[2023-06-13 21:08:07,982] [INFO] DFAST_QC pipeline started.
[2023-06-13 21:08:07,984] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 21:08:07,984] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a331f6d-8800-4d27-beaa-aef03183e4ea/dqc_reference
[2023-06-13 21:08:09,244] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 21:08:09,245] [INFO] Task started: Prodigal
[2023-06-13 21:08:09,246] [INFO] Running command: gunzip -c /var/lib/cwl/stgefa9c583-2844-45d7-940f-86fd877030d9/GCA_022781985.1_ASM2278198v1_genomic.fna.gz | prodigal -d GCA_022781985.1_ASM2278198v1_genomic.fna/cds.fna -a GCA_022781985.1_ASM2278198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 21:08:14,968] [INFO] Task succeeded: Prodigal
[2023-06-13 21:08:14,968] [INFO] Task started: HMMsearch
[2023-06-13 21:08:14,968] [INFO] Running command: hmmsearch --tblout GCA_022781985.1_ASM2278198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a331f6d-8800-4d27-beaa-aef03183e4ea/dqc_reference/reference_markers.hmm GCA_022781985.1_ASM2278198v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 21:08:15,161] [INFO] Task succeeded: HMMsearch
[2023-06-13 21:08:15,162] [INFO] Found 6/6 markers.
[2023-06-13 21:08:15,188] [INFO] Query marker FASTA was written to GCA_022781985.1_ASM2278198v1_genomic.fna/markers.fasta
[2023-06-13 21:08:15,189] [INFO] Task started: Blastn
[2023-06-13 21:08:15,189] [INFO] Running command: blastn -query GCA_022781985.1_ASM2278198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a331f6d-8800-4d27-beaa-aef03183e4ea/dqc_reference/reference_markers.fasta -out GCA_022781985.1_ASM2278198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:08:15,781] [INFO] Task succeeded: Blastn
[2023-06-13 21:08:15,785] [INFO] Selected 21 target genomes.
[2023-06-13 21:08:15,786] [INFO] Target genome list was writen to GCA_022781985.1_ASM2278198v1_genomic.fna/target_genomes.txt
[2023-06-13 21:08:15,786] [INFO] Task started: fastANI
[2023-06-13 21:08:15,787] [INFO] Running command: fastANI --query /var/lib/cwl/stgefa9c583-2844-45d7-940f-86fd877030d9/GCA_022781985.1_ASM2278198v1_genomic.fna.gz --refList GCA_022781985.1_ASM2278198v1_genomic.fna/target_genomes.txt --output GCA_022781985.1_ASM2278198v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 21:08:28,515] [INFO] Task succeeded: fastANI
[2023-06-13 21:08:28,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a331f6d-8800-4d27-beaa-aef03183e4ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 21:08:28,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a331f6d-8800-4d27-beaa-aef03183e4ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 21:08:28,528] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 21:08:28,528] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 21:08:28,528] [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
Kineothrix alysoides	strain=KNHs209	GCA_000732725.1	1469948	1469948	type	True	76.8514	126	767	95	below_threshold
Kineothrix alysoides	strain=DSM 100556	GCA_004345255.1	1469948	1469948	type	True	76.8157	125	767	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.7929	86	767	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	76.4456	91	767	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	76.2712	51	767	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.2327	105	767	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 21:08:28,530] [INFO] DFAST Taxonomy check result was written to GCA_022781985.1_ASM2278198v1_genomic.fna/tc_result.tsv
[2023-06-13 21:08:28,531] [INFO] ===== Taxonomy check completed =====
[2023-06-13 21:08:28,532] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 21:08:28,532] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a331f6d-8800-4d27-beaa-aef03183e4ea/dqc_reference/checkm_data
[2023-06-13 21:08:28,533] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 21:08:28,559] [INFO] Task started: CheckM
[2023-06-13 21:08:28,559] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022781985.1_ASM2278198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022781985.1_ASM2278198v1_genomic.fna/checkm_input GCA_022781985.1_ASM2278198v1_genomic.fna/checkm_result
[2023-06-13 21:08:51,740] [INFO] Task succeeded: CheckM
[2023-06-13 21:08:51,741] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-13 21:08:51,775] [INFO] ===== Completeness check finished =====
[2023-06-13 21:08:51,776] [INFO] ===== Start GTDB Search =====
[2023-06-13 21:08:51,776] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022781985.1_ASM2278198v1_genomic.fna/markers.fasta)
[2023-06-13 21:08:51,776] [INFO] Task started: Blastn
[2023-06-13 21:08:51,776] [INFO] Running command: blastn -query GCA_022781985.1_ASM2278198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a331f6d-8800-4d27-beaa-aef03183e4ea/dqc_reference/reference_markers_gtdb.fasta -out GCA_022781985.1_ASM2278198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:08:52,646] [INFO] Task succeeded: Blastn
[2023-06-13 21:08:52,651] [INFO] Selected 25 target genomes.
[2023-06-13 21:08:52,651] [INFO] Target genome list was writen to GCA_022781985.1_ASM2278198v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 21:08:52,652] [INFO] Task started: fastANI
[2023-06-13 21:08:52,653] [INFO] Running command: fastANI --query /var/lib/cwl/stgefa9c583-2844-45d7-940f-86fd877030d9/GCA_022781985.1_ASM2278198v1_genomic.fna.gz --refList GCA_022781985.1_ASM2278198v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022781985.1_ASM2278198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 21:09:06,330] [INFO] Task succeeded: fastANI
[2023-06-13 21:09:06,347] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 21:09:06,347] [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
GCA_017532145.1	s__Kineothrix sp017532145	78.3755	295	767	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Kineothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579935.1	s__Kineothrix sp910579935	77.1709	159	767	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Kineothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012520645.1	s__JAAYNV01 sp012520645	76.9906	94	767	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__JAAYNV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579645.1	s__Kineothrix sp910579645	76.9593	145	767	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Kineothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012520655.1	s__Kineothrix sp012520655	76.943	96	767	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Kineothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017624235.1	s__JAAYNV01 sp017624235	76.8009	88	767	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__JAAYNV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119595.1	s__Eisenbergiella merdavium	76.7646	90	767	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	98.10	98.10	0.87	0.87	2	-
GCA_003612405.1	s__UBA3282 sp003612405	76.7611	85	767	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	99.19	99.19	0.85	0.85	2	-
GCA_014804615.1	s__UBA3282 sp014804615	76.6687	95	767	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586275.1	s__Kineothrix sp910586275	76.6352	138	767	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Kineothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587715.1	s__UBA3282 sp910587715	76.5555	62	767	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003488965.1	s__Kineothrix sp003488965	76.548	93	767	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Kineothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014804645.1	s__Acetatifactor sp014804645	76.5363	79	767	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588215.1	s__UBA3282 sp910588215	76.4959	89	767	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115665.1	s__Eisenbergiella pullistercoris	76.4672	93	767	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009696275.1	s__Eisenbergiella porci	76.4456	91	767	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	97.00	96.55	0.75	0.70	10	-
GCA_009774625.1	s__VSOB01 sp009774625	76.4124	85	767	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__VSOB01	95.0	99.49	99.49	0.87	0.87	2	-
GCA_910586485.1	s__Acetatifactor sp910586485	76.3468	101	767	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578815.1	s__Acetatifactor sp910578815	76.3448	83	767	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017621075.1	s__Acetatifactor sp017621075	76.2351	82	767	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002493835.1	s__UBA3282 sp002493835	75.5696	60	767	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 21:09:06,349] [INFO] GTDB search result was written to GCA_022781985.1_ASM2278198v1_genomic.fna/result_gtdb.tsv
[2023-06-13 21:09:06,350] [INFO] ===== GTDB Search completed =====
[2023-06-13 21:09:06,353] [INFO] DFAST_QC result json was written to GCA_022781985.1_ASM2278198v1_genomic.fna/dqc_result.json
[2023-06-13 21:09:06,354] [INFO] DFAST_QC completed!
[2023-06-13 21:09:06,354] [INFO] Total running time: 0h0m58s