[2024-01-24 12:09:05,886] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:09:05,888] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:09:05,888] [INFO] DQC Reference Directory: /var/lib/cwl/stg21c88c9d-cadb-48c4-903a-feeda7b9815a/dqc_reference
[2024-01-24 12:09:07,065] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:09:07,066] [INFO] Task started: Prodigal
[2024-01-24 12:09:07,066] [INFO] Running command: gunzip -c /var/lib/cwl/stg123d5362-f508-4ccd-b232-abfb59a9c91e/GCF_001418005.1_ASM141800v1_genomic.fna.gz | prodigal -d GCF_001418005.1_ASM141800v1_genomic.fna/cds.fna -a GCF_001418005.1_ASM141800v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:09:19,944] [INFO] Task succeeded: Prodigal
[2024-01-24 12:09:19,945] [INFO] Task started: HMMsearch
[2024-01-24 12:09:19,945] [INFO] Running command: hmmsearch --tblout GCF_001418005.1_ASM141800v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21c88c9d-cadb-48c4-903a-feeda7b9815a/dqc_reference/reference_markers.hmm GCF_001418005.1_ASM141800v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:09:20,233] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:09:20,235] [INFO] Found 6/6 markers.
[2024-01-24 12:09:20,278] [INFO] Query marker FASTA was written to GCF_001418005.1_ASM141800v1_genomic.fna/markers.fasta
[2024-01-24 12:09:20,278] [INFO] Task started: Blastn
[2024-01-24 12:09:20,278] [INFO] Running command: blastn -query GCF_001418005.1_ASM141800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21c88c9d-cadb-48c4-903a-feeda7b9815a/dqc_reference/reference_markers.fasta -out GCF_001418005.1_ASM141800v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:21,353] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:21,357] [INFO] Selected 10 target genomes.
[2024-01-24 12:09:21,358] [INFO] Target genome list was writen to GCF_001418005.1_ASM141800v1_genomic.fna/target_genomes.txt
[2024-01-24 12:09:21,363] [INFO] Task started: fastANI
[2024-01-24 12:09:21,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg123d5362-f508-4ccd-b232-abfb59a9c91e/GCF_001418005.1_ASM141800v1_genomic.fna.gz --refList GCF_001418005.1_ASM141800v1_genomic.fna/target_genomes.txt --output GCF_001418005.1_ASM141800v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:09:33,264] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:33,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21c88c9d-cadb-48c4-903a-feeda7b9815a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:09:33,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21c88c9d-cadb-48c4-903a-feeda7b9815a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:09:33,275] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:09:33,275] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:09:33,276] [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 sambhunathii	strain=DSM 18167	GCA_001517345.1	363953	363953	type	True	100.0	1441	1443	95	conclusive
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001418005.1	363953	363953	type	True	100.0	1441	1443	95	conclusive
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	94.1154	1262	1443	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	87.2784	1053	1443	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	87.2533	1061	1443	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	78.2275	530	1443	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	78.1948	529	1443	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	78.1004	519	1443	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	78.0954	528	1443	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.9719	550	1443	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:09:33,277] [INFO] DFAST Taxonomy check result was written to GCF_001418005.1_ASM141800v1_genomic.fna/tc_result.tsv
[2024-01-24 12:09:33,278] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:09:33,278] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:09:33,278] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21c88c9d-cadb-48c4-903a-feeda7b9815a/dqc_reference/checkm_data
[2024-01-24 12:09:33,279] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:09:33,319] [INFO] Task started: CheckM
[2024-01-24 12:09:33,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001418005.1_ASM141800v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001418005.1_ASM141800v1_genomic.fna/checkm_input GCF_001418005.1_ASM141800v1_genomic.fna/checkm_result
[2024-01-24 12:10:14,499] [INFO] Task succeeded: CheckM
[2024-01-24 12:10:14,501] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:10:14,520] [INFO] ===== Completeness check finished =====
[2024-01-24 12:10:14,521] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:10:14,521] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001418005.1_ASM141800v1_genomic.fna/markers.fasta)
[2024-01-24 12:10:14,521] [INFO] Task started: Blastn
[2024-01-24 12:10:14,522] [INFO] Running command: blastn -query GCF_001418005.1_ASM141800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21c88c9d-cadb-48c4-903a-feeda7b9815a/dqc_reference/reference_markers_gtdb.fasta -out GCF_001418005.1_ASM141800v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:10:16,719] [INFO] Task succeeded: Blastn
[2024-01-24 12:10:16,723] [INFO] Selected 14 target genomes.
[2024-01-24 12:10:16,723] [INFO] Target genome list was writen to GCF_001418005.1_ASM141800v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:10:16,734] [INFO] Task started: fastANI
[2024-01-24 12:10:16,734] [INFO] Running command: fastANI --query /var/lib/cwl/stg123d5362-f508-4ccd-b232-abfb59a9c91e/GCF_001418005.1_ASM141800v1_genomic.fna.gz --refList GCF_001418005.1_ASM141800v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001418005.1_ASM141800v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:10:33,747] [INFO] Task succeeded: fastANI
[2024-01-24 12:10:33,764] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:10:33,765] [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_001418005.1	s__Chelatococcus_A sambhunathii	100.0	1441	1443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	99.33	99.03	0.97	0.94	5	conclusive
GCF_014196925.1	s__Chelatococcus_A caeni	94.1154	1262	1443	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_014201415.1	s__Chelatococcus_A composti	87.2649	1060	1443	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_009363855.1	s__Microvirga thermotolerans	78.9115	463	1443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009910705.1	s__Microvirga sp009910705	78.8474	465	1443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900112185.1	s__Bosea sp900112185	78.7422	588	1443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201475.1	s__Chelatococcus asaccharovorans	78.5453	489	1443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018398335.1	s__Chelatococcus sp018398335	78.3962	430	1443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003004785.1	s__Alsobacter soli	78.2542	456	1443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Alsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001043895.1	s__Methylobacterium indicum	78.2339	483	1443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.73	98.07	0.88	0.87	6	-
GCF_018398315.1	s__Chelatococcus sp018398315	78.1573	384	1443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902141855.1	s__Methylobacterium dankookense	78.1014	463	1443	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	78.0428	433	1443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040045.1	s__Methylobacterium sp008040045	77.8258	386	1443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.25	98.17	0.85	0.85	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:10:33,766] [INFO] GTDB search result was written to GCF_001418005.1_ASM141800v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:10:33,767] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:10:33,770] [INFO] DFAST_QC result json was written to GCF_001418005.1_ASM141800v1_genomic.fna/dqc_result.json
[2024-01-24 12:10:33,770] [INFO] DFAST_QC completed!
[2024-01-24 12:10:33,770] [INFO] Total running time: 0h1m28s