[2024-01-24 12:47:21,858] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:21,861] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:21,861] [INFO] DQC Reference Directory: /var/lib/cwl/stgbcd6cb55-505e-4bfb-80cf-8f96ce0c9e18/dqc_reference
[2024-01-24 12:47:23,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:23,101] [INFO] Task started: Prodigal
[2024-01-24 12:47:23,101] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8321c9c-85cc-4a9b-b8bc-4868f7e1e889/GCF_004341245.1_ASM434124v1_genomic.fna.gz | prodigal -d GCF_004341245.1_ASM434124v1_genomic.fna/cds.fna -a GCF_004341245.1_ASM434124v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:36,431] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:36,432] [INFO] Task started: HMMsearch
[2024-01-24 12:47:36,432] [INFO] Running command: hmmsearch --tblout GCF_004341245.1_ASM434124v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbcd6cb55-505e-4bfb-80cf-8f96ce0c9e18/dqc_reference/reference_markers.hmm GCF_004341245.1_ASM434124v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:36,779] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:36,781] [INFO] Found 6/6 markers.
[2024-01-24 12:47:36,825] [INFO] Query marker FASTA was written to GCF_004341245.1_ASM434124v1_genomic.fna/markers.fasta
[2024-01-24 12:47:36,825] [INFO] Task started: Blastn
[2024-01-24 12:47:36,825] [INFO] Running command: blastn -query GCF_004341245.1_ASM434124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcd6cb55-505e-4bfb-80cf-8f96ce0c9e18/dqc_reference/reference_markers.fasta -out GCF_004341245.1_ASM434124v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:37,947] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:37,951] [INFO] Selected 22 target genomes.
[2024-01-24 12:47:37,951] [INFO] Target genome list was writen to GCF_004341245.1_ASM434124v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:37,965] [INFO] Task started: fastANI
[2024-01-24 12:47:37,965] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8321c9c-85cc-4a9b-b8bc-4868f7e1e889/GCF_004341245.1_ASM434124v1_genomic.fna.gz --refList GCF_004341245.1_ASM434124v1_genomic.fna/target_genomes.txt --output GCF_004341245.1_ASM434124v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:54,982] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:54,982] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbcd6cb55-505e-4bfb-80cf-8f96ce0c9e18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:54,983] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbcd6cb55-505e-4bfb-80cf-8f96ce0c9e18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:54,999] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:54,999] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:54,999] [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
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	100.0	1431	1436	95	conclusive
Plasticicumulans acidivorans	strain=DSM 23606	GCA_003182095.1	886464	886464	type	True	80.1542	659	1436	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	77.4247	369	1436	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.3906	386	1436	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	77.3186	329	1436	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	77.2902	238	1436	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	77.2902	350	1436	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	77.211	296	1436	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	77.1378	364	1436	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	77.1171	445	1436	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	77.0787	428	1436	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	77.0196	375	1436	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	77.014	229	1436	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	77.0021	312	1436	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.9507	400	1436	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	76.943	320	1436	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	76.907	232	1436	95	below_threshold
Acidihalobacter aeolianus	strain=V6	GCA_001753165.1	2792603	2792603	type	True	76.9025	200	1436	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	76.8416	440	1436	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	76.7937	235	1436	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	76.6732	304	1436	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	76.5112	384	1436	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:55,002] [INFO] DFAST Taxonomy check result was written to GCF_004341245.1_ASM434124v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:55,003] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:55,003] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:55,004] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbcd6cb55-505e-4bfb-80cf-8f96ce0c9e18/dqc_reference/checkm_data
[2024-01-24 12:47:55,006] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:55,054] [INFO] Task started: CheckM
[2024-01-24 12:47:55,054] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004341245.1_ASM434124v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004341245.1_ASM434124v1_genomic.fna/checkm_input GCF_004341245.1_ASM434124v1_genomic.fna/checkm_result
[2024-01-24 12:48:44,384] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:44,386] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:44,409] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:44,410] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:44,410] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004341245.1_ASM434124v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:44,411] [INFO] Task started: Blastn
[2024-01-24 12:48:44,411] [INFO] Running command: blastn -query GCF_004341245.1_ASM434124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcd6cb55-505e-4bfb-80cf-8f96ce0c9e18/dqc_reference/reference_markers_gtdb.fasta -out GCF_004341245.1_ASM434124v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:46,656] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:46,661] [INFO] Selected 18 target genomes.
[2024-01-24 12:48:46,661] [INFO] Target genome list was writen to GCF_004341245.1_ASM434124v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:46,673] [INFO] Task started: fastANI
[2024-01-24 12:48:46,673] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8321c9c-85cc-4a9b-b8bc-4868f7e1e889/GCF_004341245.1_ASM434124v1_genomic.fna.gz --refList GCF_004341245.1_ASM434124v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004341245.1_ASM434124v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:59,842] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:59,859] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:59,860] [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_004341245.1	s__Plasticicumulans_A lactativorans	100.0	1431	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018240295.1	s__Plasticicumulans sp003962905	81.1906	701	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	98.50	98.50	0.84	0.84	2	-
GCF_003182095.1	s__Plasticicumulans acidivorans	80.0511	671	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716465.1	s__JADJWH01 sp016716465	77.5733	222	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JADJWH01;f__JADJWH01;g__JADJWH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	77.5205	365	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCA_013348725.1	s__GCA-013348725 sp013348725	77.4302	285	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-013348725;f__GCA-013348725;g__GCA-013348725	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011371455.1	s__DRQN01 sp011371455	77.3198	159	1436	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	-
GCA_011321775.1	s__Thiogranum sp011321775	77.2751	189	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002391525.1	s__Competibacter_A sp002391525	77.2529	251	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Competibacter_A	95.0	99.79	99.79	0.93	0.93	2	-
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	77.2142	259	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
GCF_004343155.1	s__Marichromatium gracile	77.1227	366	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	98.88	96.74	0.96	0.94	6	-
GCF_003148905.1	s__Fulvimonas soli	77.073	452	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Fulvimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_012276755.1	s__Marichromatium bheemlicum	76.9718	316	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003989075.1	s__RXIX01 sp003989075	76.9015	195	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__RXIX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583835.1	s__Thiococcus pfennigii	76.8716	312	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiococcus	95.0	98.97	98.97	0.88	0.88	2	-
GCF_000559025.1	s__Luteimonas huabeiensis	76.8397	440	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003399765.1	s__AK92 sp003399765	76.6915	64	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__AK92;g__AK92	95.0	99.97	99.97	0.99	0.99	2	-
GCF_003730135.1	s__Stagnimonas aquatica	76.5504	304	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:59,861] [INFO] GTDB search result was written to GCF_004341245.1_ASM434124v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:59,863] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:59,867] [INFO] DFAST_QC result json was written to GCF_004341245.1_ASM434124v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:59,867] [INFO] DFAST_QC completed!
[2024-01-24 12:48:59,867] [INFO] Total running time: 0h1m38s