[2024-01-25 20:13:05,761] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:05,763] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:05,763] [INFO] DQC Reference Directory: /var/lib/cwl/stg9eebcfdf-47b1-4095-9760-3c65b8804036/dqc_reference
[2024-01-25 20:13:06,898] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:06,898] [INFO] Task started: Prodigal
[2024-01-25 20:13:06,899] [INFO] Running command: gunzip -c /var/lib/cwl/stg46e4f579-fed3-4b13-b2ca-404f55737e0c/GCF_014645095.1_ASM1464509v1_genomic.fna.gz | prodigal -d GCF_014645095.1_ASM1464509v1_genomic.fna/cds.fna -a GCF_014645095.1_ASM1464509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:18,308] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:18,308] [INFO] Task started: HMMsearch
[2024-01-25 20:13:18,308] [INFO] Running command: hmmsearch --tblout GCF_014645095.1_ASM1464509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9eebcfdf-47b1-4095-9760-3c65b8804036/dqc_reference/reference_markers.hmm GCF_014645095.1_ASM1464509v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:18,585] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:18,586] [INFO] Found 6/6 markers.
[2024-01-25 20:13:18,630] [INFO] Query marker FASTA was written to GCF_014645095.1_ASM1464509v1_genomic.fna/markers.fasta
[2024-01-25 20:13:18,631] [INFO] Task started: Blastn
[2024-01-25 20:13:18,631] [INFO] Running command: blastn -query GCF_014645095.1_ASM1464509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9eebcfdf-47b1-4095-9760-3c65b8804036/dqc_reference/reference_markers.fasta -out GCF_014645095.1_ASM1464509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:19,507] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:19,509] [INFO] Selected 18 target genomes.
[2024-01-25 20:13:19,510] [INFO] Target genome list was writen to GCF_014645095.1_ASM1464509v1_genomic.fna/target_genomes.txt
[2024-01-25 20:13:19,522] [INFO] Task started: fastANI
[2024-01-25 20:13:19,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg46e4f579-fed3-4b13-b2ca-404f55737e0c/GCF_014645095.1_ASM1464509v1_genomic.fna.gz --refList GCF_014645095.1_ASM1464509v1_genomic.fna/target_genomes.txt --output GCF_014645095.1_ASM1464509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:13:36,926] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:36,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9eebcfdf-47b1-4095-9760-3c65b8804036/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:13:36,926] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9eebcfdf-47b1-4095-9760-3c65b8804036/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:13:36,938] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:13:36,938] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:13:36,938] [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
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	100.0	1542	1544	95	conclusive
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	99.9936	1540	1544	95	conclusive
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	79.7706	726	1544	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	79.7509	684	1544	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	79.7452	642	1544	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	79.6358	655	1544	95	below_threshold
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	79.5304	659	1544	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	79.4497	670	1544	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.4428	618	1544	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	79.4208	655	1544	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	79.3643	663	1544	95	below_threshold
Pseudooceanicola algae	strain=Lw-13e	GCA_003590145.2	1537215	1537215	type	True	78.9918	528	1544	95	below_threshold
Roseivivax halotolerans	strain=JCM 10271	GCA_900115815.1	93684	93684	type	True	78.7473	433	1544	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.4024	495	1544	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	78.2594	446	1544	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	78.0589	393	1544	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	77.9626	404	1544	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	77.7264	416	1544	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:13:36,940] [INFO] DFAST Taxonomy check result was written to GCF_014645095.1_ASM1464509v1_genomic.fna/tc_result.tsv
[2024-01-25 20:13:36,941] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:13:36,941] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:13:36,941] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9eebcfdf-47b1-4095-9760-3c65b8804036/dqc_reference/checkm_data
[2024-01-25 20:13:36,942] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:13:36,996] [INFO] Task started: CheckM
[2024-01-25 20:13:36,996] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645095.1_ASM1464509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645095.1_ASM1464509v1_genomic.fna/checkm_input GCF_014645095.1_ASM1464509v1_genomic.fna/checkm_result
[2024-01-25 20:14:33,892] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:33,893] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:33,908] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:33,908] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:33,909] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645095.1_ASM1464509v1_genomic.fna/markers.fasta)
[2024-01-25 20:14:33,909] [INFO] Task started: Blastn
[2024-01-25 20:14:33,910] [INFO] Running command: blastn -query GCF_014645095.1_ASM1464509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9eebcfdf-47b1-4095-9760-3c65b8804036/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645095.1_ASM1464509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:35,497] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:35,500] [INFO] Selected 17 target genomes.
[2024-01-25 20:14:35,500] [INFO] Target genome list was writen to GCF_014645095.1_ASM1464509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:35,513] [INFO] Task started: fastANI
[2024-01-25 20:14:35,513] [INFO] Running command: fastANI --query /var/lib/cwl/stg46e4f579-fed3-4b13-b2ca-404f55737e0c/GCF_014645095.1_ASM1464509v1_genomic.fna.gz --refList GCF_014645095.1_ASM1464509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645095.1_ASM1464509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:14:53,709] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:53,720] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:14:53,721] [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_000688295.1	s__Pseudooceanicola nanhaiensis	99.9936	1540	1544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002210105.1	s__Pseudooceanicola sp002210105	83.2239	1029	1544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789075.1	s__Pseudooceanicola pacificus	82.4261	620	1544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152725.1	s__Pseudooceanicola batsensis	81.5997	756	1544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638275.1	s__Pseudooceanicola flagellatus	80.9618	738	1544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222585.1	s__Pseudooceanicola sp018222585	80.2205	727	1544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	79.9989	635	1544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	79.7852	656	1544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102075.1	s__Salipiger thiooxidans	79.758	729	1544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_002300555.1	s__Salipiger sp002300555	79.6773	507	1544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827095.1	s__Pseudooceanicola sp009827095	79.6366	654	1544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900109195.1	s__Pseudooceanicola nitratireducens	79.4621	668	1544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	98.54	97.09	0.97	0.95	3	-
GCF_900116195.1	s__Salipiger pacificus	79.3669	663	1544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000379485.1	s__Wenxinia marina	79.2638	621	1544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCF_900141735.1	s__Wenxinia saemankumensis	79.0548	581	1544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590145.2	s__Pseudooceanicola algae	78.9829	529	1544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689705.1	s__HKCCE3408 sp015689705	78.887	525	1544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:14:53,722] [INFO] GTDB search result was written to GCF_014645095.1_ASM1464509v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:14:53,723] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:14:53,727] [INFO] DFAST_QC result json was written to GCF_014645095.1_ASM1464509v1_genomic.fna/dqc_result.json
[2024-01-25 20:14:53,727] [INFO] DFAST_QC completed!
[2024-01-25 20:14:53,727] [INFO] Total running time: 0h1m48s