[2024-01-24 13:22:02,289] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:02,291] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:02,291] [INFO] DQC Reference Directory: /var/lib/cwl/stgd78d3493-218e-420c-85fb-a1df75266cdf/dqc_reference
[2024-01-24 13:22:03,649] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:03,650] [INFO] Task started: Prodigal
[2024-01-24 13:22:03,650] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c82c885-946c-400c-99a8-bc59be5ce42a/GCF_014201415.1_ASM1420141v1_genomic.fna.gz | prodigal -d GCF_014201415.1_ASM1420141v1_genomic.fna/cds.fna -a GCF_014201415.1_ASM1420141v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:15,161] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:15,162] [INFO] Task started: HMMsearch
[2024-01-24 13:22:15,162] [INFO] Running command: hmmsearch --tblout GCF_014201415.1_ASM1420141v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd78d3493-218e-420c-85fb-a1df75266cdf/dqc_reference/reference_markers.hmm GCF_014201415.1_ASM1420141v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:15,455] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:15,456] [INFO] Found 6/6 markers.
[2024-01-24 13:22:15,491] [INFO] Query marker FASTA was written to GCF_014201415.1_ASM1420141v1_genomic.fna/markers.fasta
[2024-01-24 13:22:15,491] [INFO] Task started: Blastn
[2024-01-24 13:22:15,491] [INFO] Running command: blastn -query GCF_014201415.1_ASM1420141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd78d3493-218e-420c-85fb-a1df75266cdf/dqc_reference/reference_markers.fasta -out GCF_014201415.1_ASM1420141v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:16,664] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:16,694] [INFO] Selected 10 target genomes.
[2024-01-24 13:22:16,694] [INFO] Target genome list was writen to GCF_014201415.1_ASM1420141v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:16,706] [INFO] Task started: fastANI
[2024-01-24 13:22:16,706] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c82c885-946c-400c-99a8-bc59be5ce42a/GCF_014201415.1_ASM1420141v1_genomic.fna.gz --refList GCF_014201415.1_ASM1420141v1_genomic.fna/target_genomes.txt --output GCF_014201415.1_ASM1420141v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:28,533] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:28,534] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd78d3493-218e-420c-85fb-a1df75266cdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:28,534] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd78d3493-218e-420c-85fb-a1df75266cdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:28,544] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:22:28,544] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:28,544] [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 composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	100.0	1226	1228	95	conclusive
Chelatococcus composti	strain=CGMCC 1.15283	GCA_014641535.1	1743235	1743235	type	True	99.9992	1219	1228	95	conclusive
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	99.9971	1227	1228	95	conclusive
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	88.563	1080	1228	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001517345.1	363953	363953	type	True	87.458	1031	1228	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	78.0502	489	1228	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	77.9881	493	1228	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.9683	488	1228	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	77.95	517	1228	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	77.8759	438	1228	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:28,546] [INFO] DFAST Taxonomy check result was written to GCF_014201415.1_ASM1420141v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:28,546] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:28,547] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:28,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd78d3493-218e-420c-85fb-a1df75266cdf/dqc_reference/checkm_data
[2024-01-24 13:22:28,548] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:28,586] [INFO] Task started: CheckM
[2024-01-24 13:22:28,586] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201415.1_ASM1420141v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201415.1_ASM1420141v1_genomic.fna/checkm_input GCF_014201415.1_ASM1420141v1_genomic.fna/checkm_result
[2024-01-24 13:23:08,674] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:08,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:08,689] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:08,690] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:08,690] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201415.1_ASM1420141v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:08,690] [INFO] Task started: Blastn
[2024-01-24 13:23:08,690] [INFO] Running command: blastn -query GCF_014201415.1_ASM1420141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd78d3493-218e-420c-85fb-a1df75266cdf/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201415.1_ASM1420141v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:11,113] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:11,117] [INFO] Selected 14 target genomes.
[2024-01-24 13:23:11,117] [INFO] Target genome list was writen to GCF_014201415.1_ASM1420141v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:11,142] [INFO] Task started: fastANI
[2024-01-24 13:23:11,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c82c885-946c-400c-99a8-bc59be5ce42a/GCF_014201415.1_ASM1420141v1_genomic.fna.gz --refList GCF_014201415.1_ASM1420141v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201415.1_ASM1420141v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:25,968] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:25,980] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:25,981] [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_014201415.1	s__Chelatococcus_A composti	100.0	1226	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	99.84	99.53	0.99	0.98	4	conclusive
GCF_014196925.1	s__Chelatococcus_A caeni	88.589	1078	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	98.75	98.72	0.96	0.95	3	-
GCF_001418005.1	s__Chelatococcus_A sambhunathii	87.4522	1032	1228	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_009910705.1	s__Microvirga sp009910705	79.0668	443	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009363855.1	s__Microvirga thermotolerans	78.9419	442	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762225.1	s__Pseudochelatococcus lubricantis	78.5653	383	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Pseudochelatococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003004785.1	s__Alsobacter soli	78.3448	437	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Alsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398335.1	s__Chelatococcus sp018398335	78.3187	406	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201475.1	s__Chelatococcus asaccharovorans	78.3066	448	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018398315.1	s__Chelatococcus sp018398315	78.0628	335	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001043895.1	s__Methylobacterium indicum	78.0147	452	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.73	98.07	0.88	0.87	6	-
GCF_006151805.1	s__Methylobacterium sp006151805	77.9931	484	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039875.1	s__Methylobacterium sp008039875	77.9456	390	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.26	97.89	0.94	0.87	4	-
GCF_005144885.1	s__Phreatobacter stygius	77.1734	376	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:25,982] [INFO] GTDB search result was written to GCF_014201415.1_ASM1420141v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:25,983] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:25,988] [INFO] DFAST_QC result json was written to GCF_014201415.1_ASM1420141v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:25,988] [INFO] DFAST_QC completed!
[2024-01-24 13:23:25,988] [INFO] Total running time: 0h1m24s