[2024-01-25 20:04:05,579] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:04:05,580] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:04:05,581] [INFO] DQC Reference Directory: /var/lib/cwl/stg15fac639-b213-41ae-b944-55bc7104f519/dqc_reference
[2024-01-25 20:04:06,740] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:04:06,740] [INFO] Task started: Prodigal
[2024-01-25 20:04:06,740] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5e2a5f9-bb18-4b40-a6f2-3efb3418ee77/GCF_003014475.1_ASM301447v1_genomic.fna.gz | prodigal -d GCF_003014475.1_ASM301447v1_genomic.fna/cds.fna -a GCF_003014475.1_ASM301447v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:04:20,719] [INFO] Task succeeded: Prodigal
[2024-01-25 20:04:20,719] [INFO] Task started: HMMsearch
[2024-01-25 20:04:20,719] [INFO] Running command: hmmsearch --tblout GCF_003014475.1_ASM301447v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15fac639-b213-41ae-b944-55bc7104f519/dqc_reference/reference_markers.hmm GCF_003014475.1_ASM301447v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:04:20,998] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:04:20,999] [INFO] Found 6/6 markers.
[2024-01-25 20:04:21,036] [INFO] Query marker FASTA was written to GCF_003014475.1_ASM301447v1_genomic.fna/markers.fasta
[2024-01-25 20:04:21,036] [INFO] Task started: Blastn
[2024-01-25 20:04:21,037] [INFO] Running command: blastn -query GCF_003014475.1_ASM301447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15fac639-b213-41ae-b944-55bc7104f519/dqc_reference/reference_markers.fasta -out GCF_003014475.1_ASM301447v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:21,683] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:21,686] [INFO] Selected 24 target genomes.
[2024-01-25 20:04:21,686] [INFO] Target genome list was writen to GCF_003014475.1_ASM301447v1_genomic.fna/target_genomes.txt
[2024-01-25 20:04:21,714] [INFO] Task started: fastANI
[2024-01-25 20:04:21,714] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5e2a5f9-bb18-4b40-a6f2-3efb3418ee77/GCF_003014475.1_ASM301447v1_genomic.fna.gz --refList GCF_003014475.1_ASM301447v1_genomic.fna/target_genomes.txt --output GCF_003014475.1_ASM301447v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:04:39,404] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:39,405] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15fac639-b213-41ae-b944-55bc7104f519/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:04:39,405] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15fac639-b213-41ae-b944-55bc7104f519/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:04:39,417] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:04:39,418] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:04:39,418] [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
Shimia abyssi	strain=DSM 100673	GCA_003014475.1	1662395	1662395	type	True	100.0	1551	1553	95	conclusive
Shimia thalassica	strain=CECT 7735	GCA_001458215.1	1715693	1715693	type	True	78.2514	285	1553	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	78.2089	331	1553	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	78.2084	333	1553	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	77.986	386	1553	95	below_threshold
Shimia isoporae	strain=DSM 26433	GCA_004346865.1	647720	647720	type	True	77.7599	289	1553	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	77.6675	258	1553	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	77.0764	240	1553	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	77.0562	249	1553	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	77.0531	222	1553	95	below_threshold
Roseovarius aestuarii	strain=KCTC 22174	GCA_019966515.1	475083	475083	type	True	77.0166	201	1553	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	76.9807	226	1553	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	76.9722	233	1553	95	below_threshold
Thalassococcus halodurans	strain=DSM 26915	GCA_900108225.1	373675	373675	type	True	76.9426	168	1553	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	76.9314	263	1553	95	below_threshold
Aliiroseovarius pelagivivens	strain=CECT 8811	GCA_900302485.1	1639690	1639690	type	True	76.899	189	1553	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	76.7378	150	1553	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	76.6383	164	1553	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	76.611	148	1553	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	76.3209	151	1553	95	below_threshold
Rhodobacter tardus	strain=CYK-10	GCA_009925085.1	2699202	2699202	type	True	75.9792	87	1553	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:04:39,419] [INFO] DFAST Taxonomy check result was written to GCF_003014475.1_ASM301447v1_genomic.fna/tc_result.tsv
[2024-01-25 20:04:39,420] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:04:39,420] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:04:39,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15fac639-b213-41ae-b944-55bc7104f519/dqc_reference/checkm_data
[2024-01-25 20:04:39,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:04:39,466] [INFO] Task started: CheckM
[2024-01-25 20:04:39,466] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003014475.1_ASM301447v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003014475.1_ASM301447v1_genomic.fna/checkm_input GCF_003014475.1_ASM301447v1_genomic.fna/checkm_result
[2024-01-25 20:05:21,832] [INFO] Task succeeded: CheckM
[2024-01-25 20:05:21,833] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:05:21,850] [INFO] ===== Completeness check finished =====
[2024-01-25 20:05:21,850] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:05:21,850] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003014475.1_ASM301447v1_genomic.fna/markers.fasta)
[2024-01-25 20:05:21,851] [INFO] Task started: Blastn
[2024-01-25 20:05:21,851] [INFO] Running command: blastn -query GCF_003014475.1_ASM301447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15fac639-b213-41ae-b944-55bc7104f519/dqc_reference/reference_markers_gtdb.fasta -out GCF_003014475.1_ASM301447v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:22,865] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:22,868] [INFO] Selected 18 target genomes.
[2024-01-25 20:05:22,868] [INFO] Target genome list was writen to GCF_003014475.1_ASM301447v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:05:22,897] [INFO] Task started: fastANI
[2024-01-25 20:05:22,897] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5e2a5f9-bb18-4b40-a6f2-3efb3418ee77/GCF_003014475.1_ASM301447v1_genomic.fna.gz --refList GCF_003014475.1_ASM301447v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003014475.1_ASM301447v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:05:38,334] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:38,346] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:05:38,346] [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_003014475.1	s__Shimia abyssi	100.0	1551	1553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900114635.1	s__Shimia aestuarii	78.9615	543	1553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016019955.1	s__Shimia sp016019955	78.5267	514	1553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	99.56	99.56	0.93	0.93	2	-
GCF_001458215.1	s__Shimia thalassica	78.2468	286	1553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	96.93	96.93	0.94	0.94	2	-
GCF_001458175.1	s__Shimia marina	78.2294	330	1553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	98.13	96.28	0.94	0.89	3	-
GCF_017743735.1	s__Shimia sp017743735	78.0513	390	1553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	95.87	95.63	0.93	0.93	3	-
GCF_001292625.1	s__Shimia sp001292625	78.0054	385	1553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114415.1	s__Shimia haliotis	78.0019	383	1553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142085.1	s__Shimia gijangensis	77.9371	294	1553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018223085.1	s__Shimia sp018223085	77.8614	277	1553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744095.1	s__Shimia sp017744095	77.8356	340	1553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900143615.1	s__Shimia sp900143615	77.7949	362	1553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743935.1	s__Ruegeria_E sp017743935	77.3862	280	1553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	77.1512	268	1553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_010500245.1	s__Ruegeria_B sp010500245	77.0856	263	1553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458395.1	s__Leisingera aquaemixtae	77.0671	248	1553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	97.55	97.51	0.94	0.92	3	-
GCF_000511355.1	s__Leisingera methylohalidivorans	77.0667	219	1553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709405.1	s__Marinibacterium sp002709405	76.6229	159	1553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:05:38,348] [INFO] GTDB search result was written to GCF_003014475.1_ASM301447v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:05:38,348] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:05:38,352] [INFO] DFAST_QC result json was written to GCF_003014475.1_ASM301447v1_genomic.fna/dqc_result.json
[2024-01-25 20:05:38,352] [INFO] DFAST_QC completed!
[2024-01-25 20:05:38,352] [INFO] Total running time: 0h1m33s