[2023-06-13 13:52:22,611] [INFO] DFAST_QC pipeline started.
[2023-06-13 13:52:22,617] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 13:52:22,617] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a88857e-66e3-4d53-ab41-486bd51c9f87/dqc_reference
[2023-06-13 13:52:23,899] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 13:52:23,900] [INFO] Task started: Prodigal
[2023-06-13 13:52:23,900] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2f36394-3043-44ca-8e20-4c6ce1c1df9d/GCA_022797415.1_ASM2279741v1_genomic.fna.gz | prodigal -d GCA_022797415.1_ASM2279741v1_genomic.fna/cds.fna -a GCA_022797415.1_ASM2279741v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 13:52:31,569] [INFO] Task succeeded: Prodigal
[2023-06-13 13:52:31,570] [INFO] Task started: HMMsearch
[2023-06-13 13:52:31,570] [INFO] Running command: hmmsearch --tblout GCA_022797415.1_ASM2279741v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a88857e-66e3-4d53-ab41-486bd51c9f87/dqc_reference/reference_markers.hmm GCA_022797415.1_ASM2279741v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 13:52:31,840] [INFO] Task succeeded: HMMsearch
[2023-06-13 13:52:31,841] [INFO] Found 6/6 markers.
[2023-06-13 13:52:31,874] [INFO] Query marker FASTA was written to GCA_022797415.1_ASM2279741v1_genomic.fna/markers.fasta
[2023-06-13 13:52:31,874] [INFO] Task started: Blastn
[2023-06-13 13:52:31,874] [INFO] Running command: blastn -query GCA_022797415.1_ASM2279741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a88857e-66e3-4d53-ab41-486bd51c9f87/dqc_reference/reference_markers.fasta -out GCA_022797415.1_ASM2279741v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:52:32,532] [INFO] Task succeeded: Blastn
[2023-06-13 13:52:32,538] [INFO] Selected 28 target genomes.
[2023-06-13 13:52:32,538] [INFO] Target genome list was writen to GCA_022797415.1_ASM2279741v1_genomic.fna/target_genomes.txt
[2023-06-13 13:52:32,541] [INFO] Task started: fastANI
[2023-06-13 13:52:32,541] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2f36394-3043-44ca-8e20-4c6ce1c1df9d/GCA_022797415.1_ASM2279741v1_genomic.fna.gz --refList GCA_022797415.1_ASM2279741v1_genomic.fna/target_genomes.txt --output GCA_022797415.1_ASM2279741v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 13:52:48,415] [INFO] Task succeeded: fastANI
[2023-06-13 13:52:48,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a88857e-66e3-4d53-ab41-486bd51c9f87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 13:52:48,417] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a88857e-66e3-4d53-ab41-486bd51c9f87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 13:52:48,430] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 13:52:48,431] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 13:52:48,431] [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
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	77.1423	78	1004	95	below_threshold
Kineothrix alysoides	strain=DSM 100556	GCA_004345255.1	1469948	1469948	type	True	76.5376	62	1004	95	below_threshold
Kineothrix alysoides	strain=KNHs209	GCA_000732725.1	1469948	1469948	type	True	76.5051	63	1004	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.5022	85	1004	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	76.4676	53	1004	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	76.2511	101	1004	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.2373	111	1004	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	75.7473	50	1004	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 13:52:48,433] [INFO] DFAST Taxonomy check result was written to GCA_022797415.1_ASM2279741v1_genomic.fna/tc_result.tsv
[2023-06-13 13:52:48,433] [INFO] ===== Taxonomy check completed =====
[2023-06-13 13:52:48,433] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 13:52:48,434] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a88857e-66e3-4d53-ab41-486bd51c9f87/dqc_reference/checkm_data
[2023-06-13 13:52:48,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 13:52:48,471] [INFO] Task started: CheckM
[2023-06-13 13:52:48,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022797415.1_ASM2279741v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022797415.1_ASM2279741v1_genomic.fna/checkm_input GCA_022797415.1_ASM2279741v1_genomic.fna/checkm_result
[2023-06-13 13:53:17,112] [INFO] Task succeeded: CheckM
[2023-06-13 13:53:17,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.02%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 13:53:17,138] [INFO] ===== Completeness check finished =====
[2023-06-13 13:53:17,139] [INFO] ===== Start GTDB Search =====
[2023-06-13 13:53:17,139] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022797415.1_ASM2279741v1_genomic.fna/markers.fasta)
[2023-06-13 13:53:17,140] [INFO] Task started: Blastn
[2023-06-13 13:53:17,140] [INFO] Running command: blastn -query GCA_022797415.1_ASM2279741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a88857e-66e3-4d53-ab41-486bd51c9f87/dqc_reference/reference_markers_gtdb.fasta -out GCA_022797415.1_ASM2279741v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:53:18,253] [INFO] Task succeeded: Blastn
[2023-06-13 13:53:18,258] [INFO] Selected 15 target genomes.
[2023-06-13 13:53:18,258] [INFO] Target genome list was writen to GCA_022797415.1_ASM2279741v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 13:53:18,262] [INFO] Task started: fastANI
[2023-06-13 13:53:18,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2f36394-3043-44ca-8e20-4c6ce1c1df9d/GCA_022797415.1_ASM2279741v1_genomic.fna.gz --refList GCA_022797415.1_ASM2279741v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022797415.1_ASM2279741v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 13:53:29,700] [INFO] Task succeeded: fastANI
[2023-06-13 13:53:29,716] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 13:53:29,717] [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_009774175.1	s__UBA3282 sp009774175	99.2311	898	1004	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	99.14	99.14	0.87	0.87	2	conclusive
GCA_002361355.1	s__UBA3282 sp002361355	82.3739	625	1004	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	99.97	99.95	0.96	0.94	5	-
GCA_002490705.1	s__UBA3282 sp002490705	82.0777	654	1004	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	99.98	99.98	0.97	0.97	2	-
GCA_009774215.1	s__UBA3282 sp009774215	80.5035	557	1004	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	98.90	98.90	0.87	0.87	2	-
GCA_910586705.1	s__UBA3282 sp910586705	80.4689	602	1004	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_910584725.1	s__UBA3282 sp910584725	80.4129	582	1004	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_910579505.1	s__UBA3282 sp910579505	80.3429	582	1004	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_002491905.1	s__UBA3282 sp002491905	80.3391	561	1004	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_910587715.1	s__UBA3282 sp910587715	80.2969	575	1004	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_003611805.1	s__UBA3282 sp003611805	80.2555	597	1004	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	98.73	98.68	0.87	0.86	4	-
GCA_910575775.1	s__UBA3282 sp910575775	80.1882	595	1004	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	98.26	98.26	0.81	0.81	2	-
GCA_910588955.1	s__UBA3282 sp910588955	80.1095	585	1004	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_910579285.1	s__UBA3282 sp910579285	80.0505	539	1004	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_014804565.1	s__UBA3282 sp014804565	79.5092	443	1004	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_014804615.1	s__UBA3282 sp014804615	79.4498	452	1004	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 13:53:29,719] [INFO] GTDB search result was written to GCA_022797415.1_ASM2279741v1_genomic.fna/result_gtdb.tsv
[2023-06-13 13:53:29,719] [INFO] ===== GTDB Search completed =====
[2023-06-13 13:53:29,723] [INFO] DFAST_QC result json was written to GCA_022797415.1_ASM2279741v1_genomic.fna/dqc_result.json
[2023-06-13 13:53:29,723] [INFO] DFAST_QC completed!
[2023-06-13 13:53:29,723] [INFO] Total running time: 0h1m7s