[2024-01-24 13:46:03,644] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:03,657] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:03,657] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3474046-f3ca-4cfc-8bb1-09d8b9407ef0/dqc_reference
[2024-01-24 13:46:04,990] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:04,991] [INFO] Task started: Prodigal
[2024-01-24 13:46:04,991] [INFO] Running command: gunzip -c /var/lib/cwl/stg368ce9fb-b945-48d2-bf98-05a797447ab1/GCF_014651855.1_ASM1465185v1_genomic.fna.gz | prodigal -d GCF_014651855.1_ASM1465185v1_genomic.fna/cds.fna -a GCF_014651855.1_ASM1465185v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:23,751] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:23,752] [INFO] Task started: HMMsearch
[2024-01-24 13:46:23,752] [INFO] Running command: hmmsearch --tblout GCF_014651855.1_ASM1465185v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3474046-f3ca-4cfc-8bb1-09d8b9407ef0/dqc_reference/reference_markers.hmm GCF_014651855.1_ASM1465185v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:24,079] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:24,081] [INFO] Found 6/6 markers.
[2024-01-24 13:46:24,127] [INFO] Query marker FASTA was written to GCF_014651855.1_ASM1465185v1_genomic.fna/markers.fasta
[2024-01-24 13:46:24,128] [INFO] Task started: Blastn
[2024-01-24 13:46:24,128] [INFO] Running command: blastn -query GCF_014651855.1_ASM1465185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3474046-f3ca-4cfc-8bb1-09d8b9407ef0/dqc_reference/reference_markers.fasta -out GCF_014651855.1_ASM1465185v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:25,042] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:25,045] [INFO] Selected 21 target genomes.
[2024-01-24 13:46:25,046] [INFO] Target genome list was writen to GCF_014651855.1_ASM1465185v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:25,063] [INFO] Task started: fastANI
[2024-01-24 13:46:25,063] [INFO] Running command: fastANI --query /var/lib/cwl/stg368ce9fb-b945-48d2-bf98-05a797447ab1/GCF_014651855.1_ASM1465185v1_genomic.fna.gz --refList GCF_014651855.1_ASM1465185v1_genomic.fna/target_genomes.txt --output GCF_014651855.1_ASM1465185v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:44,290] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:44,290] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3474046-f3ca-4cfc-8bb1-09d8b9407ef0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:44,291] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3474046-f3ca-4cfc-8bb1-09d8b9407ef0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:44,307] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:44,307] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:44,308] [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
Saccharospirillum salsuginis	strain=KCTC 22169	GCA_014651855.1	418750	418750	type	True	100.0	1825	1828	95	conclusive
Saccharospirillum mangrovi	strain=HK-33	GCA_003054775.1	2161747	2161747	type	True	78.4299	407	1828	95	below_threshold
Saccharospirillum mangrovi	strain=HK-33	GCA_003367315.1	2161747	2161747	type	True	78.3873	417	1828	95	below_threshold
Saccharospirillum alexandrii	strain=LZ-5	GCA_004000275.1	2448477	2448477	type	True	77.9773	449	1828	95	below_threshold
Saccharospirillum impatiens	strain=DSM 12546	GCA_000423605.1	169438	169438	type	True	77.7984	373	1828	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	77.1619	178	1828	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	77.1497	232	1828	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	77.1472	230	1828	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.9895	207	1828	95	below_threshold
Pseudomonas nitroreducens	strain=NBRC 12694	GCA_002091755.1	46680	46680	suspected-type	True	76.8935	189	1828	95	below_threshold
Pseudomonas nitroreducens	strain=DSM 14399	GCA_012986245.1	46680	46680	suspected-type	True	76.8554	193	1828	95	below_threshold
Pseudomonas guariconensis	strain=LMG 27394	GCA_900102675.1	1288410	1288410	suspected-type	True	76.852	133	1828	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	76.8446	98	1828	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	76.6227	134	1828	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	76.5721	133	1828	95	below_threshold
Pseudomonas azerbaijanoriens	strain=SWRI123	GCA_019139795.1	2842350	2842350	type	True	76.523	125	1828	95	below_threshold
Reinekea blandensis	strain=MED297	GCA_000153185.1	374838	374838	type	True	76.4557	97	1828	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	76.4119	140	1828	95	below_threshold
Pseudomonas palleroniana	strain=LMG 23076	GCA_003031675.1	191390	191390	type	True	76.2607	124	1828	95	below_threshold
Pseudomonas cremoris	strain=WS 5106	GCA_014230465.1	2724178	2724178	type	True	76.2516	106	1828	95	below_threshold
Marinobacterium profundum	strain=PAMC 27536	GCA_001528745.1	1714300	1714300	type	True	76.1489	102	1828	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:44,310] [INFO] DFAST Taxonomy check result was written to GCF_014651855.1_ASM1465185v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:44,310] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:44,311] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:44,311] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3474046-f3ca-4cfc-8bb1-09d8b9407ef0/dqc_reference/checkm_data
[2024-01-24 13:46:44,312] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:44,365] [INFO] Task started: CheckM
[2024-01-24 13:46:44,366] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651855.1_ASM1465185v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651855.1_ASM1465185v1_genomic.fna/checkm_input GCF_014651855.1_ASM1465185v1_genomic.fna/checkm_result
[2024-01-24 13:47:36,880] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:36,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:36,899] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:36,900] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:36,900] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651855.1_ASM1465185v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:36,900] [INFO] Task started: Blastn
[2024-01-24 13:47:36,900] [INFO] Running command: blastn -query GCF_014651855.1_ASM1465185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3474046-f3ca-4cfc-8bb1-09d8b9407ef0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651855.1_ASM1465185v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:38,389] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:38,392] [INFO] Selected 20 target genomes.
[2024-01-24 13:47:38,393] [INFO] Target genome list was writen to GCF_014651855.1_ASM1465185v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:38,418] [INFO] Task started: fastANI
[2024-01-24 13:47:38,418] [INFO] Running command: fastANI --query /var/lib/cwl/stg368ce9fb-b945-48d2-bf98-05a797447ab1/GCF_014651855.1_ASM1465185v1_genomic.fna.gz --refList GCF_014651855.1_ASM1465185v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651855.1_ASM1465185v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:55,991] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:56,006] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:56,007] [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_014651855.1	s__Saccharospirillum salsuginis	100.0	1825	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003367315.1	s__Saccharospirillum mangrovi	78.3958	417	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003054965.1	s__Saccharospirillum sp003054965	78.1553	291	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402545.1	s__Saccharospirillum sp018402545	78.0507	419	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000275.1	s__Saccharospirillum alexandrii	77.9673	453	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423605.1	s__Saccharospirillum impatiens	77.8288	372	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	77.2985	171	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCF_000761545.1	s__Pseudomonas_E sp000761545	77.1157	181	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004327985.1	s__Marinobacter_A halodurans	77.0834	172	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017491605.1	s__Pseudomonas sp017491605	77.057	205	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003205495.1	s__Pseudomonas_E alcaligenes_B	77.0196	190	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000313755.1	s__Pseudomonas nitroreducens_A	76.9734	179	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	96.60	96.60	0.86	0.86	2	-
GCF_002091755.1	s__Pseudomonas nitroreducens	76.8918	188	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	98.47	95.19	0.93	0.83	16	-
GCF_009883635.2	s__Pseudomonas_E putida_W	76.8068	167	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452115.1	s__Pseudomonas nitroreducens_B	76.8064	184	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741075.1	s__Pseudomonas_E putida_T	76.7471	153	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.21	95.06	0.91	0.90	4	-
GCF_900536025.1	s__Pseudomonas_E reidholzensis	76.5097	166	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013386115.1	s__Pseudomonas_E gingeri_B	76.4421	158	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.74	98.43	0.94	0.92	9	-
GCF_009905435.1	s__Pseudomonas_E sp009905435	76.3122	130	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001528745.1	s__Marinobacterium_A profundum	76.1648	101	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:56,008] [INFO] GTDB search result was written to GCF_014651855.1_ASM1465185v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:56,009] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:56,013] [INFO] DFAST_QC result json was written to GCF_014651855.1_ASM1465185v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:56,013] [INFO] DFAST_QC completed!
[2024-01-24 13:47:56,013] [INFO] Total running time: 0h1m52s