[2024-01-24 13:23:10,888] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:23:10,890] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:23:10,890] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbb50ca2-c199-4896-945d-c453fe012f8a/dqc_reference
[2024-01-24 13:23:12,133] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:23:12,134] [INFO] Task started: Prodigal
[2024-01-24 13:23:12,134] [INFO] Running command: gunzip -c /var/lib/cwl/stga13b2179-b1e7-4500-8794-0789a7a8e058/GCF_003992665.1_ASM399266v1_genomic.fna.gz | prodigal -d GCF_003992665.1_ASM399266v1_genomic.fna/cds.fna -a GCF_003992665.1_ASM399266v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:24,229] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:24,229] [INFO] Task started: HMMsearch
[2024-01-24 13:23:24,229] [INFO] Running command: hmmsearch --tblout GCF_003992665.1_ASM399266v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbb50ca2-c199-4896-945d-c453fe012f8a/dqc_reference/reference_markers.hmm GCF_003992665.1_ASM399266v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:24,447] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:24,448] [INFO] Found 6/6 markers.
[2024-01-24 13:23:24,485] [INFO] Query marker FASTA was written to GCF_003992665.1_ASM399266v1_genomic.fna/markers.fasta
[2024-01-24 13:23:24,486] [INFO] Task started: Blastn
[2024-01-24 13:23:24,486] [INFO] Running command: blastn -query GCF_003992665.1_ASM399266v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbb50ca2-c199-4896-945d-c453fe012f8a/dqc_reference/reference_markers.fasta -out GCF_003992665.1_ASM399266v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:25,406] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:25,409] [INFO] Selected 14 target genomes.
[2024-01-24 13:23:25,409] [INFO] Target genome list was writen to GCF_003992665.1_ASM399266v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:25,414] [INFO] Task started: fastANI
[2024-01-24 13:23:25,415] [INFO] Running command: fastANI --query /var/lib/cwl/stga13b2179-b1e7-4500-8794-0789a7a8e058/GCF_003992665.1_ASM399266v1_genomic.fna.gz --refList GCF_003992665.1_ASM399266v1_genomic.fna/target_genomes.txt --output GCF_003992665.1_ASM399266v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:35,829] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:35,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbb50ca2-c199-4896-945d-c453fe012f8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:35,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbb50ca2-c199-4896-945d-c453fe012f8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:35,841] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:35,841] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:35,841] [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
Pelagibacterium montanilacus	strain=CCL18	GCA_003992665.1	2185280	2185280	type	True	100.0	1239	1245	95	conclusive
Pelagibacterium lacus	strain=XYN52	GCA_003345525.1	2282655	2282655	type	True	79.5647	477	1245	95	below_threshold
Pelagibacterium sediminicola	strain=IMCC34151	GCA_003390885.1	2248761	2248761	type	True	79.2043	456	1245	95	below_threshold
Pelagibacterium halotolerans	strain=B2	GCA_000230555.1	531813	531813	type	True	79.0687	429	1245	95	below_threshold
Pelagibacterium xiamenense	strain=HS1C4-1	GCA_021166475.1	2901140	2901140	type	True	78.7814	415	1245	95	below_threshold
Pelagibacterium luteolum	strain=CGMCC 1.10267	GCA_900100665.1	440168	440168	type	True	78.3676	393	1245	95	below_threshold
Pelagibacterium lentulum	strain=B2	GCA_003992625.1	2029865	2029865	type	True	78.0871	315	1245	95	below_threshold
Pelagibacterium lentulum	strain=CGMCC 1.15896	GCA_014643755.1	2029865	2029865	type	True	77.8961	311	1245	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	77.2361	138	1245	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	77.0269	176	1245	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	76.9478	145	1245	95	below_threshold
Martelella mediterranea	strain=DSM 17316	GCA_000376125.1	293089	293089	type	True	76.8482	173	1245	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	76.6378	154	1245	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	76.4195	146	1245	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:35,843] [INFO] DFAST Taxonomy check result was written to GCF_003992665.1_ASM399266v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:35,843] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:35,843] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:35,843] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbb50ca2-c199-4896-945d-c453fe012f8a/dqc_reference/checkm_data
[2024-01-24 13:23:35,844] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:35,880] [INFO] Task started: CheckM
[2024-01-24 13:23:35,881] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003992665.1_ASM399266v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003992665.1_ASM399266v1_genomic.fna/checkm_input GCF_003992665.1_ASM399266v1_genomic.fna/checkm_result
[2024-01-24 13:24:12,192] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:12,193] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:12,214] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:12,215] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:12,215] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003992665.1_ASM399266v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:12,216] [INFO] Task started: Blastn
[2024-01-24 13:24:12,216] [INFO] Running command: blastn -query GCF_003992665.1_ASM399266v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbb50ca2-c199-4896-945d-c453fe012f8a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003992665.1_ASM399266v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:13,922] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:13,925] [INFO] Selected 13 target genomes.
[2024-01-24 13:24:13,925] [INFO] Target genome list was writen to GCF_003992665.1_ASM399266v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:13,985] [INFO] Task started: fastANI
[2024-01-24 13:24:13,985] [INFO] Running command: fastANI --query /var/lib/cwl/stga13b2179-b1e7-4500-8794-0789a7a8e058/GCF_003992665.1_ASM399266v1_genomic.fna.gz --refList GCF_003992665.1_ASM399266v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003992665.1_ASM399266v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:24,899] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:24,910] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:24,910] [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_003992665.1	s__Pelagibacterium montanilacus	100.0	1239	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003345525.1	s__Pelagibacterium lacus	79.6263	480	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390885.1	s__Pelagibacterium sp003390885	79.2289	454	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000230555.1	s__Pelagibacterium halotolerans	79.1139	430	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCA_002723255.1	s__Pelagibacterium sp002723255	78.7383	368	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	98.69	98.23	0.81	0.73	4	-
GCA_002337455.1	s__Pelagibacterium sp002337455	78.6956	405	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.90	99.87	0.93	0.91	4	-
GCA_002375765.1	s__Pelagibacterium sp002375765	78.5119	419	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.84	99.84	0.95	0.95	2	-
GCF_015694405.1	s__Pelagibacterium limicola	78.4082	382	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100665.1	s__Pelagibacterium luteolum	78.3449	396	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992625.1	s__Pelagibacterium lentulum	78.1902	317	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000472865.1	s__Bradyrhizobium elkanii_A	76.6746	135	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.78	96.35	0.83	0.83	3	-
GCF_000379145.1	s__Bradyrhizobium elkanii	76.5251	153	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.89	95.57	0.89	0.83	18	-
GCF_001189245.1	s__Bradyrhizobium pachyrhizi	76.4076	147	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.66	95.38	0.85	0.82	8	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:24,912] [INFO] GTDB search result was written to GCF_003992665.1_ASM399266v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:24,913] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:24,916] [INFO] DFAST_QC result json was written to GCF_003992665.1_ASM399266v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:24,916] [INFO] DFAST_QC completed!
[2024-01-24 13:24:24,916] [INFO] Total running time: 0h1m14s