[2024-01-24 14:06:18,147] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:18,148] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:18,149] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1a9e428-fbb5-42b8-a79e-37ea4eed2b3b/dqc_reference
[2024-01-24 14:06:19,483] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:19,484] [INFO] Task started: Prodigal
[2024-01-24 14:06:19,484] [INFO] Running command: gunzip -c /var/lib/cwl/stg7bdb5f75-68bb-42b8-b96a-f60e61fc48d8/GCF_003932505.1_ASM393250v1_genomic.fna.gz | prodigal -d GCF_003932505.1_ASM393250v1_genomic.fna/cds.fna -a GCF_003932505.1_ASM393250v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:29,888] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:29,889] [INFO] Task started: HMMsearch
[2024-01-24 14:06:29,889] [INFO] Running command: hmmsearch --tblout GCF_003932505.1_ASM393250v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1a9e428-fbb5-42b8-a79e-37ea4eed2b3b/dqc_reference/reference_markers.hmm GCF_003932505.1_ASM393250v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:30,232] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:30,234] [INFO] Found 6/6 markers.
[2024-01-24 14:06:30,267] [INFO] Query marker FASTA was written to GCF_003932505.1_ASM393250v1_genomic.fna/markers.fasta
[2024-01-24 14:06:30,267] [INFO] Task started: Blastn
[2024-01-24 14:06:30,267] [INFO] Running command: blastn -query GCF_003932505.1_ASM393250v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1a9e428-fbb5-42b8-a79e-37ea4eed2b3b/dqc_reference/reference_markers.fasta -out GCF_003932505.1_ASM393250v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:31,412] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:31,415] [INFO] Selected 23 target genomes.
[2024-01-24 14:06:31,416] [INFO] Target genome list was writen to GCF_003932505.1_ASM393250v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:31,448] [INFO] Task started: fastANI
[2024-01-24 14:06:31,448] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bdb5f75-68bb-42b8-b96a-f60e61fc48d8/GCF_003932505.1_ASM393250v1_genomic.fna.gz --refList GCF_003932505.1_ASM393250v1_genomic.fna/target_genomes.txt --output GCF_003932505.1_ASM393250v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:48,144] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:48,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1a9e428-fbb5-42b8-a79e-37ea4eed2b3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:48,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1a9e428-fbb5-42b8-a79e-37ea4eed2b3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:48,163] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:48,163] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:48,163] [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
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	100.0	1099	1099	95	conclusive
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	78.5706	333	1099	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	78.2791	328	1099	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	78.1058	239	1099	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	77.8215	236	1099	95	below_threshold
Halorhodospira neutriphila	strain=DSM 15116	GCA_016584055.1	168379	168379	type	True	77.3828	159	1099	95	below_threshold
Aquisalimonas asiatica	strain=CGMCC 1.6291	GCA_900110585.1	406100	406100	type	True	77.3507	172	1099	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	77.3422	222	1099	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	77.2648	168	1099	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	77.2445	198	1099	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	77.2237	178	1099	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	77.2102	229	1099	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	77.165	188	1099	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.1519	222	1099	95	below_threshold
Ectothiorhodospira magna	strain=B7-7	GCA_900110965.1	867345	867345	type	True	77.1436	135	1099	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	76.9849	195	1099	95	below_threshold
Methylomagnum ishizawai	strain=RS11D-Pr	GCA_019670005.1	1760988	1760988	type	True	76.8696	147	1099	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.7949	181	1099	95	below_threshold
Halomonas pacifica	strain=NBRC 102220	GCA_007989625.1	77098	77098	type	True	76.6547	180	1099	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	76.5673	203	1099	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	76.2477	176	1099	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	76.1815	177	1099	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	76.1586	167	1099	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:48,165] [INFO] DFAST Taxonomy check result was written to GCF_003932505.1_ASM393250v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:48,166] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:48,166] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:48,166] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1a9e428-fbb5-42b8-a79e-37ea4eed2b3b/dqc_reference/checkm_data
[2024-01-24 14:06:48,167] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:48,200] [INFO] Task started: CheckM
[2024-01-24 14:06:48,200] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003932505.1_ASM393250v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003932505.1_ASM393250v1_genomic.fna/checkm_input GCF_003932505.1_ASM393250v1_genomic.fna/checkm_result
[2024-01-24 14:07:21,178] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:21,210] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:21,286] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:21,286] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:21,287] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003932505.1_ASM393250v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:21,287] [INFO] Task started: Blastn
[2024-01-24 14:07:21,287] [INFO] Running command: blastn -query GCF_003932505.1_ASM393250v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1a9e428-fbb5-42b8-a79e-37ea4eed2b3b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003932505.1_ASM393250v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:23,005] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:23,008] [INFO] Selected 15 target genomes.
[2024-01-24 14:07:23,008] [INFO] Target genome list was writen to GCF_003932505.1_ASM393250v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:23,023] [INFO] Task started: fastANI
[2024-01-24 14:07:23,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bdb5f75-68bb-42b8-b96a-f60e61fc48d8/GCF_003932505.1_ASM393250v1_genomic.fna.gz --refList GCF_003932505.1_ASM393250v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003932505.1_ASM393250v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:32,624] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:32,640] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:32,640] [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_003932505.1	s__Thiohalobacter thiocyanaticus	100.0	1099	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	87.9297	877	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
GCA_002699185.1	s__Thiohalobacter sp002699185	87.8235	676	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702725.1	s__BRH-c0 sp002702725	78.9819	67	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__BRH-c0	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	78.9019	344	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003695825.1	s__J048 sp003695825	78.7781	248	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__J048;f__J048;g__J048	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	78.5704	333	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494295.1	s__Thiogranum sp015494295	78.4231	291	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	99.47	99.47	0.86	0.86	2	-
GCF_003337735.1	s__Thioalbus denitrificans	78.2289	333	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-26407;f__DSM-26407;g__Thioalbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011371455.1	s__DRQN01 sp011371455	78.0919	200	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__DRQN01	95.0	97.38	97.35	0.90	0.88	5	-
GCF_900114895.1	s__Ectothiorhodospira mobilis_A	77.922	225	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378965.1	s__Thioalkalivibrio_A thiocyanodenitrificans	77.7934	238	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002376325.1	s__Sulfurivermis sp002376325	77.7593	167	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819175.1	s__JAHJQQ01 sp018819175	77.1708	202	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JAHJQQ01;f__JAHJQQ01;g__JAHJQQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859305.1	s__Luteimonas wenzhouensis	77.1337	184	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.47	99.47	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:32,642] [INFO] GTDB search result was written to GCF_003932505.1_ASM393250v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:32,643] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:32,647] [INFO] DFAST_QC result json was written to GCF_003932505.1_ASM393250v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:32,648] [INFO] DFAST_QC completed!
[2024-01-24 14:07:32,648] [INFO] Total running time: 0h1m15s