[2024-01-24 14:10:13,725] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:10:13,727] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:10:13,727] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2022b24-e24a-44b1-ba89-713dc2376f67/dqc_reference
[2024-01-24 14:10:14,893] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:10:14,894] [INFO] Task started: Prodigal
[2024-01-24 14:10:14,894] [INFO] Running command: gunzip -c /var/lib/cwl/stg290ff910-b834-4b36-b73a-7686d718bfcf/GCF_025175675.1_ASM2517567v1_genomic.fna.gz | prodigal -d GCF_025175675.1_ASM2517567v1_genomic.fna/cds.fna -a GCF_025175675.1_ASM2517567v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:10:27,914] [INFO] Task succeeded: Prodigal
[2024-01-24 14:10:27,914] [INFO] Task started: HMMsearch
[2024-01-24 14:10:27,914] [INFO] Running command: hmmsearch --tblout GCF_025175675.1_ASM2517567v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2022b24-e24a-44b1-ba89-713dc2376f67/dqc_reference/reference_markers.hmm GCF_025175675.1_ASM2517567v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:10:28,148] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:10:28,149] [INFO] Found 6/6 markers.
[2024-01-24 14:10:28,187] [INFO] Query marker FASTA was written to GCF_025175675.1_ASM2517567v1_genomic.fna/markers.fasta
[2024-01-24 14:10:28,188] [INFO] Task started: Blastn
[2024-01-24 14:10:28,188] [INFO] Running command: blastn -query GCF_025175675.1_ASM2517567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2022b24-e24a-44b1-ba89-713dc2376f67/dqc_reference/reference_markers.fasta -out GCF_025175675.1_ASM2517567v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:10:28,987] [INFO] Task succeeded: Blastn
[2024-01-24 14:10:28,990] [INFO] Selected 24 target genomes.
[2024-01-24 14:10:28,990] [INFO] Target genome list was writen to GCF_025175675.1_ASM2517567v1_genomic.fna/target_genomes.txt
[2024-01-24 14:10:29,040] [INFO] Task started: fastANI
[2024-01-24 14:10:29,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg290ff910-b834-4b36-b73a-7686d718bfcf/GCF_025175675.1_ASM2517567v1_genomic.fna.gz --refList GCF_025175675.1_ASM2517567v1_genomic.fna/target_genomes.txt --output GCF_025175675.1_ASM2517567v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:10:44,901] [INFO] Task succeeded: fastANI
[2024-01-24 14:10:44,901] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2022b24-e24a-44b1-ba89-713dc2376f67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:10:44,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2022b24-e24a-44b1-ba89-713dc2376f67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:10:44,919] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:10:44,919] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:10:44,919] [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
Sedimenticola selenatireducens	strain=DSM 17993	GCA_000428045.1	191960	191960	type	True	83.0075	957	1504	95	below_threshold
Sedimenticola thiotaurini	strain=SIP-G1	GCA_001007875.1	1543721	1543721	type	True	80.9633	792	1504	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	77.8692	299	1504	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	77.4676	208	1504	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	77.3638	231	1504	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	77.354	247	1504	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	77.2494	201	1504	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	77.2289	240	1504	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	77.1779	251	1504	95	below_threshold
Thiohalocapsa halophila	strain=DSM 6210	GCA_016583825.1	69359	69359	type	True	76.9724	213	1504	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.894	133	1504	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.8803	204	1504	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	76.7361	133	1504	95	below_threshold
Thiohalophilus thiocyanatoxydans	strain=DSM 16326	GCA_004366735.1	381308	381308	type	True	76.6986	135	1504	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	76.6018	162	1504	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.5491	167	1504	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	76.499	154	1504	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.4902	172	1504	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	76.3964	139	1504	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	76.3901	170	1504	95	below_threshold
Plasticicumulans acidivorans	strain=DSM 23606	GCA_003182095.1	886464	886464	type	True	76.2747	148	1504	95	below_threshold
Aeromonas diversa	strain=CECT 4254	GCA_000819805.1	502790	502790	type	True	76.0295	110	1504	95	below_threshold
Pseudomonas flavescens	strain=NBRC 103044	GCA_002091575.1	29435	29435	type	True	75.9128	123	1504	95	below_threshold
Pseudomonas flavescens	strain=LMG 18387	GCA_900100535.1	29435	29435	type	True	75.9128	123	1504	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:10:44,921] [INFO] DFAST Taxonomy check result was written to GCF_025175675.1_ASM2517567v1_genomic.fna/tc_result.tsv
[2024-01-24 14:10:44,922] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:10:44,922] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:10:44,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2022b24-e24a-44b1-ba89-713dc2376f67/dqc_reference/checkm_data
[2024-01-24 14:10:44,923] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:10:44,968] [INFO] Task started: CheckM
[2024-01-24 14:10:44,969] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025175675.1_ASM2517567v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025175675.1_ASM2517567v1_genomic.fna/checkm_input GCF_025175675.1_ASM2517567v1_genomic.fna/checkm_result
[2024-01-24 14:11:25,141] [INFO] Task succeeded: CheckM
[2024-01-24 14:11:25,142] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:11:25,161] [INFO] ===== Completeness check finished =====
[2024-01-24 14:11:25,162] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:11:25,162] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025175675.1_ASM2517567v1_genomic.fna/markers.fasta)
[2024-01-24 14:11:25,162] [INFO] Task started: Blastn
[2024-01-24 14:11:25,162] [INFO] Running command: blastn -query GCF_025175675.1_ASM2517567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2022b24-e24a-44b1-ba89-713dc2376f67/dqc_reference/reference_markers_gtdb.fasta -out GCF_025175675.1_ASM2517567v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:11:26,852] [INFO] Task succeeded: Blastn
[2024-01-24 14:11:26,860] [INFO] Selected 15 target genomes.
[2024-01-24 14:11:26,860] [INFO] Target genome list was writen to GCF_025175675.1_ASM2517567v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:11:26,950] [INFO] Task started: fastANI
[2024-01-24 14:11:26,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg290ff910-b834-4b36-b73a-7686d718bfcf/GCF_025175675.1_ASM2517567v1_genomic.fna.gz --refList GCF_025175675.1_ASM2517567v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025175675.1_ASM2517567v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:11:36,647] [INFO] Task succeeded: fastANI
[2024-01-24 14:11:36,660] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:11:36,661] [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_000428045.1	s__Sedimenticola selenatireducens	83.0365	953	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola	95.0	98.15	98.15	0.90	0.90	2	-
GCF_001007875.1	s__Sedimenticola thiotaurini	80.9531	793	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051715.1	s__HyVt-443 sp011051715	79.1775	415	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__HyVt-443	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003062205.1	s__Sedimenticola_A endophacoides	78.6586	367	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola_A	95.0	99.88	99.76	0.97	0.95	6	-
GCF_007625115.1	s__Sedimenticola selenatireducens_A	78.2268	328	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007713595.1	s__Sedimenticola thiotaurini_A	78.1786	374	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002020805.1	s__GCF-002020805 sp002020805	78.0108	223	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__GCF-002020805	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003972985.1	s__Thiolapillus sp003972985	77.8225	197	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiolapillus	95.0	99.52	99.52	0.88	0.88	2	-
GCA_011051655.1	s__DRKS01 sp011051655	77.8038	230	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__DRKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	77.49	234	1504	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	77.1282	183	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011947365.2	s__QGON01 sp011947365	77.0195	172	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__QGON01	95.0	97.47	97.46	0.87	0.84	3	-
GCA_003696905.1	s__MONJU sp003696905	76.9924	162	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__MONJU	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016842065.1	s__Thiodiazotropha sp016842065	76.6553	136	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182095.1	s__Plasticicumulans acidivorans	76.2629	149	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:11:36,662] [INFO] GTDB search result was written to GCF_025175675.1_ASM2517567v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:11:36,663] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:11:36,668] [INFO] DFAST_QC result json was written to GCF_025175675.1_ASM2517567v1_genomic.fna/dqc_result.json
[2024-01-24 14:11:36,668] [INFO] DFAST_QC completed!
[2024-01-24 14:11:36,668] [INFO] Total running time: 0h1m23s