[2024-01-24 12:47:14,126] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:14,129] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:14,130] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f8fdedb-e118-40dd-bf00-0e44f2986550/dqc_reference
[2024-01-24 12:47:15,481] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:15,482] [INFO] Task started: Prodigal
[2024-01-24 12:47:15,482] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b80c501-df32-41de-bfcf-790b9a1ca161/GCF_009695585.1_ASM969558v1_genomic.fna.gz | prodigal -d GCF_009695585.1_ASM969558v1_genomic.fna/cds.fna -a GCF_009695585.1_ASM969558v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:23,751] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:23,752] [INFO] Task started: HMMsearch
[2024-01-24 12:47:23,752] [INFO] Running command: hmmsearch --tblout GCF_009695585.1_ASM969558v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f8fdedb-e118-40dd-bf00-0e44f2986550/dqc_reference/reference_markers.hmm GCF_009695585.1_ASM969558v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:24,034] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:24,038] [INFO] Found 6/6 markers.
[2024-01-24 12:47:24,075] [INFO] Query marker FASTA was written to GCF_009695585.1_ASM969558v1_genomic.fna/markers.fasta
[2024-01-24 12:47:24,076] [INFO] Task started: Blastn
[2024-01-24 12:47:24,076] [INFO] Running command: blastn -query GCF_009695585.1_ASM969558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f8fdedb-e118-40dd-bf00-0e44f2986550/dqc_reference/reference_markers.fasta -out GCF_009695585.1_ASM969558v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:24,685] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:24,687] [INFO] Selected 18 target genomes.
[2024-01-24 12:47:24,688] [INFO] Target genome list was writen to GCF_009695585.1_ASM969558v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:24,694] [INFO] Task started: fastANI
[2024-01-24 12:47:24,694] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b80c501-df32-41de-bfcf-790b9a1ca161/GCF_009695585.1_ASM969558v1_genomic.fna.gz --refList GCF_009695585.1_ASM969558v1_genomic.fna/target_genomes.txt --output GCF_009695585.1_ASM969558v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:34,137] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:34,137] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f8fdedb-e118-40dd-bf00-0e44f2986550/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:34,138] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f8fdedb-e118-40dd-bf00-0e44f2986550/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:34,143] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:34,144] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:34,144] [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
Anaerovibrio slackiae	strain=WCA-693-APC-5D-A	GCA_009695585.1	2652309	2652309	type	True	100.0	968	973	95	conclusive
Selenomonas ruminantium subsp. ruminantium	strain=ATCC 12561	GCA_000424065.1	114196	971	type	True	77.0325	85	973	95	below_threshold
Mitsuokella multacida	strain=DSM 20544	GCA_000155955.1	52226	52226	type	True	76.8408	57	973	95	below_threshold
Mitsuokella jalaludinii	strain=DSM 13811	GCA_000702905.1	187979	187979	type	True	76.7002	55	973	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:34,147] [INFO] DFAST Taxonomy check result was written to GCF_009695585.1_ASM969558v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:34,147] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:34,147] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:34,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f8fdedb-e118-40dd-bf00-0e44f2986550/dqc_reference/checkm_data
[2024-01-24 12:47:34,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:34,182] [INFO] Task started: CheckM
[2024-01-24 12:47:34,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009695585.1_ASM969558v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009695585.1_ASM969558v1_genomic.fna/checkm_input GCF_009695585.1_ASM969558v1_genomic.fna/checkm_result
[2024-01-24 12:48:04,163] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:04,165] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:04,185] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:04,186] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:04,186] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009695585.1_ASM969558v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:04,187] [INFO] Task started: Blastn
[2024-01-24 12:48:04,187] [INFO] Running command: blastn -query GCF_009695585.1_ASM969558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f8fdedb-e118-40dd-bf00-0e44f2986550/dqc_reference/reference_markers_gtdb.fasta -out GCF_009695585.1_ASM969558v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:05,071] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:05,075] [INFO] Selected 11 target genomes.
[2024-01-24 12:48:05,075] [INFO] Target genome list was writen to GCF_009695585.1_ASM969558v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:05,085] [INFO] Task started: fastANI
[2024-01-24 12:48:05,085] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b80c501-df32-41de-bfcf-790b9a1ca161/GCF_009695585.1_ASM969558v1_genomic.fna.gz --refList GCF_009695585.1_ASM969558v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009695585.1_ASM969558v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:11,255] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:11,271] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:11,271] [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_009695585.1	s__Anaerovibrio slackiae	100.0	968	973	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	98.28	97.88	0.95	0.93	10	conclusive
GCA_016302095.1	s__Anaerovibrio sp016302095	94.388	333	973	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900768695.1	s__Anaerovibrio sp900768695	85.9516	376	973	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548165.1	s__Anaerovibrio sp900548165	79.5464	287	973	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	96.97	96.65	0.86	0.85	4	-
GCF_002100115.1	s__Anaerovibrio sp002100115	78.9407	197	973	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622005.1	s__Anaerovibrio sp000622005	78.2137	188	973	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902786545.1	s__Anaerovibrio sp902786545	77.998	139	973	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	97.48	96.70	0.88	0.86	3	-
GCA_017390245.1	s__Anaerovibrio sp017390245	77.7706	159	973	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017475925.1	s__Anaerovibrio sp017475925	77.2315	102	973	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	97.54	97.54	0.79	0.79	2	-
GCF_000702545.1	s__Selenomonas_B ruminantium_A	77.0124	148	973	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_B	95.0	96.24	95.81	0.75	0.73	3	-
GCA_905234515.1	s__Selenomonas_B sp905234515	76.8471	101	973	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:11,273] [INFO] GTDB search result was written to GCF_009695585.1_ASM969558v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:11,274] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:11,277] [INFO] DFAST_QC result json was written to GCF_009695585.1_ASM969558v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:11,277] [INFO] DFAST_QC completed!
[2024-01-24 12:48:11,277] [INFO] Total running time: 0h0m57s