[2024-01-24 12:13:28,778] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:28,780] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:28,780] [INFO] DQC Reference Directory: /var/lib/cwl/stg0cf39d30-2ff4-44f5-b0fa-eafdb723c4eb/dqc_reference
[2024-01-24 12:13:30,331] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:30,332] [INFO] Task started: Prodigal
[2024-01-24 12:13:30,332] [INFO] Running command: gunzip -c /var/lib/cwl/stg79771ddd-7a16-49ec-a718-50f416f494d9/GCF_003258905.1_ASM325890v1_genomic.fna.gz | prodigal -d GCF_003258905.1_ASM325890v1_genomic.fna/cds.fna -a GCF_003258905.1_ASM325890v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:42,016] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:42,016] [INFO] Task started: HMMsearch
[2024-01-24 12:13:42,017] [INFO] Running command: hmmsearch --tblout GCF_003258905.1_ASM325890v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0cf39d30-2ff4-44f5-b0fa-eafdb723c4eb/dqc_reference/reference_markers.hmm GCF_003258905.1_ASM325890v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:42,348] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:42,349] [INFO] Found 6/6 markers.
[2024-01-24 12:13:42,385] [INFO] Query marker FASTA was written to GCF_003258905.1_ASM325890v1_genomic.fna/markers.fasta
[2024-01-24 12:13:42,386] [INFO] Task started: Blastn
[2024-01-24 12:13:42,386] [INFO] Running command: blastn -query GCF_003258905.1_ASM325890v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0cf39d30-2ff4-44f5-b0fa-eafdb723c4eb/dqc_reference/reference_markers.fasta -out GCF_003258905.1_ASM325890v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:43,364] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:43,367] [INFO] Selected 11 target genomes.
[2024-01-24 12:13:43,368] [INFO] Target genome list was writen to GCF_003258905.1_ASM325890v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:43,373] [INFO] Task started: fastANI
[2024-01-24 12:13:43,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg79771ddd-7a16-49ec-a718-50f416f494d9/GCF_003258905.1_ASM325890v1_genomic.fna.gz --refList GCF_003258905.1_ASM325890v1_genomic.fna/target_genomes.txt --output GCF_003258905.1_ASM325890v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:53,149] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:53,150] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0cf39d30-2ff4-44f5-b0fa-eafdb723c4eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:53,150] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0cf39d30-2ff4-44f5-b0fa-eafdb723c4eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:53,159] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:13:53,159] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:53,159] [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
Afifella marina	strain=DSM 2698	GCA_003258905.1	1080	1080	type	True	100.0	1303	1303	95	conclusive
Afifella marina	strain=DSM 2698	GCA_016584015.1	1080	1080	type	True	99.9985	1294	1303	95	conclusive
Afifella marina	strain=DSM 2698	GCA_900102695.1	1080	1080	type	True	99.9984	1297	1303	95	conclusive
Afifella aestuarii	strain=JA968	GCA_004023665.1	1909496	1909496	type	True	93.2713	1189	1303	95	below_threshold
Afifella pfennigii	strain=DSM 17143	GCA_000688515.1	209897	209897	type	True	79.9385	629	1303	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	77.4915	294	1303	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.2638	288	1303	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	77.0524	198	1303	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	77.019	183	1303	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	76.6274	224	1303	95	below_threshold
Jannaschia marina	strain=SHC163	GCA_013404595.1	2741674	2741674	type	True	75.9794	108	1303	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:53,161] [INFO] DFAST Taxonomy check result was written to GCF_003258905.1_ASM325890v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:53,162] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:53,162] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:53,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0cf39d30-2ff4-44f5-b0fa-eafdb723c4eb/dqc_reference/checkm_data
[2024-01-24 12:13:53,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:53,207] [INFO] Task started: CheckM
[2024-01-24 12:13:53,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003258905.1_ASM325890v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003258905.1_ASM325890v1_genomic.fna/checkm_input GCF_003258905.1_ASM325890v1_genomic.fna/checkm_result
[2024-01-24 12:14:32,787] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:32,788] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:32,813] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:32,813] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:32,814] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003258905.1_ASM325890v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:32,814] [INFO] Task started: Blastn
[2024-01-24 12:14:32,814] [INFO] Running command: blastn -query GCF_003258905.1_ASM325890v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0cf39d30-2ff4-44f5-b0fa-eafdb723c4eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003258905.1_ASM325890v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:34,561] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:34,564] [INFO] Selected 15 target genomes.
[2024-01-24 12:14:34,564] [INFO] Target genome list was writen to GCF_003258905.1_ASM325890v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:34,581] [INFO] Task started: fastANI
[2024-01-24 12:14:34,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg79771ddd-7a16-49ec-a718-50f416f494d9/GCF_003258905.1_ASM325890v1_genomic.fna.gz --refList GCF_003258905.1_ASM325890v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003258905.1_ASM325890v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:47,251] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:47,266] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:47,266] [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_900102695.1	s__Afifella marina	99.9984	1297	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Afifella	95.0	99.99	99.99	1.00	0.99	5	conclusive
GCF_004023665.1	s__Afifella aestuarii	93.2825	1188	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Afifella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688515.1	s__Afifella pfennigii	79.9479	628	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Afifella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009866965.1	s__Propylenella binzhouense	77.7681	309	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Propylenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258835.1	s__Rhodobium orientis	77.6454	292	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	99.99	99.98	0.99	0.98	3	-
GCA_900110915.1	s__Propylenella sp900110915	77.3227	238	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Propylenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053845.1	s__Breoghania corrubedonensis	77.1598	234	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Breoghania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305635.1	s__Bauldia sp017305635	77.1018	236	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Bauldia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610575.1	s__Stappia sp003610575	77.0188	279	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	98.18	0.97	0.97	2	-
GCF_000496075.1	s__Lutibaculum baratangense	76.9737	223	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Tepidamorphaceae;g__Lutibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017875275.1	s__Xanthobacter flavus	76.7926	182	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812985.1	s__Propylenella sp013812985	76.7762	136	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Propylenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900148505.1	s__Pseudoxanthobacter soli	76.6742	226	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pseudoxanthobacteraceae;g__Pseudoxanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882975.1	s__Maritimibacter harenae	76.2705	89	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013404595.1	s__Jannaschia marina	75.9834	108	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:47,268] [INFO] GTDB search result was written to GCF_003258905.1_ASM325890v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:47,268] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:47,271] [INFO] DFAST_QC result json was written to GCF_003258905.1_ASM325890v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:47,272] [INFO] DFAST_QC completed!
[2024-01-24 12:14:47,272] [INFO] Total running time: 0h1m18s