[2024-01-24 14:11:50,843] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:50,847] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:50,848] [INFO] DQC Reference Directory: /var/lib/cwl/stgf85f7610-f02e-416c-8db3-a877cd1b7248/dqc_reference
[2024-01-24 14:11:52,410] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:52,411] [INFO] Task started: Prodigal
[2024-01-24 14:11:52,411] [INFO] Running command: gunzip -c /var/lib/cwl/stg27979cd4-5f35-46bc-8c56-57e84afe74a4/GCF_000092205.1_ASM9220v1_genomic.fna.gz | prodigal -d GCF_000092205.1_ASM9220v1_genomic.fna/cds.fna -a GCF_000092205.1_ASM9220v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:02,516] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:02,516] [INFO] Task started: HMMsearch
[2024-01-24 14:12:02,517] [INFO] Running command: hmmsearch --tblout GCF_000092205.1_ASM9220v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf85f7610-f02e-416c-8db3-a877cd1b7248/dqc_reference/reference_markers.hmm GCF_000092205.1_ASM9220v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:02,916] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:02,917] [INFO] Found 6/6 markers.
[2024-01-24 14:12:02,947] [INFO] Query marker FASTA was written to GCF_000092205.1_ASM9220v1_genomic.fna/markers.fasta
[2024-01-24 14:12:02,947] [INFO] Task started: Blastn
[2024-01-24 14:12:02,947] [INFO] Running command: blastn -query GCF_000092205.1_ASM9220v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf85f7610-f02e-416c-8db3-a877cd1b7248/dqc_reference/reference_markers.fasta -out GCF_000092205.1_ASM9220v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:04,993] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:05,000] [INFO] Selected 21 target genomes.
[2024-01-24 14:12:05,000] [INFO] Target genome list was writen to GCF_000092205.1_ASM9220v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:05,010] [INFO] Task started: fastANI
[2024-01-24 14:12:05,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg27979cd4-5f35-46bc-8c56-57e84afe74a4/GCF_000092205.1_ASM9220v1_genomic.fna.gz --refList GCF_000092205.1_ASM9220v1_genomic.fna/target_genomes.txt --output GCF_000092205.1_ASM9220v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:20,125] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:20,125] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf85f7610-f02e-416c-8db3-a877cd1b7248/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:20,126] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf85f7610-f02e-416c-8db3-a877cd1b7248/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:20,181] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:20,181] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:20,182] [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
Desulfurivibrio alkaliphilus	strain=AHT 2	GCA_000092205.1	427923	427923	type	True	100.0	1031	1032	95	conclusive
Desulfobulbus elongatus	strain=DSM 2908	GCA_000621145.1	53332	53332	type	True	76.893	108	1032	95	below_threshold
Desulfobulbus propionicus	strain=DSM 2032	GCA_000186885.1	894	894	type	True	76.4594	83	1032	95	below_threshold
Desulfoprunum benzoelyticum	strain=DSM 28570	GCA_016918515.1	1506996	1506996	type	True	76.3545	71	1032	95	below_threshold
Megalodesulfovibrio gigas	strain=DSM 1382	GCA_000429285.1	879	879	type	True	76.306	50	1032	95	below_threshold
Desulfoprunum benzoelyticum	strain=DSM 28570	GCA_014201505.1	1506996	1506996	type	True	76.2696	75	1032	95	below_threshold
Megalodesulfovibrio gigas	strain=ATCC 19364	GCA_000468495.1	879	879	type	True	76.1661	50	1032	95	below_threshold
Desulfogranum mediterraneum	strain=DSM 13871	GCA_000429965.1	160661	160661	type	True	75.9927	114	1032	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	75.8047	64	1032	95	below_threshold
Desulfobulbus alkaliphilus	strain=DSM 24258	GCA_016918545.1	869814	869814	type	True	75.7778	51	1032	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:20,185] [INFO] DFAST Taxonomy check result was written to GCF_000092205.1_ASM9220v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:20,186] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:20,186] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:20,187] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf85f7610-f02e-416c-8db3-a877cd1b7248/dqc_reference/checkm_data
[2024-01-24 14:12:20,193] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:20,234] [INFO] Task started: CheckM
[2024-01-24 14:12:20,234] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000092205.1_ASM9220v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000092205.1_ASM9220v1_genomic.fna/checkm_input GCF_000092205.1_ASM9220v1_genomic.fna/checkm_result
[2024-01-24 14:12:53,818] [INFO] Task succeeded: CheckM
[2024-01-24 14:12:53,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:12:53,839] [INFO] ===== Completeness check finished =====
[2024-01-24 14:12:53,839] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:12:53,840] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000092205.1_ASM9220v1_genomic.fna/markers.fasta)
[2024-01-24 14:12:53,840] [INFO] Task started: Blastn
[2024-01-24 14:12:53,841] [INFO] Running command: blastn -query GCF_000092205.1_ASM9220v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf85f7610-f02e-416c-8db3-a877cd1b7248/dqc_reference/reference_markers_gtdb.fasta -out GCF_000092205.1_ASM9220v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:55,208] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:55,213] [INFO] Selected 17 target genomes.
[2024-01-24 14:12:55,213] [INFO] Target genome list was writen to GCF_000092205.1_ASM9220v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:12:55,244] [INFO] Task started: fastANI
[2024-01-24 14:12:55,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg27979cd4-5f35-46bc-8c56-57e84afe74a4/GCF_000092205.1_ASM9220v1_genomic.fna.gz --refList GCF_000092205.1_ASM9220v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000092205.1_ASM9220v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:04,256] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:04,294] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:04,294] [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_000092205.1	s__Desulfurivibrio alkaliphilus	100.0	1031	1032	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__Desulfurivibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003557565.1	s__Desulfurivibrio sp003557565	81.0204	394	1032	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__Desulfurivibrio	95.0	98.36	98.36	0.83	0.83	2	-
GCA_011048585.1	s__Desulfurivibrio alkaliphilus_A	79.5315	289	1032	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__Desulfurivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002421565.1	s__UBA5628 sp002421565	78.2477	176	1032	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__UBA5628	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018830485.1	s__UBA2262 sp018830485	77.3323	189	1032	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__UBA2262	95.0	99.86	99.86	0.95	0.94	3	-
GCA_004332195.1	s__Desulfurivibrio sp004332195	77.2768	178	1032	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__Desulfurivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002347095.1	s__UBA2262 sp002347095	77.1788	190	1032	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__UBA2262	95.0	98.22	98.22	0.94	0.94	2	-
GCA_002841785.1	s__UBA2262 sp002841785	76.8696	157	1032	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__UBA2262	95.0	98.87	98.69	0.72	0.70	5	-
GCA_002414225.1	s__UBA5123 sp002414225	76.783	190	1032	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__UBA5123	95.0	99.93	99.93	0.96	0.96	2	-
GCA_002347185.1	s__UBA2262 sp002347185	76.7684	177	1032	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__UBA2262	95.0	99.47	99.47	0.90	0.90	2	-
GCA_002415465.1	s__UBA5123 sp002415465	76.4081	122	1032	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__UBA5123	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016208225.1	s__SURF-16 sp016208225	76.1587	106	1032	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__SURF-16	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:04,296] [INFO] GTDB search result was written to GCF_000092205.1_ASM9220v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:04,297] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:04,302] [INFO] DFAST_QC result json was written to GCF_000092205.1_ASM9220v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:04,303] [INFO] DFAST_QC completed!
[2024-01-24 14:13:04,303] [INFO] Total running time: 0h1m13s