[2024-01-24 12:52:26,283] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:26,285] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:26,285] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b5c475e-c4f1-475a-9d63-946067e7da01/dqc_reference
[2024-01-24 12:52:27,558] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:27,559] [INFO] Task started: Prodigal
[2024-01-24 12:52:27,560] [INFO] Running command: gunzip -c /var/lib/cwl/stg2839a9f8-1cca-499b-a846-cafb67e25abd/GCF_003721225.1_ASM372122v1_genomic.fna.gz | prodigal -d GCF_003721225.1_ASM372122v1_genomic.fna/cds.fna -a GCF_003721225.1_ASM372122v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:52:35,861] [INFO] Task succeeded: Prodigal
[2024-01-24 12:52:35,861] [INFO] Task started: HMMsearch
[2024-01-24 12:52:35,861] [INFO] Running command: hmmsearch --tblout GCF_003721225.1_ASM372122v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b5c475e-c4f1-475a-9d63-946067e7da01/dqc_reference/reference_markers.hmm GCF_003721225.1_ASM372122v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:52:36,129] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:52:36,130] [INFO] Found 6/6 markers.
[2024-01-24 12:52:36,155] [INFO] Query marker FASTA was written to GCF_003721225.1_ASM372122v1_genomic.fna/markers.fasta
[2024-01-24 12:52:36,156] [INFO] Task started: Blastn
[2024-01-24 12:52:36,156] [INFO] Running command: blastn -query GCF_003721225.1_ASM372122v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b5c475e-c4f1-475a-9d63-946067e7da01/dqc_reference/reference_markers.fasta -out GCF_003721225.1_ASM372122v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:36,807] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:36,811] [INFO] Selected 26 target genomes.
[2024-01-24 12:52:36,811] [INFO] Target genome list was writen to GCF_003721225.1_ASM372122v1_genomic.fna/target_genomes.txt
[2024-01-24 12:52:36,848] [INFO] Task started: fastANI
[2024-01-24 12:52:36,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg2839a9f8-1cca-499b-a846-cafb67e25abd/GCF_003721225.1_ASM372122v1_genomic.fna.gz --refList GCF_003721225.1_ASM372122v1_genomic.fna/target_genomes.txt --output GCF_003721225.1_ASM372122v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:52:54,540] [INFO] Task succeeded: fastANI
[2024-01-24 12:52:54,540] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b5c475e-c4f1-475a-9d63-946067e7da01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:52:54,541] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b5c475e-c4f1-475a-9d63-946067e7da01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:52:54,554] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:52:54,554] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:52:54,555] [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
Acidithiobacillus sulfuriphilus	strain=CJ-2	GCA_003721225.1	1867749	1867749	type	True	100.0	825	843	95	conclusive
Acidithiobacillus ferrooxidans	strain=ATCC 23270	GCA_000021485.1	920	920	type	True	80.5111	256	843	95	below_threshold
Acidithiobacillus ferridurans	strain=JCM 18981	GCA_003966655.1	1232575	1232575	type	True	79.8793	254	843	95	below_threshold
Acidithiobacillus ferrianus	strain=MG	GCA_010378095.1	2678518	2678518	type	True	78.4758	223	843	95	below_threshold
Acidithiobacillus thiooxidans	strain=ATCC 19377	GCA_000227215.2	930	930	suspected-type	True	78.2531	109	843	95	below_threshold
Acidithiobacillus caldus	strain=ATCC 51756	GCA_000175575.2	33059	33059	type	True	77.7867	168	843	95	below_threshold
Acidithiobacillus caldus	strain=DSM 8584	GCA_018853615.1	33059	33059	type	True	77.689	162	843	95	below_threshold
Thermithiobacillus tepidarius	strain=DSM 3134	GCA_000423825.1	929	929	type	True	77.3444	125	843	95	below_threshold
Acidithiobacillus thiooxidans	strain=ATCC 19377	GCA_006718285.1	930	930	suspected-type	True	77.2146	110	843	95	below_threshold
Acidithiobacillus thiooxidans	strain=ATCC 19377	GCA_009662475.1	930	930	suspected-type	True	77.0218	107	843	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	76.3438	73	843	95	below_threshold
Thiohalospira halophila	strain=HL 3	GCA_900112605.1	381300	381300	type	True	76.1971	51	843	95	below_threshold
Bordetella pseudohinzii	strain=8-296-03	GCA_000657795.2	1331258	1331258	type	True	75.7143	50	843	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:52:54,557] [INFO] DFAST Taxonomy check result was written to GCF_003721225.1_ASM372122v1_genomic.fna/tc_result.tsv
[2024-01-24 12:52:54,558] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:52:54,558] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:52:54,558] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b5c475e-c4f1-475a-9d63-946067e7da01/dqc_reference/checkm_data
[2024-01-24 12:52:54,560] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:52:54,595] [INFO] Task started: CheckM
[2024-01-24 12:52:54,596] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003721225.1_ASM372122v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003721225.1_ASM372122v1_genomic.fna/checkm_input GCF_003721225.1_ASM372122v1_genomic.fna/checkm_result
[2024-01-24 12:53:23,314] [INFO] Task succeeded: CheckM
[2024-01-24 12:53:23,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:53:23,340] [INFO] ===== Completeness check finished =====
[2024-01-24 12:53:23,340] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:53:23,341] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003721225.1_ASM372122v1_genomic.fna/markers.fasta)
[2024-01-24 12:53:23,341] [INFO] Task started: Blastn
[2024-01-24 12:53:23,341] [INFO] Running command: blastn -query GCF_003721225.1_ASM372122v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b5c475e-c4f1-475a-9d63-946067e7da01/dqc_reference/reference_markers_gtdb.fasta -out GCF_003721225.1_ASM372122v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:24,387] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:24,391] [INFO] Selected 23 target genomes.
[2024-01-24 12:53:24,391] [INFO] Target genome list was writen to GCF_003721225.1_ASM372122v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:53:24,454] [INFO] Task started: fastANI
[2024-01-24 12:53:24,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg2839a9f8-1cca-499b-a846-cafb67e25abd/GCF_003721225.1_ASM372122v1_genomic.fna.gz --refList GCF_003721225.1_ASM372122v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003721225.1_ASM372122v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:53:37,249] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:37,268] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:53:37,269] [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_003721225.1	s__Acidithiobacillus_B sulfuriphilus	100.0	825	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000021485.1	s__Acidithiobacillus ferrooxidans	80.5111	256	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	98.94	96.59	0.87	0.73	15	-
GCF_018854495.1	s__Acidithiobacillus ferrooxidans_C	79.9577	243	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966655.1	s__Acidithiobacillus ferridurans	79.8949	254	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	99.15	97.49	0.87	0.83	8	-
GCF_018853935.1	s__Acidithiobacillus ferrivorans	79.2031	198	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	96.97	95.59	0.71	0.67	8	-
GCF_010378095.1	s__Acidithiobacillus ferrianus	78.4585	224	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000175575.2	s__Acidithiobacillus_A caldus	77.7867	168	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus_A	95.0	99.11	98.61	0.89	0.82	17	-
GCF_018853815.1	s__Acidithiobacillus sp018853815	77.6192	98	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018854025.1	s__UBA2486 sp018854025	77.4076	122	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__UBA2486	95.0	99.54	99.39	0.91	0.89	6	-
GCF_000423825.1	s__Thermithiobacillus tepidarius	77.3681	124	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Thermithiobacillaceae;g__Thermithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002847505.1	s__Acidithiobacillus sp002847505	77.281	120	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018853465.1	s__Acidithiobacillus sp018853465	77.1901	127	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	99.74	99.74	0.91	0.91	2	-
GCF_009662475.1	s__Acidithiobacillus thiooxidans	77.0259	106	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	97.93	97.09	0.77	0.70	22	-
GCA_019136395.1	s__M0108 sp019136395	76.5705	53	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__M0108	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112605.1	s__Thiohalospira halophila	76.1971	51	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalospirales;f__Thiohalospiraceae;g__Thiohalospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018435665.1	s__M0108 sp018435665	75.8956	55	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__M0108	95.0	99.16	99.16	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:53:37,270] [INFO] GTDB search result was written to GCF_003721225.1_ASM372122v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:53:37,271] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:53:37,275] [INFO] DFAST_QC result json was written to GCF_003721225.1_ASM372122v1_genomic.fna/dqc_result.json
[2024-01-24 12:53:37,275] [INFO] DFAST_QC completed!
[2024-01-24 12:53:37,275] [INFO] Total running time: 0h1m11s