[2024-01-24 11:43:42,230] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:42,232] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:42,232] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ed8ee77-a4ab-4765-b11f-c3792503f5b8/dqc_reference
[2024-01-24 11:43:43,646] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:43,647] [INFO] Task started: Prodigal
[2024-01-24 11:43:43,647] [INFO] Running command: gunzip -c /var/lib/cwl/stg4df0c348-20e4-44ff-b7ae-99f3a1c35e43/GCF_015694405.1_ASM1569440v1_genomic.fna.gz | prodigal -d GCF_015694405.1_ASM1569440v1_genomic.fna/cds.fna -a GCF_015694405.1_ASM1569440v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:54,789] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:54,789] [INFO] Task started: HMMsearch
[2024-01-24 11:43:54,790] [INFO] Running command: hmmsearch --tblout GCF_015694405.1_ASM1569440v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ed8ee77-a4ab-4765-b11f-c3792503f5b8/dqc_reference/reference_markers.hmm GCF_015694405.1_ASM1569440v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:55,108] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:55,109] [INFO] Found 6/6 markers.
[2024-01-24 11:43:55,140] [INFO] Query marker FASTA was written to GCF_015694405.1_ASM1569440v1_genomic.fna/markers.fasta
[2024-01-24 11:43:55,140] [INFO] Task started: Blastn
[2024-01-24 11:43:55,140] [INFO] Running command: blastn -query GCF_015694405.1_ASM1569440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ed8ee77-a4ab-4765-b11f-c3792503f5b8/dqc_reference/reference_markers.fasta -out GCF_015694405.1_ASM1569440v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:56,043] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:56,046] [INFO] Selected 15 target genomes.
[2024-01-24 11:43:56,046] [INFO] Target genome list was writen to GCF_015694405.1_ASM1569440v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:56,051] [INFO] Task started: fastANI
[2024-01-24 11:43:56,051] [INFO] Running command: fastANI --query /var/lib/cwl/stg4df0c348-20e4-44ff-b7ae-99f3a1c35e43/GCF_015694405.1_ASM1569440v1_genomic.fna.gz --refList GCF_015694405.1_ASM1569440v1_genomic.fna/target_genomes.txt --output GCF_015694405.1_ASM1569440v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:07,046] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:07,046] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ed8ee77-a4ab-4765-b11f-c3792503f5b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:07,046] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ed8ee77-a4ab-4765-b11f-c3792503f5b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:07,059] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:07,059] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:07,060] [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 limicola	strain=NAJP-14	GCA_015694405.1	2791022	2791022	type	True	100.0	1152	1152	95	conclusive
Pelagibacterium sediminicola	strain=IMCC34151	GCA_003390885.1	2248761	2248761	type	True	80.7163	554	1152	95	below_threshold
Pelagibacterium lacus	strain=XYN52	GCA_003345525.1	2282655	2282655	type	True	79.1179	407	1152	95	below_threshold
Pelagibacterium halotolerans	strain=B2	GCA_000230555.1	531813	531813	type	True	78.9478	437	1152	95	below_threshold
Pelagibacterium xiamenense	strain=HS1C4-1	GCA_021166475.1	2901140	2901140	type	True	78.7883	400	1152	95	below_threshold
Pelagibacterium montanilacus	strain=CCL18	GCA_003992665.1	2185280	2185280	type	True	78.592	364	1152	95	below_threshold
Pelagibacterium luteolum	strain=CGMCC 1.10267	GCA_900100665.1	440168	440168	type	True	78.3393	393	1152	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	77.6221	254	1152	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	77.5947	249	1152	95	below_threshold
Devosia chinhatensis	strain=IPL18	GCA_000969445.1	429727	429727	type	True	77.5069	218	1152	95	below_threshold
Youhaiella tibetensis	strain=fig4	GCA_008000755.1	1447062	1447062	type	True	77.4238	265	1152	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	77.3579	228	1152	95	below_threshold
Youhaiella tibetensis	strain=CGMCC 1.12719	GCA_014638565.1	1447062	1447062	type	True	77.3562	263	1152	95	below_threshold
Devosia geojensis	strain=BD-c194	GCA_000969415.1	443610	443610	type	True	77.3404	288	1152	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	77.2349	243	1152	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:07,061] [INFO] DFAST Taxonomy check result was written to GCF_015694405.1_ASM1569440v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:07,062] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:07,062] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:07,062] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ed8ee77-a4ab-4765-b11f-c3792503f5b8/dqc_reference/checkm_data
[2024-01-24 11:44:07,064] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:07,102] [INFO] Task started: CheckM
[2024-01-24 11:44:07,102] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015694405.1_ASM1569440v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015694405.1_ASM1569440v1_genomic.fna/checkm_input GCF_015694405.1_ASM1569440v1_genomic.fna/checkm_result
[2024-01-24 11:44:42,932] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:42,933] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:42,961] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:42,961] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:42,962] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015694405.1_ASM1569440v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:42,962] [INFO] Task started: Blastn
[2024-01-24 11:44:42,962] [INFO] Running command: blastn -query GCF_015694405.1_ASM1569440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ed8ee77-a4ab-4765-b11f-c3792503f5b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_015694405.1_ASM1569440v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:44,704] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:44,708] [INFO] Selected 13 target genomes.
[2024-01-24 11:44:44,708] [INFO] Target genome list was writen to GCF_015694405.1_ASM1569440v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:44,717] [INFO] Task started: fastANI
[2024-01-24 11:44:44,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg4df0c348-20e4-44ff-b7ae-99f3a1c35e43/GCF_015694405.1_ASM1569440v1_genomic.fna.gz --refList GCF_015694405.1_ASM1569440v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015694405.1_ASM1569440v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:53,773] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:53,788] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:53,788] [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_015694405.1	s__Pelagibacterium limicola	100.0	1152	1152	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_003390885.1	s__Pelagibacterium sp003390885	80.7095	555	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003345525.1	s__Pelagibacterium lacus	79.1212	407	1152	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	78.9374	438	1152	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	78.8078	349	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	98.69	98.23	0.81	0.73	4	-
GCA_002375765.1	s__Pelagibacterium sp002375765	78.4809	423	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.84	99.84	0.95	0.95	2	-
GCF_900100665.1	s__Pelagibacterium luteolum	78.3481	391	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650025.1	s__Devosia elaeis	77.5773	249	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969445.1	s__Devosia chinhatensis	77.5069	218	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008000755.1	s__Youhaiella tibetensis	77.4238	265	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Youhaiella	95.0	99.26	98.52	0.98	0.97	3	-
GCF_016801025.1	s__Paradevosia shaoguanensis	77.287	266	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Paradevosia	95.0	97.16	97.13	0.92	0.92	4	-
GCA_017307495.1	s__Devosia_A sp017307495	77.1833	222	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	98.70	98.70	0.95	0.95	2	-
GCA_900470445.1	s__Devosia sp900470445	77.0309	239	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	95.41	95.41	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:53,790] [INFO] GTDB search result was written to GCF_015694405.1_ASM1569440v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:53,790] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:53,794] [INFO] DFAST_QC result json was written to GCF_015694405.1_ASM1569440v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:53,794] [INFO] DFAST_QC completed!
[2024-01-24 11:44:53,794] [INFO] Total running time: 0h1m12s