[2024-01-24 12:13:59,187] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:59,190] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:59,190] [INFO] DQC Reference Directory: /var/lib/cwl/stg4445ffea-f1d4-474f-9167-8edc37765b4c/dqc_reference
[2024-01-24 12:14:00,669] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:00,670] [INFO] Task started: Prodigal
[2024-01-24 12:14:00,670] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f37aa95-7061-4cb0-b7c3-0703b0d1a5bf/GCF_022179305.1_ASM2217930v1_genomic.fna.gz | prodigal -d GCF_022179305.1_ASM2217930v1_genomic.fna/cds.fna -a GCF_022179305.1_ASM2217930v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:15,291] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:15,291] [INFO] Task started: HMMsearch
[2024-01-24 12:14:15,292] [INFO] Running command: hmmsearch --tblout GCF_022179305.1_ASM2217930v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4445ffea-f1d4-474f-9167-8edc37765b4c/dqc_reference/reference_markers.hmm GCF_022179305.1_ASM2217930v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:15,635] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:15,636] [INFO] Found 6/6 markers.
[2024-01-24 12:14:15,694] [INFO] Query marker FASTA was written to GCF_022179305.1_ASM2217930v1_genomic.fna/markers.fasta
[2024-01-24 12:14:15,695] [INFO] Task started: Blastn
[2024-01-24 12:14:15,695] [INFO] Running command: blastn -query GCF_022179305.1_ASM2217930v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4445ffea-f1d4-474f-9167-8edc37765b4c/dqc_reference/reference_markers.fasta -out GCF_022179305.1_ASM2217930v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:16,805] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:16,808] [INFO] Selected 15 target genomes.
[2024-01-24 12:14:16,808] [INFO] Target genome list was writen to GCF_022179305.1_ASM2217930v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:16,816] [INFO] Task started: fastANI
[2024-01-24 12:14:16,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f37aa95-7061-4cb0-b7c3-0703b0d1a5bf/GCF_022179305.1_ASM2217930v1_genomic.fna.gz --refList GCF_022179305.1_ASM2217930v1_genomic.fna/target_genomes.txt --output GCF_022179305.1_ASM2217930v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:35,279] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:35,280] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4445ffea-f1d4-474f-9167-8edc37765b4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:35,280] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4445ffea-f1d4-474f-9167-8edc37765b4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:35,292] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:35,292] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:35,293] [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 iners	strain=DSM 19015	GCA_022179305.1	418707	418707	type	True	100.0	1733	1740	95	conclusive
Methylobacterium oxalidis	strain=NBRC 107715	GCA_007992195.1	944322	944322	type	True	82.4757	895	1740	95	below_threshold
Methylobacterium oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	82.4097	900	1740	95	below_threshold
Methylobacterium dankookense	strain=SW08-7	GCA_902141855.1	560405	560405	type	True	82.3335	919	1740	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	82.3129	880	1740	95	below_threshold
Methylobacterium jeotgali	strain=LMG 23639	GCA_022179345.1	381630	381630	type	True	82.1974	804	1740	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	82.1619	861	1740	95	below_threshold
Methylobacterium durans	strain=17SD2-17	GCA_003173715.1	2202825	2202825	type	True	82.1607	924	1740	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	82.0211	738	1740	95	below_threshold
Methylobacterium bullatum	strain=DSM 21893	GCA_022179105.1	570505	570505	type	True	81.9789	860	1740	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	81.9315	903	1740	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	81.8923	895	1740	95	below_threshold
Methylobacterium adhaesivum	strain=DSM 17169	GCA_022179065.1	333297	333297	type	True	81.8606	834	1740	95	below_threshold
Methylobacterium bullatum	strain=LMG 24788	GCA_014845095.1	570505	570505	type	True	81.8597	788	1740	95	below_threshold
Methylobacterium gossipiicola	strain=Gh-105	GCA_900113485.1	582675	582675	type	True	81.615	825	1740	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:35,294] [INFO] DFAST Taxonomy check result was written to GCF_022179305.1_ASM2217930v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:35,295] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:35,295] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:35,295] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4445ffea-f1d4-474f-9167-8edc37765b4c/dqc_reference/checkm_data
[2024-01-24 12:14:35,296] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:35,351] [INFO] Task started: CheckM
[2024-01-24 12:14:35,351] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022179305.1_ASM2217930v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022179305.1_ASM2217930v1_genomic.fna/checkm_input GCF_022179305.1_ASM2217930v1_genomic.fna/checkm_result
[2024-01-24 12:15:19,266] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:19,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:19,293] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:19,293] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:19,293] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022179305.1_ASM2217930v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:19,294] [INFO] Task started: Blastn
[2024-01-24 12:15:19,294] [INFO] Running command: blastn -query GCF_022179305.1_ASM2217930v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4445ffea-f1d4-474f-9167-8edc37765b4c/dqc_reference/reference_markers_gtdb.fasta -out GCF_022179305.1_ASM2217930v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:21,473] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:21,477] [INFO] Selected 18 target genomes.
[2024-01-24 12:15:21,477] [INFO] Target genome list was writen to GCF_022179305.1_ASM2217930v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:21,490] [INFO] Task started: fastANI
[2024-01-24 12:15:21,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f37aa95-7061-4cb0-b7c3-0703b0d1a5bf/GCF_022179305.1_ASM2217930v1_genomic.fna.gz --refList GCF_022179305.1_ASM2217930v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022179305.1_ASM2217930v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:42,288] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:42,305] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:15:42,306] [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_001423265.1	s__Methylobacterium sp001423265	82.9409	929	1740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.78	98.73	0.95	0.94	3	-
GCF_001422885.1	s__Methylobacterium sp001422885	82.6431	909	1740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422375.1	s__Methylobacterium sp001422375	82.4659	892	1740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.25	98.25	0.90	0.90	2	-
GCF_003217615.1	s__Methylobacterium sp003217615	82.4059	901	1740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007992195.1	s__Methylobacterium oxalidis	82.35	907	1740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424705.1	s__Methylobacterium sp001424705	82.3267	923	1740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.56	98.52	0.92	0.91	5	-
GCF_902141855.1	s__Methylobacterium dankookense	82.3164	921	1740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423085.1	s__Methylobacterium sp001423085	82.1688	902	1740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.83	97.83	0.87	0.87	2	-
GCF_008039875.1	s__Methylobacterium sp008039875	81.9921	899	1740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.26	97.89	0.94	0.87	4	-
GCF_001423295.1	s__Methylobacterium sp001423295	81.9833	866	1740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.75	98.70	0.92	0.92	5	-
GCF_014845095.1	s__Methylobacterium bullatum	81.8661	789	1740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.58	95.73	0.88	0.87	6	-
GCF_001422985.1	s__Methylobacterium sp001422985	81.7876	875	1740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.40	98.40	0.91	0.91	2	-
GCF_000519085.1	s__Methylobacterium sp000519085	81.7391	853	1740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113485.1	s__Methylobacterium gossipiicola	81.6183	824	1740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422815.1	s__Methylobacterium sp001422815	81.2115	858	1740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.57	97.58	0.90	0.88	3	-
GCF_001653715.1	s__Methylobacterium platani	80.915	834	1740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.94	99.94	0.97	0.97	2	-
GCF_004004555.2	s__Methylobacterium sp004004555	80.7728	825	1740	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	80.3745	858	1740	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 12:15:42,308] [INFO] GTDB search result was written to GCF_022179305.1_ASM2217930v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:42,308] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:42,312] [INFO] DFAST_QC result json was written to GCF_022179305.1_ASM2217930v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:42,312] [INFO] DFAST_QC completed!
[2024-01-24 12:15:42,312] [INFO] Total running time: 0h1m43s