[2024-01-25 17:37:51,137] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:37:51,146] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:37:51,146] [INFO] DQC Reference Directory: /var/lib/cwl/stge6da33b3-9dd2-40ac-a321-3ab4d7517bea/dqc_reference
[2024-01-25 17:37:52,321] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:37:52,322] [INFO] Task started: Prodigal
[2024-01-25 17:37:52,323] [INFO] Running command: gunzip -c /var/lib/cwl/stg083e1cfd-0c00-4940-9e23-695cba8cf122/GCF_003385955.1_ASM338595v1_genomic.fna.gz | prodigal -d GCF_003385955.1_ASM338595v1_genomic.fna/cds.fna -a GCF_003385955.1_ASM338595v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:38:06,009] [INFO] Task succeeded: Prodigal
[2024-01-25 17:38:06,009] [INFO] Task started: HMMsearch
[2024-01-25 17:38:06,009] [INFO] Running command: hmmsearch --tblout GCF_003385955.1_ASM338595v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6da33b3-9dd2-40ac-a321-3ab4d7517bea/dqc_reference/reference_markers.hmm GCF_003385955.1_ASM338595v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:38:06,320] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:38:06,321] [INFO] Found 6/6 markers.
[2024-01-25 17:38:06,368] [INFO] Query marker FASTA was written to GCF_003385955.1_ASM338595v1_genomic.fna/markers.fasta
[2024-01-25 17:38:06,369] [INFO] Task started: Blastn
[2024-01-25 17:38:06,369] [INFO] Running command: blastn -query GCF_003385955.1_ASM338595v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6da33b3-9dd2-40ac-a321-3ab4d7517bea/dqc_reference/reference_markers.fasta -out GCF_003385955.1_ASM338595v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:07,097] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:07,106] [INFO] Selected 25 target genomes.
[2024-01-25 17:38:07,106] [INFO] Target genome list was writen to GCF_003385955.1_ASM338595v1_genomic.fna/target_genomes.txt
[2024-01-25 17:38:07,117] [INFO] Task started: fastANI
[2024-01-25 17:38:07,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg083e1cfd-0c00-4940-9e23-695cba8cf122/GCF_003385955.1_ASM338595v1_genomic.fna.gz --refList GCF_003385955.1_ASM338595v1_genomic.fna/target_genomes.txt --output GCF_003385955.1_ASM338595v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:38:27,704] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:27,704] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6da33b3-9dd2-40ac-a321-3ab4d7517bea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:38:27,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6da33b3-9dd2-40ac-a321-3ab4d7517bea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:38:27,715] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:38:27,715] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:38:27,715] [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
Aestuariispira insulae	strain=CECT 8488	GCA_003385955.1	1461337	1461337	type	True	100.0	1580	1581	95	conclusive
Aestuariispira ectoiniformans	strain=SWCN16	GCA_025136295.1	2775080	2775080	type	True	77.4247	279	1581	95	below_threshold
Thalassospira tepidiphila	strain=DSM 18888	GCA_011927685.1	393657	393657	type	True	76.4052	81	1581	95	below_threshold
Pacificispira spongiicola	strain=KN72	GCA_012926505.1	2729598	2729598	type	True	76.2147	120	1581	95	below_threshold
Hwanghaeella grinnelliae	strain=Gri0909	GCA_004005845.1	2500179	2500179	type	True	76.201	102	1581	95	below_threshold
Thalassospira profundimaris	strain=WP0211	GCA_000300275.1	502049	502049	suspected-type	True	76.1732	70	1581	95	below_threshold
Thalassospira tepidiphila	strain=MCCC 1A03514	GCA_001662875.1	393657	393657	type	True	76.1727	77	1581	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	76.1611	76	1581	95	below_threshold
Marivibrio halodurans	strain=CGMCC 1.15697	GCA_017963645.1	2039722	2039722	type	True	76.1479	96	1581	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	75.8357	81	1581	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	75.7146	77	1581	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	75.6918	85	1581	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	75.4348	50	1581	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.4294	80	1581	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:38:27,716] [INFO] DFAST Taxonomy check result was written to GCF_003385955.1_ASM338595v1_genomic.fna/tc_result.tsv
[2024-01-25 17:38:27,718] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:38:27,718] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:38:27,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6da33b3-9dd2-40ac-a321-3ab4d7517bea/dqc_reference/checkm_data
[2024-01-25 17:38:27,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:38:27,764] [INFO] Task started: CheckM
[2024-01-25 17:38:27,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003385955.1_ASM338595v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003385955.1_ASM338595v1_genomic.fna/checkm_input GCF_003385955.1_ASM338595v1_genomic.fna/checkm_result
[2024-01-25 17:39:10,973] [INFO] Task succeeded: CheckM
[2024-01-25 17:39:10,974] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:39:10,993] [INFO] ===== Completeness check finished =====
[2024-01-25 17:39:10,993] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:39:10,993] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003385955.1_ASM338595v1_genomic.fna/markers.fasta)
[2024-01-25 17:39:10,993] [INFO] Task started: Blastn
[2024-01-25 17:39:10,993] [INFO] Running command: blastn -query GCF_003385955.1_ASM338595v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6da33b3-9dd2-40ac-a321-3ab4d7517bea/dqc_reference/reference_markers_gtdb.fasta -out GCF_003385955.1_ASM338595v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:12,318] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:12,321] [INFO] Selected 26 target genomes.
[2024-01-25 17:39:12,321] [INFO] Target genome list was writen to GCF_003385955.1_ASM338595v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:39:12,333] [INFO] Task started: fastANI
[2024-01-25 17:39:12,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg083e1cfd-0c00-4940-9e23-695cba8cf122/GCF_003385955.1_ASM338595v1_genomic.fna.gz --refList GCF_003385955.1_ASM338595v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003385955.1_ASM338595v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:39:31,392] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:31,402] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:39:31,403] [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_003385955.1	s__Aestuariispira insulae	100.0	1580	1581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__Aestuariispira	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017792345.1	s__GCA-2696645 sp017792345	76.6433	137	1581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	95.39	95.37	0.96	0.95	3	-
GCA_012926505.1	s__GCA-2696645 sp012926505	76.2147	120	1581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005845.1	s__Hwanghaeella grinnelliae	76.201	102	1581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__Hwanghaeella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300275.1	s__Thalassospira profundimaris	76.1732	70	1581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	N/A	N/A	N/A	N/A	1	-
GCF_001662875.1	s__Thalassospira tepidiphila	76.1727	77	1581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	96.58	95.57	0.94	0.88	15	-
GCA_002696645.1	s__GCA-2696645 sp002696645	76.128	92	1581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	99.85	99.85	0.96	0.96	2	-
GCF_000948415.1	s__Thalassospira sp000948415	76.0726	79	1581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003403095.1	s__Thalassospira indica	76.0684	77	1581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006385175.1	s__Emcibacter nanhaiensis	75.9674	61	1581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Emcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006844765.1	s__SPJV01 sp006844765	75.8166	50	1581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__SPJV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006980715.1	s__Oleiliquidispirillum nitrogeniifigens	75.8051	81	1581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Oleiliquidispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018336035.1	s__Ferrovibrio sp018336035	75.6693	67	1581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482765.1	s__Ferrovibrio sp002482765	75.5409	68	1581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	95.40	95.40	0.86	0.86	2	-
GCF_000423185.1	s__Inquilinus limosus	75.4429	79	1581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355985.1	s__Desertibacter sp017355985	75.4167	51	1581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Desertibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654615.1	s__Telmatospirillum sp015654615	75.3815	53	1581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:39:31,404] [INFO] GTDB search result was written to GCF_003385955.1_ASM338595v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:39:31,405] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:39:31,408] [INFO] DFAST_QC result json was written to GCF_003385955.1_ASM338595v1_genomic.fna/dqc_result.json
[2024-01-25 17:39:31,408] [INFO] DFAST_QC completed!
[2024-01-25 17:39:31,408] [INFO] Total running time: 0h1m40s