[2023-06-19 14:15:44,161] [INFO] DFAST_QC pipeline started.
[2023-06-19 14:15:44,163] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 14:15:44,164] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b975bf4-b776-4cf0-9449-4f2d5c12640a/dqc_reference
[2023-06-19 14:15:45,501] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 14:15:45,502] [INFO] Task started: Prodigal
[2023-06-19 14:15:45,502] [INFO] Running command: gunzip -c /var/lib/cwl/stg548605df-00b9-4250-ad6f-d5210d34c73d/GCA_014804745.1_ASM1480474v1_genomic.fna.gz | prodigal -d GCA_014804745.1_ASM1480474v1_genomic.fna/cds.fna -a GCA_014804745.1_ASM1480474v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 14:15:57,560] [INFO] Task succeeded: Prodigal
[2023-06-19 14:15:57,561] [INFO] Task started: HMMsearch
[2023-06-19 14:15:57,561] [INFO] Running command: hmmsearch --tblout GCA_014804745.1_ASM1480474v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b975bf4-b776-4cf0-9449-4f2d5c12640a/dqc_reference/reference_markers.hmm GCA_014804745.1_ASM1480474v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 14:15:57,898] [INFO] Task succeeded: HMMsearch
[2023-06-19 14:15:57,900] [INFO] Found 6/6 markers.
[2023-06-19 14:15:57,947] [INFO] Query marker FASTA was written to GCA_014804745.1_ASM1480474v1_genomic.fna/markers.fasta
[2023-06-19 14:15:57,947] [INFO] Task started: Blastn
[2023-06-19 14:15:57,947] [INFO] Running command: blastn -query GCA_014804745.1_ASM1480474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b975bf4-b776-4cf0-9449-4f2d5c12640a/dqc_reference/reference_markers.fasta -out GCA_014804745.1_ASM1480474v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:15:58,622] [INFO] Task succeeded: Blastn
[2023-06-19 14:15:58,629] [INFO] Selected 25 target genomes.
[2023-06-19 14:15:58,629] [INFO] Target genome list was writen to GCA_014804745.1_ASM1480474v1_genomic.fna/target_genomes.txt
[2023-06-19 14:15:58,636] [INFO] Task started: fastANI
[2023-06-19 14:15:58,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg548605df-00b9-4250-ad6f-d5210d34c73d/GCA_014804745.1_ASM1480474v1_genomic.fna.gz --refList GCA_014804745.1_ASM1480474v1_genomic.fna/target_genomes.txt --output GCA_014804745.1_ASM1480474v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 14:16:15,099] [INFO] Task succeeded: fastANI
[2023-06-19 14:16:15,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b975bf4-b776-4cf0-9449-4f2d5c12640a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 14:16:15,100] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b975bf4-b776-4cf0-9449-4f2d5c12640a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 14:16:15,112] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 14:16:15,112] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 14:16:15,112] [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	77.5444	142	1529	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	77.1653	83	1529	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.9279	93	1529	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	76.7068	97	1529	95	below_threshold
Kineothrix alysoides	strain=DSM 100556	GCA_004345255.1	1469948	1469948	type	True	76.6282	77	1529	95	below_threshold
Kineothrix alysoides	strain=KNHs209	GCA_000732725.1	1469948	1469948	type	True	76.6278	77	1529	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	76.4878	73	1529	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 14:16:15,121] [INFO] DFAST Taxonomy check result was written to GCA_014804745.1_ASM1480474v1_genomic.fna/tc_result.tsv
[2023-06-19 14:16:15,123] [INFO] ===== Taxonomy check completed =====
[2023-06-19 14:16:15,123] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 14:16:15,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b975bf4-b776-4cf0-9449-4f2d5c12640a/dqc_reference/checkm_data
[2023-06-19 14:16:15,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 14:16:15,174] [INFO] Task started: CheckM
[2023-06-19 14:16:15,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014804745.1_ASM1480474v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014804745.1_ASM1480474v1_genomic.fna/checkm_input GCA_014804745.1_ASM1480474v1_genomic.fna/checkm_result
[2023-06-19 14:16:54,136] [INFO] Task succeeded: CheckM
[2023-06-19 14:16:54,137] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 14:16:54,167] [INFO] ===== Completeness check finished =====
[2023-06-19 14:16:54,167] [INFO] ===== Start GTDB Search =====
[2023-06-19 14:16:54,168] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014804745.1_ASM1480474v1_genomic.fna/markers.fasta)
[2023-06-19 14:16:54,168] [INFO] Task started: Blastn
[2023-06-19 14:16:54,168] [INFO] Running command: blastn -query GCA_014804745.1_ASM1480474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b975bf4-b776-4cf0-9449-4f2d5c12640a/dqc_reference/reference_markers_gtdb.fasta -out GCA_014804745.1_ASM1480474v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:16:55,231] [INFO] Task succeeded: Blastn
[2023-06-19 14:16:55,238] [INFO] Selected 15 target genomes.
[2023-06-19 14:16:55,238] [INFO] Target genome list was writen to GCA_014804745.1_ASM1480474v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 14:16:55,247] [INFO] Task started: fastANI
[2023-06-19 14:16:55,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg548605df-00b9-4250-ad6f-d5210d34c73d/GCA_014804745.1_ASM1480474v1_genomic.fna.gz --refList GCA_014804745.1_ASM1480474v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014804745.1_ASM1480474v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 14:17:05,321] [INFO] Task succeeded: fastANI
[2023-06-19 14:17:05,347] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 14:17:05,348] [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_014804445.1	s__CAG-510 sp014804445	93.6749	944	1529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510	95.0	97.73	97.61	0.86	0.84	3	-
GCA_910578335.1	s__CAG-510 sp910578335	81.9809	755	1529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013316825.1	s__CAG-510 sp003979355	81.938	556	1529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510	95.0	99.67	99.65	0.84	0.73	3	-
GCA_900551115.1	s__CAG-510 sp900551115	78.0935	301	1529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577015.1	s__CAG-510 sp910577015	78.0542	303	1529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017482205.1	s__CAG-510 sp017482205	77.8639	170	1529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510	95.0	98.99	98.99	0.84	0.84	2	-
GCA_910577105.1	s__CAG-510 sp910577105	77.7823	293	1529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002432425.1	s__CAG-510 sp002432425	77.5465	167	1529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510	95.0	97.90	96.14	0.90	0.83	7	-
GCA_900550475.1	s__CAG-510 sp900550475	77.4699	215	1529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510	95.0	99.15	99.15	0.91	0.91	2	-
GCA_017476665.1	s__Acetatifactor sp017476665	77.3804	78	1529	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_017626325.1	s__UBA3282 sp017626325	76.9833	81	1529	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_910586775.1	s__Acetatifactor sp910586775	76.8163	94	1529	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_002490995.1	s__Acetatifactor sp002490995	76.7194	80	1529	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_910587555.1	s__Acetatifactor sp910587555	76.5801	88	1529	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	76.4168	88	1529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 14:17:05,350] [INFO] GTDB search result was written to GCA_014804745.1_ASM1480474v1_genomic.fna/result_gtdb.tsv
[2023-06-19 14:17:05,351] [INFO] ===== GTDB Search completed =====
[2023-06-19 14:17:05,354] [INFO] DFAST_QC result json was written to GCA_014804745.1_ASM1480474v1_genomic.fna/dqc_result.json
[2023-06-19 14:17:05,354] [INFO] DFAST_QC completed!
[2023-06-19 14:17:05,354] [INFO] Total running time: 0h1m21s