[2024-01-25 18:07:50,353] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:07:50,354] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:07:50,354] [INFO] DQC Reference Directory: /var/lib/cwl/stgc56501d5-6763-414f-9e31-a8e9a35126fb/dqc_reference
[2024-01-25 18:07:51,482] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:07:51,482] [INFO] Task started: Prodigal
[2024-01-25 18:07:51,482] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f2b5052-05a6-44f5-92f7-c4e6a5bd25b4/GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna/cds.fna -a GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:02,565] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:02,565] [INFO] Task started: HMMsearch
[2024-01-25 18:08:02,565] [INFO] Running command: hmmsearch --tblout GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc56501d5-6763-414f-9e31-a8e9a35126fb/dqc_reference/reference_markers.hmm GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:02,786] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:02,787] [INFO] Found 6/6 markers.
[2024-01-25 18:08:02,826] [INFO] Query marker FASTA was written to GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 18:08:02,826] [INFO] Task started: Blastn
[2024-01-25 18:08:02,826] [INFO] Running command: blastn -query GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc56501d5-6763-414f-9e31-a8e9a35126fb/dqc_reference/reference_markers.fasta -out GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:03,705] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:03,708] [INFO] Selected 13 target genomes.
[2024-01-25 18:08:03,708] [INFO] Target genome list was writen to GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 18:08:03,728] [INFO] Task started: fastANI
[2024-01-25 18:08:03,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f2b5052-05a6-44f5-92f7-c4e6a5bd25b4/GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna.gz --refList GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:08:19,802] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:19,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc56501d5-6763-414f-9e31-a8e9a35126fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:08:19,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc56501d5-6763-414f-9e31-a8e9a35126fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:08:19,813] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:08:19,813] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:08:19,813] [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 gossipiicola	strain=Gh-105	GCA_900113485.1	582675	582675	type	True	100.0	1462	1466	95	conclusive
Methylobacterium adhaesivum	strain=DSM 17169	GCA_022179065.1	333297	333297	type	True	88.4898	1138	1466	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	83.2411	935	1466	95	below_threshold
Methylobacterium bullatum	strain=DSM 21893	GCA_022179105.1	570505	570505	type	True	82.3352	921	1466	95	below_threshold
Methylobacterium bullatum	strain=LMG 24788	GCA_014845095.1	570505	570505	type	True	82.296	850	1466	95	below_threshold
Methylobacterium iners	strain=DSM 19015	GCA_022179305.1	418707	418707	type	True	81.5421	817	1466	95	below_threshold
Methylobacterium soli	strain=YIM 48816	GCA_008806385.1	553447	553447	type	True	81.5328	899	1466	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	81.521	860	1466	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	81.3889	707	1466	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	81.1039	907	1466	95	below_threshold
Methylobacterium tardum	strain=DSM 19566	GCA_023546765.1	374432	374432	type	True	80.5291	804	1466	95	below_threshold
Methylobacterium aquaticum	strain=DSM 16371	GCA_001043915.1	270351	270351	type	True	80.029	804	1466	95	below_threshold
Methylobacterium crusticola	strain=MIMD6	GCA_003574465.1	1697972	1697972	type	True	79.9512	759	1466	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:08:19,815] [INFO] DFAST Taxonomy check result was written to GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 18:08:19,819] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:08:19,820] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:08:19,820] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc56501d5-6763-414f-9e31-a8e9a35126fb/dqc_reference/checkm_data
[2024-01-25 18:08:19,821] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:08:19,868] [INFO] Task started: CheckM
[2024-01-25 18:08:19,868] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna/checkm_input GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 18:08:56,738] [INFO] Task succeeded: CheckM
[2024-01-25 18:08:56,739] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:08:56,754] [INFO] ===== Completeness check finished =====
[2024-01-25 18:08:56,754] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:08:56,755] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 18:08:56,755] [INFO] Task started: Blastn
[2024-01-25 18:08:56,755] [INFO] Running command: blastn -query GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc56501d5-6763-414f-9e31-a8e9a35126fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:58,305] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:58,308] [INFO] Selected 9 target genomes.
[2024-01-25 18:08:58,308] [INFO] Target genome list was writen to GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:08:58,321] [INFO] Task started: fastANI
[2024-01-25 18:08:58,321] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f2b5052-05a6-44f5-92f7-c4e6a5bd25b4/GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna.gz --refList GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:09:09,361] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:09,368] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:09:09,368] [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_900113485.1	s__Methylobacterium gossipiicola	100.0	1462	1466	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_001422375.1	s__Methylobacterium sp001422375	87.2233	1109	1466	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.25	98.25	0.90	0.90	2	-
GCF_001423295.1	s__Methylobacterium sp001423295	86.6027	1092	1466	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.75	98.70	0.92	0.92	5	-
GCF_001422885.1	s__Methylobacterium sp001422885	83.5639	980	1466	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	83.3455	992	1466	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.56	98.52	0.92	0.91	5	-
GCF_003217615.1	s__Methylobacterium sp003217615	83.2734	966	1466	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001423085.1	s__Methylobacterium sp001423085	83.1422	960	1466	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.83	97.83	0.87	0.87	2	-
GCF_001422985.1	s__Methylobacterium sp001422985	82.8342	961	1466	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.40	98.40	0.91	0.91	2	-
GCF_000372825.1	s__Methylobacterium sp000372825	82.1979	898	1466	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:09:09,369] [INFO] GTDB search result was written to GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 18:09:09,370] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:09:09,373] [INFO] DFAST_QC result json was written to GCF_900113485.1_IMG-taxon_2651870128_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 18:09:09,373] [INFO] DFAST_QC completed!
[2024-01-25 18:09:09,373] [INFO] Total running time: 0h1m19s