[2024-01-25 19:56:35,667] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:56:35,671] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:56:35,671] [INFO] DQC Reference Directory: /var/lib/cwl/stgdfe080d0-f85d-4eaa-a1ae-0eb94818562c/dqc_reference
[2024-01-25 19:56:36,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:56:36,787] [INFO] Task started: Prodigal
[2024-01-25 19:56:36,787] [INFO] Running command: gunzip -c /var/lib/cwl/stg93eab1af-86a9-43cb-a265-e95dfc09e2d6/GCF_014905135.1_ASM1490513v1_genomic.fna.gz | prodigal -d GCF_014905135.1_ASM1490513v1_genomic.fna/cds.fna -a GCF_014905135.1_ASM1490513v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:56:41,114] [INFO] Task succeeded: Prodigal
[2024-01-25 19:56:41,115] [INFO] Task started: HMMsearch
[2024-01-25 19:56:41,115] [INFO] Running command: hmmsearch --tblout GCF_014905135.1_ASM1490513v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdfe080d0-f85d-4eaa-a1ae-0eb94818562c/dqc_reference/reference_markers.hmm GCF_014905135.1_ASM1490513v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:56:41,297] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:56:41,298] [INFO] Found 6/6 markers.
[2024-01-25 19:56:41,319] [INFO] Query marker FASTA was written to GCF_014905135.1_ASM1490513v1_genomic.fna/markers.fasta
[2024-01-25 19:56:41,320] [INFO] Task started: Blastn
[2024-01-25 19:56:41,320] [INFO] Running command: blastn -query GCF_014905135.1_ASM1490513v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfe080d0-f85d-4eaa-a1ae-0eb94818562c/dqc_reference/reference_markers.fasta -out GCF_014905135.1_ASM1490513v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:41,857] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:41,859] [INFO] Selected 11 target genomes.
[2024-01-25 19:56:41,859] [INFO] Target genome list was writen to GCF_014905135.1_ASM1490513v1_genomic.fna/target_genomes.txt
[2024-01-25 19:56:41,885] [INFO] Task started: fastANI
[2024-01-25 19:56:41,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg93eab1af-86a9-43cb-a265-e95dfc09e2d6/GCF_014905135.1_ASM1490513v1_genomic.fna.gz --refList GCF_014905135.1_ASM1490513v1_genomic.fna/target_genomes.txt --output GCF_014905135.1_ASM1490513v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:56:46,569] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:46,570] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdfe080d0-f85d-4eaa-a1ae-0eb94818562c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:56:46,570] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdfe080d0-f85d-4eaa-a1ae-0eb94818562c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:56:46,577] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:56:46,577] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:56:46,578] [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
Sulfurimonas paralvinellae	strain=GO25	GCA_014905135.1	317658	317658	type	True	100.0	691	692	95	conclusive
Sulfurimonas indica	strain=NW8N	GCA_009192995.1	2508707	2508707	type	True	80.6873	374	692	95	below_threshold
Sulfurimonas autotrophica	strain=DSM 16294	GCA_000147355.1	202747	202747	type	True	79.3553	292	692	95	below_threshold
Sulfurimonas sediminis	strain=S2-6	GCA_014905115.1	2590020	2590020	type	True	78.8543	256	692	95	below_threshold
Sulfurimonas hydrogeniphila	strain=NW10	GCA_009068765.1	2509341	2509341	type	True	78.7686	270	692	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	78.5574	146	692	95	below_threshold
Sulfurimonas gotlandica	strain=GD1	GCA_000242915.2	1176482	1176482	type	True	78.55	144	692	95	below_threshold
Sulfurimonas xiamenensis	strain=1-1N	GCA_009258045.1	2590021	2590021	type	True	78.2353	116	692	95	below_threshold
Sulfurimonas crateris	strain=SN118	GCA_005217605.1	2574727	2574727	type	True	77.7534	121	692	95	below_threshold
Sulfurimonas denitrificans	strain=DSM 1251	GCA_000012965.1	39766	39766	type	True	77.5869	117	692	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:56:46,579] [INFO] DFAST Taxonomy check result was written to GCF_014905135.1_ASM1490513v1_genomic.fna/tc_result.tsv
[2024-01-25 19:56:46,579] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:56:46,579] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:56:46,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdfe080d0-f85d-4eaa-a1ae-0eb94818562c/dqc_reference/checkm_data
[2024-01-25 19:56:46,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:56:46,603] [INFO] Task started: CheckM
[2024-01-25 19:56:46,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014905135.1_ASM1490513v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014905135.1_ASM1490513v1_genomic.fna/checkm_input GCF_014905135.1_ASM1490513v1_genomic.fna/checkm_result
[2024-01-25 19:57:05,718] [INFO] Task succeeded: CheckM
[2024-01-25 19:57:05,719] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:57:05,743] [INFO] ===== Completeness check finished =====
[2024-01-25 19:57:05,744] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:57:05,744] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014905135.1_ASM1490513v1_genomic.fna/markers.fasta)
[2024-01-25 19:57:05,744] [INFO] Task started: Blastn
[2024-01-25 19:57:05,744] [INFO] Running command: blastn -query GCF_014905135.1_ASM1490513v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfe080d0-f85d-4eaa-a1ae-0eb94818562c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014905135.1_ASM1490513v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:06,574] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:06,576] [INFO] Selected 14 target genomes.
[2024-01-25 19:57:06,576] [INFO] Target genome list was writen to GCF_014905135.1_ASM1490513v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:57:06,606] [INFO] Task started: fastANI
[2024-01-25 19:57:06,606] [INFO] Running command: fastANI --query /var/lib/cwl/stg93eab1af-86a9-43cb-a265-e95dfc09e2d6/GCF_014905135.1_ASM1490513v1_genomic.fna.gz --refList GCF_014905135.1_ASM1490513v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014905135.1_ASM1490513v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:57:12,967] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:12,976] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:57:12,976] [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_014905135.1	s__Sulfurimonas paralvinellae	100.0	691	692	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013607665.1	s__Sulfurimonas sp013607665	81.545	339	692	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009192995.1	s__Sulfurimonas indica	80.6873	374	692	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000147355.1	s__Sulfurimonas autotrophica	79.3751	293	692	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014905115.1	s__Sulfurimonas sediminis	78.8489	255	692	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009068765.1	s__Sulfurimonas sp009068765	78.6748	270	692	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009883775.1	s__Sulfurimonas sp002452895	78.2653	113	692	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	98.89	98.30	0.92	0.92	4	-
GCF_017357825.1	s__Sulfurimonas sp017357825	78.1645	151	692	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005217605.1	s__Sulfurimonas crateris	77.7905	119	692	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013607635.1	s__Sulfurimonas sp013607635	77.7575	137	692	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487265.1	s__Sulfurimonas sp015487265	77.5503	158	692	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013791885.1	s__Sulfurimonas sp013791885	77.5331	153	692	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.38	98.60	0.95	0.92	8	-
GCA_015663215.1	s__Sulfurimonas sp015663215	77.4202	100	692	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001873135.1	s__Sulfurimonas sp001873135	77.055	101	692	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:57:12,977] [INFO] GTDB search result was written to GCF_014905135.1_ASM1490513v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:57:12,978] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:57:12,980] [INFO] DFAST_QC result json was written to GCF_014905135.1_ASM1490513v1_genomic.fna/dqc_result.json
[2024-01-25 19:57:12,980] [INFO] DFAST_QC completed!
[2024-01-25 19:57:12,981] [INFO] Total running time: 0h0m37s