[2024-01-24 12:54:22,614] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:22,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:22,617] [INFO] DQC Reference Directory: /var/lib/cwl/stg93cef1f4-4665-46d9-af57-81572302ee72/dqc_reference
[2024-01-24 12:54:24,205] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:24,206] [INFO] Task started: Prodigal
[2024-01-24 12:54:24,206] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d2c93c6-36a7-4bad-88d2-0936d0bb064e/GCF_000355765.4_ASM35576v4_genomic.fna.gz | prodigal -d GCF_000355765.4_ASM35576v4_genomic.fna/cds.fna -a GCF_000355765.4_ASM35576v4_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:34,304] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:34,304] [INFO] Task started: HMMsearch
[2024-01-24 12:54:34,304] [INFO] Running command: hmmsearch --tblout GCF_000355765.4_ASM35576v4_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93cef1f4-4665-46d9-af57-81572302ee72/dqc_reference/reference_markers.hmm GCF_000355765.4_ASM35576v4_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:34,572] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:34,573] [INFO] Found 6/6 markers.
[2024-01-24 12:54:34,610] [INFO] Query marker FASTA was written to GCF_000355765.4_ASM35576v4_genomic.fna/markers.fasta
[2024-01-24 12:54:34,611] [INFO] Task started: Blastn
[2024-01-24 12:54:34,611] [INFO] Running command: blastn -query GCF_000355765.4_ASM35576v4_genomic.fna/markers.fasta -db /var/lib/cwl/stg93cef1f4-4665-46d9-af57-81572302ee72/dqc_reference/reference_markers.fasta -out GCF_000355765.4_ASM35576v4_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:35,256] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:35,260] [INFO] Selected 20 target genomes.
[2024-01-24 12:54:35,261] [INFO] Target genome list was writen to GCF_000355765.4_ASM35576v4_genomic.fna/target_genomes.txt
[2024-01-24 12:54:35,272] [INFO] Task started: fastANI
[2024-01-24 12:54:35,273] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d2c93c6-36a7-4bad-88d2-0936d0bb064e/GCF_000355765.4_ASM35576v4_genomic.fna.gz --refList GCF_000355765.4_ASM35576v4_genomic.fna/target_genomes.txt --output GCF_000355765.4_ASM35576v4_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:47,123] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:47,123] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93cef1f4-4665-46d9-af57-81572302ee72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:47,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93cef1f4-4665-46d9-af57-81572302ee72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:47,134] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:47,135] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:47,135] [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
Nitrosospira lacus	strain=APG3	GCA_000355765.4	1288494	1288494	type	True	100.0	1084	1087	95	conclusive
Nitrosospira briensis	strain=C-128	GCA_000619905.2	35799	35799	reftype	True	78.5656	415	1087	95	below_threshold
Nitrosospira multiformis	strain=ATCC 25196	GCA_000196355.1	1231	1231	suspected-type	True	77.6771	229	1087	95	below_threshold
Sulfuriferula plumbiphila	strain=Gro7	GCA_009938015.1	171865	171865	type	True	76.6039	55	1087	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	76.5051	60	1087	95	below_threshold
Nitrosomonas oligotropha	strain=Nm45	GCA_009833085.1	42354	42354	type	True	76.0695	78	1087	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:47,136] [INFO] DFAST Taxonomy check result was written to GCF_000355765.4_ASM35576v4_genomic.fna/tc_result.tsv
[2024-01-24 12:54:47,137] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:47,137] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:47,137] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93cef1f4-4665-46d9-af57-81572302ee72/dqc_reference/checkm_data
[2024-01-24 12:54:47,138] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:47,178] [INFO] Task started: CheckM
[2024-01-24 12:54:47,178] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000355765.4_ASM35576v4_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000355765.4_ASM35576v4_genomic.fna/checkm_input GCF_000355765.4_ASM35576v4_genomic.fna/checkm_result
[2024-01-24 12:55:21,242] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:21,243] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:21,263] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:21,263] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:21,264] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000355765.4_ASM35576v4_genomic.fna/markers.fasta)
[2024-01-24 12:55:21,264] [INFO] Task started: Blastn
[2024-01-24 12:55:21,265] [INFO] Running command: blastn -query GCF_000355765.4_ASM35576v4_genomic.fna/markers.fasta -db /var/lib/cwl/stg93cef1f4-4665-46d9-af57-81572302ee72/dqc_reference/reference_markers_gtdb.fasta -out GCF_000355765.4_ASM35576v4_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:22,253] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:22,258] [INFO] Selected 10 target genomes.
[2024-01-24 12:55:22,258] [INFO] Target genome list was writen to GCF_000355765.4_ASM35576v4_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:22,268] [INFO] Task started: fastANI
[2024-01-24 12:55:22,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d2c93c6-36a7-4bad-88d2-0936d0bb064e/GCF_000355765.4_ASM35576v4_genomic.fna.gz --refList GCF_000355765.4_ASM35576v4_genomic.fna/target_genomes_gtdb.txt --output GCF_000355765.4_ASM35576v4_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:29,490] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:29,498] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:29,499] [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_000355765.4	s__Nitrosospira lacus	100.0	1085	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosospira	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900103165.1	s__Nitrosospira multiformis_D	87.4206	861	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosospira	95.0	98.83	96.49	0.95	0.85	4	-
GCF_000832065.1	s__Nitrosospira sp000832065	84.908	795	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102495.1	s__Nitrosospira sp900102495	79.5909	534	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013697655.1	s__Nitrosospira sp013697655	79.014	473	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053905.1	s__Nitrosospira sp003053905	78.5686	417	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosospira	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000619905.2	s__Nitrosospira briensis	78.5351	420	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosospira	95.0	95.54	95.29	0.88	0.87	3	-
GCF_003046405.1	s__Nitrosospira sp003046405	78.4028	416	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110495.1	s__Nitrosospira sp900110495	78.3479	425	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosospira	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001899235.1	s__Nitrosospira sp001899235	77.3989	266	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosospira	95.0	99.98	99.98	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:29,500] [INFO] GTDB search result was written to GCF_000355765.4_ASM35576v4_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:29,501] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:29,503] [INFO] DFAST_QC result json was written to GCF_000355765.4_ASM35576v4_genomic.fna/dqc_result.json
[2024-01-24 12:55:29,503] [INFO] DFAST_QC completed!
[2024-01-24 12:55:29,504] [INFO] Total running time: 0h1m7s