[2023-06-04 21:46:05,884] [INFO] DFAST_QC pipeline started.
[2023-06-04 21:46:05,890] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 21:46:05,891] [INFO] DQC Reference Directory: /var/lib/cwl/stg1194951c-1dc6-4c59-a46c-29d05a8b088c/dqc_reference
[2023-06-04 21:46:09,120] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 21:46:09,121] [INFO] Task started: Prodigal
[2023-06-04 21:46:09,121] [INFO] Running command: gunzip -c /var/lib/cwl/stg792b356c-9774-4c56-a117-7265bbbe4ee6/GCA_004554745.1_ASM455474v1_genomic.fna.gz | prodigal -d GCA_004554745.1_ASM455474v1_genomic.fna/cds.fna -a GCA_004554745.1_ASM455474v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 21:46:15,400] [INFO] Task succeeded: Prodigal
[2023-06-04 21:46:15,400] [INFO] Task started: HMMsearch
[2023-06-04 21:46:15,400] [INFO] Running command: hmmsearch --tblout GCA_004554745.1_ASM455474v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1194951c-1dc6-4c59-a46c-29d05a8b088c/dqc_reference/reference_markers.hmm GCA_004554745.1_ASM455474v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 21:46:15,615] [INFO] Task succeeded: HMMsearch
[2023-06-04 21:46:15,616] [INFO] Found 6/6 markers.
[2023-06-04 21:46:15,647] [INFO] Query marker FASTA was written to GCA_004554745.1_ASM455474v1_genomic.fna/markers.fasta
[2023-06-04 21:46:15,648] [INFO] Task started: Blastn
[2023-06-04 21:46:15,648] [INFO] Running command: blastn -query GCA_004554745.1_ASM455474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1194951c-1dc6-4c59-a46c-29d05a8b088c/dqc_reference/reference_markers.fasta -out GCA_004554745.1_ASM455474v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:46:16,352] [INFO] Task succeeded: Blastn
[2023-06-04 21:46:16,357] [INFO] Selected 8 target genomes.
[2023-06-04 21:46:16,358] [INFO] Target genome list was writen to GCA_004554745.1_ASM455474v1_genomic.fna/target_genomes.txt
[2023-06-04 21:46:16,367] [INFO] Task started: fastANI
[2023-06-04 21:46:16,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg792b356c-9774-4c56-a117-7265bbbe4ee6/GCA_004554745.1_ASM455474v1_genomic.fna.gz --refList GCA_004554745.1_ASM455474v1_genomic.fna/target_genomes.txt --output GCA_004554745.1_ASM455474v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 21:46:20,149] [INFO] Task succeeded: fastANI
[2023-06-04 21:46:20,149] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1194951c-1dc6-4c59-a46c-29d05a8b088c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 21:46:20,150] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1194951c-1dc6-4c59-a46c-29d05a8b088c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 21:46:20,157] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 21:46:20,157] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 21:46:20,158] [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
Mitsuokella jalaludinii	strain=DSM 13811	GCA_000702905.1	187979	187979	type	True	80.8692	339	715	95	below_threshold
Mitsuokella multacida	strain=DSM 20544	GCA_000155955.1	52226	52226	type	True	80.6275	366	715	95	below_threshold
Selenomonas montiformis	strain=WCA-380-WT-3B3	GCA_009697385.1	2652285	2652285	type	True	79.3531	164	715	95	below_threshold
Selenomonas sputigena	strain=ATCC 35185	GCA_000160495.1	69823	69823	neotype	True	78.3968	238	715	95	below_threshold
Selenomonas sputigena	strain=ATCC 35185	GCA_000208405.1	69823	69823	neotype	True	78.3568	239	715	95	below_threshold
Selenomonas artemidis	strain=DSM 19719	GCA_000426665.1	671224	671224	type	True	77.8696	163	715	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 21:46:20,160] [INFO] DFAST Taxonomy check result was written to GCA_004554745.1_ASM455474v1_genomic.fna/tc_result.tsv
[2023-06-04 21:46:20,160] [INFO] ===== Taxonomy check completed =====
[2023-06-04 21:46:20,160] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 21:46:20,161] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1194951c-1dc6-4c59-a46c-29d05a8b088c/dqc_reference/checkm_data
[2023-06-04 21:46:20,162] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 21:46:20,190] [INFO] Task started: CheckM
[2023-06-04 21:46:20,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004554745.1_ASM455474v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004554745.1_ASM455474v1_genomic.fna/checkm_input GCA_004554745.1_ASM455474v1_genomic.fna/checkm_result
[2023-06-04 21:46:44,513] [INFO] Task succeeded: CheckM
[2023-06-04 21:46:44,515] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 21:46:44,537] [INFO] ===== Completeness check finished =====
[2023-06-04 21:46:44,538] [INFO] ===== Start GTDB Search =====
[2023-06-04 21:46:44,538] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004554745.1_ASM455474v1_genomic.fna/markers.fasta)
[2023-06-04 21:46:44,539] [INFO] Task started: Blastn
[2023-06-04 21:46:44,539] [INFO] Running command: blastn -query GCA_004554745.1_ASM455474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1194951c-1dc6-4c59-a46c-29d05a8b088c/dqc_reference/reference_markers_gtdb.fasta -out GCA_004554745.1_ASM455474v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:46:45,622] [INFO] Task succeeded: Blastn
[2023-06-04 21:46:45,627] [INFO] Selected 8 target genomes.
[2023-06-04 21:46:45,627] [INFO] Target genome list was writen to GCA_004554745.1_ASM455474v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 21:46:45,635] [INFO] Task started: fastANI
[2023-06-04 21:46:45,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg792b356c-9774-4c56-a117-7265bbbe4ee6/GCA_004554745.1_ASM455474v1_genomic.fna.gz --refList GCA_004554745.1_ASM455474v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004554745.1_ASM455474v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 21:46:51,207] [INFO] Task succeeded: fastANI
[2023-06-04 21:46:51,223] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 21:46:51,223] [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_000381005.1	s__Selenomonas_C bovis	95.9227	601	715	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_C	95.0	97.36	95.92	0.90	0.82	11	conclusive
GCA_902763085.1	s__Selenomonas_C sp002351185	88.057	484	715	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_C	95.0	98.44	97.41	0.83	0.79	3	-
GCA_902780535.1	s__Selenomonas_C sp902780535	82.469	390	715	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_C	95.0	97.25	96.14	0.82	0.79	5	-
GCA_900318215.1	s__Selenomonas_C sp900318215	82.1832	360	715	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_C	95.0	98.35	97.85	0.83	0.79	6	-
GCA_900315575.1	s__Selenomonas_C sp900315575	81.983	395	715	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_C	95.0	98.35	97.63	0.83	0.78	4	-
GCA_900314825.1	s__Selenomonas_C sp900314825	81.7089	419	715	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_C	95.0	99.95	99.95	0.95	0.95	2	-
GCF_000702905.1	s__Mitsuokella jalaludinii	80.8503	340	715	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella	95.0	98.12	97.46	0.90	0.85	11	-
GCF_000469545.1	s__Mitsuokella sp000469545	79.2794	240	715	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella	95.0	98.87	98.87	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-04 21:46:51,226] [INFO] GTDB search result was written to GCA_004554745.1_ASM455474v1_genomic.fna/result_gtdb.tsv
[2023-06-04 21:46:51,226] [INFO] ===== GTDB Search completed =====
[2023-06-04 21:46:51,231] [INFO] DFAST_QC result json was written to GCA_004554745.1_ASM455474v1_genomic.fna/dqc_result.json
[2023-06-04 21:46:51,232] [INFO] DFAST_QC completed!
[2023-06-04 21:46:51,232] [INFO] Total running time: 0h0m45s