[2024-01-24 14:40:03,015] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:40:03,020] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:40:03,021] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b22b886-4655-412e-bbdb-a20a283337a6/dqc_reference
[2024-01-24 14:40:04,411] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:40:04,412] [INFO] Task started: Prodigal
[2024-01-24 14:40:04,412] [INFO] Running command: gunzip -c /var/lib/cwl/stg65ad4e10-2e25-4d60-8cc4-d6d924661136/GCF_014196925.1_ASM1419692v1_genomic.fna.gz | prodigal -d GCF_014196925.1_ASM1419692v1_genomic.fna/cds.fna -a GCF_014196925.1_ASM1419692v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:20,872] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:20,872] [INFO] Task started: HMMsearch
[2024-01-24 14:40:20,872] [INFO] Running command: hmmsearch --tblout GCF_014196925.1_ASM1419692v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b22b886-4655-412e-bbdb-a20a283337a6/dqc_reference/reference_markers.hmm GCF_014196925.1_ASM1419692v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:21,209] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:21,211] [INFO] Found 6/6 markers.
[2024-01-24 14:40:21,269] [INFO] Query marker FASTA was written to GCF_014196925.1_ASM1419692v1_genomic.fna/markers.fasta
[2024-01-24 14:40:21,270] [INFO] Task started: Blastn
[2024-01-24 14:40:21,270] [INFO] Running command: blastn -query GCF_014196925.1_ASM1419692v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b22b886-4655-412e-bbdb-a20a283337a6/dqc_reference/reference_markers.fasta -out GCF_014196925.1_ASM1419692v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:22,452] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:22,456] [INFO] Selected 10 target genomes.
[2024-01-24 14:40:22,456] [INFO] Target genome list was writen to GCF_014196925.1_ASM1419692v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:22,467] [INFO] Task started: fastANI
[2024-01-24 14:40:22,467] [INFO] Running command: fastANI --query /var/lib/cwl/stg65ad4e10-2e25-4d60-8cc4-d6d924661136/GCF_014196925.1_ASM1419692v1_genomic.fna.gz --refList GCF_014196925.1_ASM1419692v1_genomic.fna/target_genomes.txt --output GCF_014196925.1_ASM1419692v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:35,885] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:35,885] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b22b886-4655-412e-bbdb-a20a283337a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:35,886] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b22b886-4655-412e-bbdb-a20a283337a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:35,896] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:35,896] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:35,896] [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
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	100.0	1798	1799	95	conclusive
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001517345.1	363953	363953	type	True	93.9811	1273	1799	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001418005.1	363953	363953	type	True	93.9811	1273	1799	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	88.4079	1087	1799	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	88.3556	1091	1799	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	78.4824	670	1799	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	78.4036	668	1799	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	78.3887	652	1799	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	78.3543	675	1799	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	78.3494	632	1799	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:35,898] [INFO] DFAST Taxonomy check result was written to GCF_014196925.1_ASM1419692v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:35,898] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:35,899] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:35,899] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b22b886-4655-412e-bbdb-a20a283337a6/dqc_reference/checkm_data
[2024-01-24 14:40:35,900] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:35,954] [INFO] Task started: CheckM
[2024-01-24 14:40:35,954] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196925.1_ASM1419692v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196925.1_ASM1419692v1_genomic.fna/checkm_input GCF_014196925.1_ASM1419692v1_genomic.fna/checkm_result
[2024-01-24 14:41:31,043] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:31,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:31,068] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:31,068] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:31,069] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196925.1_ASM1419692v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:31,069] [INFO] Task started: Blastn
[2024-01-24 14:41:31,069] [INFO] Running command: blastn -query GCF_014196925.1_ASM1419692v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b22b886-4655-412e-bbdb-a20a283337a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196925.1_ASM1419692v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:33,499] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:33,503] [INFO] Selected 14 target genomes.
[2024-01-24 14:41:33,504] [INFO] Target genome list was writen to GCF_014196925.1_ASM1419692v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:33,528] [INFO] Task started: fastANI
[2024-01-24 14:41:33,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg65ad4e10-2e25-4d60-8cc4-d6d924661136/GCF_014196925.1_ASM1419692v1_genomic.fna.gz --refList GCF_014196925.1_ASM1419692v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196925.1_ASM1419692v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:50,103] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:50,118] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:50,119] [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_014196925.1	s__Chelatococcus_A caeni	100.0	1798	1799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	98.75	98.72	0.96	0.95	3	conclusive
GCF_001418005.1	s__Chelatococcus_A sambhunathii	93.9811	1273	1799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	99.33	99.03	0.97	0.94	5	-
GCF_014201415.1	s__Chelatococcus_A composti	88.4206	1086	1799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	99.84	99.53	0.99	0.98	4	-
GCF_009910705.1	s__Microvirga sp009910705	79.2602	549	1799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003201475.1	s__Chelatococcus asaccharovorans	79.0881	553	1799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003004785.1	s__Alsobacter soli	78.7042	519	1799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Alsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645695.1	s__Salinarimonas ramus	78.5464	655	1799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Salinarimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398335.1	s__Chelatococcus sp018398335	78.4793	524	1799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039875.1	s__Methylobacterium sp008039875	78.4593	486	1799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.26	97.89	0.94	0.87	4	-
GCF_001043895.1	s__Methylobacterium indicum	78.4297	604	1799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.73	98.07	0.88	0.87	6	-
GCF_007992195.1	s__Methylobacterium oxalidis	78.3196	517	1799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902141845.1	s__Methylobacterium symbioticum	78.2985	522	1799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735605.1	s__Bosea sp000735605	78.2806	552	1799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398315.1	s__Chelatococcus sp018398315	78.1877	457	1799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:50,120] [INFO] GTDB search result was written to GCF_014196925.1_ASM1419692v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:50,121] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:50,124] [INFO] DFAST_QC result json was written to GCF_014196925.1_ASM1419692v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:50,125] [INFO] DFAST_QC completed!
[2024-01-24 14:41:50,125] [INFO] Total running time: 0h1m47s