[2024-01-24 12:31:20,820] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:20,822] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:20,822] [INFO] DQC Reference Directory: /var/lib/cwl/stg531f66c0-19ec-4326-bf75-5ab59231d690/dqc_reference
[2024-01-24 12:31:22,083] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:22,084] [INFO] Task started: Prodigal
[2024-01-24 12:31:22,084] [INFO] Running command: gunzip -c /var/lib/cwl/stg33965e2c-824b-4a2f-acf4-7a0db2c34e48/GCF_005281615.1_ASM528161v1_genomic.fna.gz | prodigal -d GCF_005281615.1_ASM528161v1_genomic.fna/cds.fna -a GCF_005281615.1_ASM528161v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:40,112] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:40,112] [INFO] Task started: HMMsearch
[2024-01-24 12:31:40,112] [INFO] Running command: hmmsearch --tblout GCF_005281615.1_ASM528161v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg531f66c0-19ec-4326-bf75-5ab59231d690/dqc_reference/reference_markers.hmm GCF_005281615.1_ASM528161v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:40,397] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:40,399] [INFO] Found 6/6 markers.
[2024-01-24 12:31:40,444] [INFO] Query marker FASTA was written to GCF_005281615.1_ASM528161v1_genomic.fna/markers.fasta
[2024-01-24 12:31:40,445] [INFO] Task started: Blastn
[2024-01-24 12:31:40,445] [INFO] Running command: blastn -query GCF_005281615.1_ASM528161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg531f66c0-19ec-4326-bf75-5ab59231d690/dqc_reference/reference_markers.fasta -out GCF_005281615.1_ASM528161v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:41,356] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:41,359] [INFO] Selected 22 target genomes.
[2024-01-24 12:31:41,360] [INFO] Target genome list was writen to GCF_005281615.1_ASM528161v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:41,367] [INFO] Task started: fastANI
[2024-01-24 12:31:41,368] [INFO] Running command: fastANI --query /var/lib/cwl/stg33965e2c-824b-4a2f-acf4-7a0db2c34e48/GCF_005281615.1_ASM528161v1_genomic.fna.gz --refList GCF_005281615.1_ASM528161v1_genomic.fna/target_genomes.txt --output GCF_005281615.1_ASM528161v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:59,853] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:59,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg531f66c0-19ec-4326-bf75-5ab59231d690/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:59,854] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg531f66c0-19ec-4326-bf75-5ab59231d690/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:59,869] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:59,870] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:59,870] [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
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	100.0	1816	1817	95	conclusive
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	77.9604	199	1817	95	below_threshold
Rhodoligotrophos appendicifer	strain=120-1	GCA_007474605.1	987056	987056	type	True	77.8564	410	1817	95	below_threshold
Kaustia mangrovi	strain=R1DC25	GCA_015482775.1	2593653	2593653	type	True	77.803	352	1817	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.2636	309	1817	95	below_threshold
Aestuariivirga litoralis	strain=KCTC 52945	GCA_003234965.1	2650924	2650924	type	True	77.1776	236	1817	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	77.1148	223	1817	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	76.9877	258	1817	95	below_threshold
Xanthobacter autotrophicus	strain=DSM 432	GCA_005871085.1	280	280	type	True	76.9481	232	1817	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	76.9473	247	1817	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_016653375.1	34017	34017	type	True	76.9458	264	1817	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	76.9276	261	1817	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	76.9239	270	1817	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	76.8538	239	1817	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	76.6356	201	1817	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	76.544	256	1817	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	76.4483	196	1817	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	76.4146	177	1817	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.2602	279	1817	95	below_threshold
Afifella marina	strain=DSM 2698	GCA_900102695.1	1080	1080	type	True	76.1851	144	1817	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	75.9765	175	1817	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.9295	195	1817	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:59,872] [INFO] DFAST Taxonomy check result was written to GCF_005281615.1_ASM528161v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:59,873] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:59,873] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:59,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg531f66c0-19ec-4326-bf75-5ab59231d690/dqc_reference/checkm_data
[2024-01-24 12:31:59,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:59,923] [INFO] Task started: CheckM
[2024-01-24 12:31:59,924] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005281615.1_ASM528161v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005281615.1_ASM528161v1_genomic.fna/checkm_input GCF_005281615.1_ASM528161v1_genomic.fna/checkm_result
[2024-01-24 12:32:50,430] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:50,431] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:50,454] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:50,454] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:50,454] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005281615.1_ASM528161v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:50,454] [INFO] Task started: Blastn
[2024-01-24 12:32:50,454] [INFO] Running command: blastn -query GCF_005281615.1_ASM528161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg531f66c0-19ec-4326-bf75-5ab59231d690/dqc_reference/reference_markers_gtdb.fasta -out GCF_005281615.1_ASM528161v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:52,092] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:52,096] [INFO] Selected 20 target genomes.
[2024-01-24 12:32:52,096] [INFO] Target genome list was writen to GCF_005281615.1_ASM528161v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:52,126] [INFO] Task started: fastANI
[2024-01-24 12:32:52,126] [INFO] Running command: fastANI --query /var/lib/cwl/stg33965e2c-824b-4a2f-acf4-7a0db2c34e48/GCF_005281615.1_ASM528161v1_genomic.fna.gz --refList GCF_005281615.1_ASM528161v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005281615.1_ASM528161v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:07,860] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:07,875] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:07,875] [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_005281615.1	s__Rhodoligotrophos sp005281615	100.0	1816	1817	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Im1;g__Rhodoligotrophos	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007474605.1	s__Rhodoligotrophos appendicifer	77.8484	411	1817	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Im1;g__Rhodoligotrophos	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015482775.1	s__Kaustia mangrovi	77.8127	351	1817	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Im1;g__Kaustia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000192745.1	s__Polymorphum gilvum	77.4017	235	1817	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Polymorphum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003234965.1	s__Aestuariivirga litoralis	77.1876	235	1817	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Aestuariivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576695.1	s__Nordella sp003576695	77.0955	287	1817	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003574785.1	s__Nordella sp003574785	77.0787	280	1817	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702305.1	s__GCF-000702305 sp000702305	77.0602	243	1817	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__GCF-000702305	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007559435.1	s__Starkeya sp007559435	77.0537	241	1817	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	98.55	98.55	0.95	0.95	2	-
GCF_018390635.1	s__Ancylobacter_C lacus	76.9367	250	1817	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258835.1	s__Rhodobium orientis	76.9093	263	1817	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	99.99	99.98	0.99	0.98	3	-
GCA_017307955.1	s__Kaistia sp017307955	76.8396	229	1817	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005502925.1	s__Nordella sp005502925	76.7928	304	1817	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella	95.0	100.00	100.00	1.00	1.00	3	-
GCF_009600605.1	s__Pseudoxanthobacter spirostomi	76.7852	230	1817	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pseudoxanthobacteraceae;g__Pseudoxanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898115.1	s__Bosea sp001898115	76.6801	209	1817	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.21	98.43	0.96	0.93	3	-
GCF_014199915.1	s__Prosthecomicrobium pneumaticum	76.6563	224	1817	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Prosthecomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185245.1	s__Aestuariivirga sp016185245	76.5723	207	1817	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Aestuariivirga	95.0	99.81	99.81	0.97	0.97	2	-
GCA_007118805.1	s__SKQW01 sp007118805	76.5145	148	1817	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Tepidamorphaceae;g__SKQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124525.1	s__Oceanicella actignis	76.4366	175	1817	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
GCA_001464235.1	s__Phreatobacter sp001464235	76.3961	205	1817	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:07,877] [INFO] GTDB search result was written to GCF_005281615.1_ASM528161v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:07,877] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:07,881] [INFO] DFAST_QC result json was written to GCF_005281615.1_ASM528161v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:07,881] [INFO] DFAST_QC completed!
[2024-01-24 12:33:07,882] [INFO] Total running time: 0h1m47s