[2024-01-24 13:49:44,762] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:44,765] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:44,765] [INFO] DQC Reference Directory: /var/lib/cwl/stg9928709f-7f70-4a6a-94d3-4f404c72a90f/dqc_reference
[2024-01-24 13:49:46,075] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:46,076] [INFO] Task started: Prodigal
[2024-01-24 13:49:46,076] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe113fec-fee0-4a10-91a3-f83d4cd45f2c/GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna/cds.fna -a GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:00,324] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:00,325] [INFO] Task started: HMMsearch
[2024-01-24 13:50:00,325] [INFO] Running command: hmmsearch --tblout GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9928709f-7f70-4a6a-94d3-4f404c72a90f/dqc_reference/reference_markers.hmm GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:00,641] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:00,642] [INFO] Found 6/6 markers.
[2024-01-24 13:50:00,685] [INFO] Query marker FASTA was written to GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:50:00,686] [INFO] Task started: Blastn
[2024-01-24 13:50:00,686] [INFO] Running command: blastn -query GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9928709f-7f70-4a6a-94d3-4f404c72a90f/dqc_reference/reference_markers.fasta -out GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:01,878] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:01,883] [INFO] Selected 10 target genomes.
[2024-01-24 13:50:01,884] [INFO] Target genome list was writen to GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:50:01,889] [INFO] Task started: fastANI
[2024-01-24 13:50:01,890] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe113fec-fee0-4a10-91a3-f83d4cd45f2c/GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna.gz --refList GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:16,199] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:16,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9928709f-7f70-4a6a-94d3-4f404c72a90f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:16,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9928709f-7f70-4a6a-94d3-4f404c72a90f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:16,214] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:16,214] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:16,214] [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
Methylorubrum salsuginis	strain=CGMCC 1.6474	GCA_900114375.1	414703	414703	type	True	100.0	1744	1746	95	conclusive
Methylorubrum rhodinum	strain=DSM 2163	GCA_014199935.1	29428	29428	type	True	90.4505	1359	1746	95	below_threshold
Methylorubrum suomiense	strain=DSM 14458	GCA_022179765.1	144191	144191	type	True	87.4408	1292	1746	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	85.9396	922	1746	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	85.3148	1219	1746	95	below_threshold
Methylorubrum rhodesianum	strain=DSM 5687	GCA_014199985.1	29427	29427	type	True	85.2367	1224	1746	95	below_threshold
Methylorubrum extorquens	strain=TK 0001	GCA_900234795.1	408	408	type	True	85.1821	1219	1746	95	below_threshold
Methylorubrum zatmanii	strain=LMG 6087	GCA_014845115.1	29429	29429	type	True	85.1063	1063	1746	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	81.5272	768	1746	95	below_threshold
Methylobacterium gnaphalii	strain=DSM 24027	GCA_022179205.1	1010610	1010610	type	True	81.4	814	1746	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:16,216] [INFO] DFAST Taxonomy check result was written to GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:50:16,217] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:16,217] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:16,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9928709f-7f70-4a6a-94d3-4f404c72a90f/dqc_reference/checkm_data
[2024-01-24 13:50:16,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:16,277] [INFO] Task started: CheckM
[2024-01-24 13:50:16,277] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna/checkm_input GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:51:00,382] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:00,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:00,405] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:00,406] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:00,406] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:51:00,407] [INFO] Task started: Blastn
[2024-01-24 13:51:00,407] [INFO] Running command: blastn -query GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9928709f-7f70-4a6a-94d3-4f404c72a90f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:02,574] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:02,578] [INFO] Selected 10 target genomes.
[2024-01-24 13:51:02,578] [INFO] Target genome list was writen to GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:02,595] [INFO] Task started: fastANI
[2024-01-24 13:51:02,595] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe113fec-fee0-4a10-91a3-f83d4cd45f2c/GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna.gz --refList GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:17,515] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:17,530] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:17,530] [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_900114375.1	s__Methylobacterium salsuginis	100.0	1744	1746	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_001425465.1	s__Methylobacterium sp001425465	91.169	1406	1746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199935.1	s__Methylobacterium rhodinum	90.4751	1357	1746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005502455.1	s__Methylobacterium sp005502455	87.4005	1259	1746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355515.1	s__Methylobacterium populi_A	85.5611	1207	1746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201865.1	s__Methylobacterium sp003201865	85.3916	1198	1746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199985.1	s__Methylobacterium rhodesianum	85.2629	1218	1746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.84	98.11	0.88	0.84	5	-
GCF_001423405.1	s__Methylobacterium sp001423405	85.2628	1210	1746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900234795.1	s__Methylobacterium extorquens	85.1769	1219	1746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.03	96.19	0.88	0.73	17	-
GCF_014845115.1	s__Methylobacterium zatmanii	85.0845	1065	1746	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 13:51:17,532] [INFO] GTDB search result was written to GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:17,532] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:17,535] [INFO] DFAST_QC result json was written to GCF_900114375.1_IMG-taxon_2617270908_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:51:17,535] [INFO] DFAST_QC completed!
[2024-01-24 13:51:17,535] [INFO] Total running time: 0h1m33s