/dqc_reference/reference_markers_gtdb.fasta -out GCF_003173755.1_ASM317375v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:44,234] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:44,238] [INFO] Selected 13 target genomes.
[2024-01-24 12:15:44,238] [INFO] Target genome list was writen to GCF_003173755.1_ASM317375v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:44,241] [INFO] Task started: fastANI
[2024-01-24 12:15:44,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg952ad2c9-7774-414d-af28-5806f431888f/GCF_003173755.1_ASM317375v1_genomic.fna.gz --refList GCF_003173755.1_ASM317375v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003173755.1_ASM317375v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:13,107] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:13,131] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:13,131] [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_003173755.1	s__Methylobacterium terrae	100.0	2054	2054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001653715.1	s__Methylobacterium platani	91.9601	1697	2054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.94	99.94	0.97	0.97	2	-
GCF_011043735.1	s__Methylobacterium sp011043735	91.5999	1690	2054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006151805.1	s__Methylobacterium sp006151805	91.5131	1730	2054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173775.1	s__Methylobacterium sp003173775	90.9753	1704	2054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	95.16	95.16	0.87	0.87	2	-
GCF_001043955.1	s__Methylobacterium tarhaniae	90.9085	1503	2054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058325.1	s__Methylobacterium currus	90.7367	1710	2054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019216885.1	s__Methylobacterium sp019216885	90.643	1706	2054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016804325.1	s__Methylobacterium aquaticum_C	90.6065	1688	2054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745635.1	s__Methylobacterium sp004745635	90.4057	1671	2054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016613415.1	s__Methylobacterium ajmalii	90.3769	1555	2054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.55	96.20	0.90	0.83	5	-
GCF_001043895.1	s__Methylobacterium indicum	90.366	1463	2054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.73	98.07	0.88	0.87	6	-
GCF_001043975.1	s__Methylobacterium variabile	90.2456	1469	2054	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 12:16:13,133] [INFO] GTDB search result was written to GCF_003173755.1_ASM317375v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:13,134] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:13,140] [INFO] DFAST_QC result json was written to GCF_003173755.1_ASM317375v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:13,140] [INFO] DFAST_QC completed!
[2024-01-24 12:16:13,140] [INFO] Total running time: 0h2m15s