[2024-01-24 11:34:38,690] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:38,693] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:38,693] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e3e66bc-d66c-400f-893e-b97e80e9de75/dqc_reference
[2024-01-24 11:34:41,321] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:41,324] [INFO] Task started: Prodigal
[2024-01-24 11:34:41,324] [INFO] Running command: gunzip -c /var/lib/cwl/stg99b397a8-e429-4034-a651-a487ffcf5d02/GCF_009938015.1_ASM993801v1_genomic.fna.gz | prodigal -d GCF_009938015.1_ASM993801v1_genomic.fna/cds.fna -a GCF_009938015.1_ASM993801v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:53,463] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:53,464] [INFO] Task started: HMMsearch
[2024-01-24 11:34:53,464] [INFO] Running command: hmmsearch --tblout GCF_009938015.1_ASM993801v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e3e66bc-d66c-400f-893e-b97e80e9de75/dqc_reference/reference_markers.hmm GCF_009938015.1_ASM993801v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:53,782] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:53,784] [INFO] Found 6/6 markers.
[2024-01-24 11:34:53,817] [INFO] Query marker FASTA was written to GCF_009938015.1_ASM993801v1_genomic.fna/markers.fasta
[2024-01-24 11:34:53,817] [INFO] Task started: Blastn
[2024-01-24 11:34:53,817] [INFO] Running command: blastn -query GCF_009938015.1_ASM993801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e3e66bc-d66c-400f-893e-b97e80e9de75/dqc_reference/reference_markers.fasta -out GCF_009938015.1_ASM993801v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:54,752] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:54,755] [INFO] Selected 17 target genomes.
[2024-01-24 11:34:54,755] [INFO] Target genome list was writen to GCF_009938015.1_ASM993801v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:54,762] [INFO] Task started: fastANI
[2024-01-24 11:34:54,762] [INFO] Running command: fastANI --query /var/lib/cwl/stg99b397a8-e429-4034-a651-a487ffcf5d02/GCF_009938015.1_ASM993801v1_genomic.fna.gz --refList GCF_009938015.1_ASM993801v1_genomic.fna/target_genomes.txt --output GCF_009938015.1_ASM993801v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:06,027] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:06,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e3e66bc-d66c-400f-893e-b97e80e9de75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:06,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e3e66bc-d66c-400f-893e-b97e80e9de75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:06,040] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:06,041] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:06,041] [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
Sulfuriferula plumbiphila	strain=Gro7	GCA_009938015.1	171865	171865	type	True	100.0	1148	1150	95	conclusive
Sulfuriferula plumbiphila	strain=NBRC 107929	GCA_007992375.1	171865	171865	type	True	99.9353	1080	1150	95	conclusive
Sulfuriferula multivorans	strain=TTN	GCA_003851125.1	1559896	1559896	type	True	86.6138	757	1150	95	below_threshold
Thiobacillus denitrificans	strain=DSM 12475	GCA_000376425.1	36861	36861	type	True	78.356	249	1150	95	below_threshold
Sulfuricella denitrificans	strain=skB26	GCA_000297055.2	649841	649841	type	True	78.12	154	1150	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	77.8542	221	1150	95	below_threshold
Thiobacillus thioparus	strain=DSM 505	GCA_000373385.1	931	931	type	True	77.6171	237	1150	95	below_threshold
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	77.3012	151	1150	95	below_threshold
Sulfuriferula thiophila	strain=mst6	GCA_003864975.1	1781211	1781211	type	True	76.9233	178	1150	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	76.7296	150	1150	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	76.6157	126	1150	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	76.3519	105	1150	95	below_threshold
Andreprevotia chitinilytica	strain=DSM 18519	GCA_000711875.1	396808	396808	type	True	76.2422	88	1150	95	below_threshold
Janthinobacterium psychrotolerans	strain=S3-2	GCA_001677885.1	1747903	1747903	type	True	76.229	153	1150	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:06,042] [INFO] DFAST Taxonomy check result was written to GCF_009938015.1_ASM993801v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:06,043] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:06,043] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:06,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e3e66bc-d66c-400f-893e-b97e80e9de75/dqc_reference/checkm_data
[2024-01-24 11:35:06,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:06,082] [INFO] Task started: CheckM
[2024-01-24 11:35:06,082] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009938015.1_ASM993801v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009938015.1_ASM993801v1_genomic.fna/checkm_input GCF_009938015.1_ASM993801v1_genomic.fna/checkm_result
[2024-01-24 11:35:45,271] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:45,273] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:45,290] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:45,290] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:45,290] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009938015.1_ASM993801v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:45,291] [INFO] Task started: Blastn
[2024-01-24 11:35:45,291] [INFO] Running command: blastn -query GCF_009938015.1_ASM993801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e3e66bc-d66c-400f-893e-b97e80e9de75/dqc_reference/reference_markers_gtdb.fasta -out GCF_009938015.1_ASM993801v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:47,122] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:47,125] [INFO] Selected 20 target genomes.
[2024-01-24 11:35:47,125] [INFO] Target genome list was writen to GCF_009938015.1_ASM993801v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:47,141] [INFO] Task started: fastANI
[2024-01-24 11:35:47,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg99b397a8-e429-4034-a651-a487ffcf5d02/GCF_009938015.1_ASM993801v1_genomic.fna.gz --refList GCF_009938015.1_ASM993801v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009938015.1_ASM993801v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:58,305] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:58,325] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:58,325] [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_009938015.1	s__Sulfuriferula plumbiphila	100.0	1148	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuriferulaceae;g__Sulfuriferula	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003851125.1	s__Sulfuriferula multivorans	86.6269	756	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuriferulaceae;g__Sulfuriferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003455595.1	s__Sulfuriferula sp003455595	80.661	368	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuriferulaceae;g__Sulfuriferula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002162035.1	s__Sulfuriferula_A sp002162035	78.1207	246	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuriferulaceae;g__Sulfuriferula_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002421825.1	s__UBA6918 sp002421825	77.9301	175	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__UBA6918	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764585.1	s__Sulfurimicrobium lacus	77.8542	221	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__Sulfurimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002343685.1	s__Thiobacillus denitrificans_A	77.8135	229	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	97.48	97.29	0.88	0.86	5	-
GCA_018823025.1	s__Sulfuricella sp018823025	77.6125	161	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__Sulfuricella	95.0	99.85	99.85	0.92	0.92	2	-
GCA_002424845.1	s__Thiobacillus denitrificans_F	77.2948	150	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549295.1	s__Azonexus sp900549295	77.1936	119	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	99.94	99.94	0.93	0.93	2	-
GCA_001899775.1	s__Thiobacillus sp001899775	77.1389	198	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003864975.1	s__Sulfuriferula_A thiophila	76.9233	178	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuriferulaceae;g__Sulfuriferula_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112435.1	s__Novimethylophilus kurashikiensis	76.8191	104	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Novimethylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903835655.1	s__PFJX01 sp903835655	76.7678	139	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	99.87	99.69	0.96	0.90	25	-
GCA_016791205.1	s__Desulfobacillus sp016791205	76.6944	138	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310185.1	s__Thauera aminoaromatica	76.6719	120	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.62	98.32	0.86	0.80	8	-
GCA_009782025.1	s__Azonexus sp009782025	76.2376	92	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016214175.1	s__JACRPB01 sp016214175	76.1948	102	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JACRPB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:58,327] [INFO] GTDB search result was written to GCF_009938015.1_ASM993801v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:58,327] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:58,335] [INFO] DFAST_QC result json was written to GCF_009938015.1_ASM993801v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:58,335] [INFO] DFAST_QC completed!
[2024-01-24 11:35:58,335] [INFO] Total running time: 0h1m20s