[2024-01-24 14:22:15,282] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:15,284] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:15,284] [INFO] DQC Reference Directory: /var/lib/cwl/stg6db08352-f691-440b-a744-7e6fbf9159ae/dqc_reference
[2024-01-24 14:22:16,531] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:16,532] [INFO] Task started: Prodigal
[2024-01-24 14:22:16,532] [INFO] Running command: gunzip -c /var/lib/cwl/stga852c32d-4baa-4e8f-ae05-53bbb6a4e52f/GCF_003345525.1_ASM334552v1_genomic.fna.gz | prodigal -d GCF_003345525.1_ASM334552v1_genomic.fna/cds.fna -a GCF_003345525.1_ASM334552v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:26,467] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:26,467] [INFO] Task started: HMMsearch
[2024-01-24 14:22:26,467] [INFO] Running command: hmmsearch --tblout GCF_003345525.1_ASM334552v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6db08352-f691-440b-a744-7e6fbf9159ae/dqc_reference/reference_markers.hmm GCF_003345525.1_ASM334552v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:26,730] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:26,733] [INFO] Found 6/6 markers.
[2024-01-24 14:22:26,762] [INFO] Query marker FASTA was written to GCF_003345525.1_ASM334552v1_genomic.fna/markers.fasta
[2024-01-24 14:22:26,763] [INFO] Task started: Blastn
[2024-01-24 14:22:26,763] [INFO] Running command: blastn -query GCF_003345525.1_ASM334552v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6db08352-f691-440b-a744-7e6fbf9159ae/dqc_reference/reference_markers.fasta -out GCF_003345525.1_ASM334552v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:27,743] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:27,748] [INFO] Selected 14 target genomes.
[2024-01-24 14:22:27,749] [INFO] Target genome list was writen to GCF_003345525.1_ASM334552v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:27,755] [INFO] Task started: fastANI
[2024-01-24 14:22:27,755] [INFO] Running command: fastANI --query /var/lib/cwl/stga852c32d-4baa-4e8f-ae05-53bbb6a4e52f/GCF_003345525.1_ASM334552v1_genomic.fna.gz --refList GCF_003345525.1_ASM334552v1_genomic.fna/target_genomes.txt --output GCF_003345525.1_ASM334552v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:39,382] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:39,382] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6db08352-f691-440b-a744-7e6fbf9159ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:39,383] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6db08352-f691-440b-a744-7e6fbf9159ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:39,394] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:39,394] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:39,394] [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 lacus	strain=XYN52	GCA_003345525.1	2282655	2282655	type	True	100.0	1044	1048	95	conclusive
Pelagibacterium halotolerans	strain=B2	GCA_000230555.1	531813	531813	type	True	80.9941	577	1048	95	below_threshold
Pelagibacterium sediminicola	strain=IMCC34151	GCA_003390885.1	2248761	2248761	type	True	80.4117	526	1048	95	below_threshold
Pelagibacterium luteolum	strain=CGMCC 1.10267	GCA_900100665.1	440168	440168	type	True	80.127	536	1048	95	below_threshold
Pelagibacterium montanilacus	strain=CCL18	GCA_003992665.1	2185280	2185280	type	True	79.7144	472	1048	95	below_threshold
Pelagibacterium xiamenense	strain=HS1C4-1	GCA_021166475.1	2901140	2901140	type	True	79.3281	440	1048	95	below_threshold
Pelagibacterium limicola	strain=NAJP-14	GCA_015694405.1	2791022	2791022	type	True	78.8844	421	1048	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	78.3928	365	1048	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	78.1894	313	1048	95	below_threshold
Pelagibacterium lentulum	strain=B2	GCA_003992625.1	2029865	2029865	type	True	78.1465	336	1048	95	below_threshold
Pelagibacterium lentulum	strain=CGMCC 1.15896	GCA_014643755.1	2029865	2029865	type	True	78.0256	334	1048	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	77.3661	181	1048	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	76.5325	196	1048	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	76.3189	140	1048	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:39,396] [INFO] DFAST Taxonomy check result was written to GCF_003345525.1_ASM334552v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:39,397] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:39,397] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:39,397] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6db08352-f691-440b-a744-7e6fbf9159ae/dqc_reference/checkm_data
[2024-01-24 14:22:39,398] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:39,432] [INFO] Task started: CheckM
[2024-01-24 14:22:39,432] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003345525.1_ASM334552v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003345525.1_ASM334552v1_genomic.fna/checkm_input GCF_003345525.1_ASM334552v1_genomic.fna/checkm_result
[2024-01-24 14:23:12,104] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:12,106] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:12,126] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:12,126] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:12,126] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003345525.1_ASM334552v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:12,127] [INFO] Task started: Blastn
[2024-01-24 14:23:12,127] [INFO] Running command: blastn -query GCF_003345525.1_ASM334552v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6db08352-f691-440b-a744-7e6fbf9159ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_003345525.1_ASM334552v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:13,841] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:13,844] [INFO] Selected 12 target genomes.
[2024-01-24 14:23:13,844] [INFO] Target genome list was writen to GCF_003345525.1_ASM334552v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:13,853] [INFO] Task started: fastANI
[2024-01-24 14:23:13,853] [INFO] Running command: fastANI --query /var/lib/cwl/stga852c32d-4baa-4e8f-ae05-53bbb6a4e52f/GCF_003345525.1_ASM334552v1_genomic.fna.gz --refList GCF_003345525.1_ASM334552v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003345525.1_ASM334552v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:22,618] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:22,628] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:22,628] [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_003345525.1	s__Pelagibacterium lacus	100.0	1045	1048	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_000230555.1	s__Pelagibacterium halotolerans	80.9902	578	1048	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	80.7818	480	1048	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	80.593	563	1048	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	80.5392	552	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.84	99.84	0.95	0.95	2	-
GCF_003390885.1	s__Pelagibacterium sp003390885	80.4115	526	1048	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	80.1373	535	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992665.1	s__Pelagibacterium montanilacus	79.6973	473	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713105.1	s__Devosia_A sp016713105	78.1687	310	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992625.1	s__Pelagibacterium lentulum	78.1059	334	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCA_015657675.1	s__Devosia_A sp015657675	77.3105	264	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337565.1	s__Paracoccus lutimaris	76.3321	139	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:22,631] [INFO] GTDB search result was written to GCF_003345525.1_ASM334552v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:22,632] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:22,635] [INFO] DFAST_QC result json was written to GCF_003345525.1_ASM334552v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:22,636] [INFO] DFAST_QC completed!
[2024-01-24 14:23:22,636] [INFO] Total running time: 0h1m7s