[2023-06-28 17:56:56,309] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:56:56,314] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:56:56,314] [INFO] DQC Reference Directory: /var/lib/cwl/stg7537bc53-1283-45e2-b68d-1a1638ccff24/dqc_reference
[2023-06-28 17:56:57,803] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:56:57,804] [INFO] Task started: Prodigal
[2023-06-28 17:56:57,804] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9f72ada-220a-45d9-b9b9-5eb6ef5464fc/GCA_017561085.1_ASM1756108v1_genomic.fna.gz | prodigal -d GCA_017561085.1_ASM1756108v1_genomic.fna/cds.fna -a GCA_017561085.1_ASM1756108v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:57:04,291] [INFO] Task succeeded: Prodigal
[2023-06-28 17:57:04,291] [INFO] Task started: HMMsearch
[2023-06-28 17:57:04,291] [INFO] Running command: hmmsearch --tblout GCA_017561085.1_ASM1756108v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7537bc53-1283-45e2-b68d-1a1638ccff24/dqc_reference/reference_markers.hmm GCA_017561085.1_ASM1756108v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:57:04,563] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:57:04,565] [INFO] Found 6/6 markers.
[2023-06-28 17:57:04,592] [INFO] Query marker FASTA was written to GCA_017561085.1_ASM1756108v1_genomic.fna/markers.fasta
[2023-06-28 17:57:04,592] [INFO] Task started: Blastn
[2023-06-28 17:57:04,592] [INFO] Running command: blastn -query GCA_017561085.1_ASM1756108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7537bc53-1283-45e2-b68d-1a1638ccff24/dqc_reference/reference_markers.fasta -out GCA_017561085.1_ASM1756108v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:57:05,232] [INFO] Task succeeded: Blastn
[2023-06-28 17:57:05,241] [INFO] Selected 27 target genomes.
[2023-06-28 17:57:05,242] [INFO] Target genome list was writen to GCA_017561085.1_ASM1756108v1_genomic.fna/target_genomes.txt
[2023-06-28 17:57:05,243] [INFO] Task started: fastANI
[2023-06-28 17:57:05,244] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9f72ada-220a-45d9-b9b9-5eb6ef5464fc/GCA_017561085.1_ASM1756108v1_genomic.fna.gz --refList GCA_017561085.1_ASM1756108v1_genomic.fna/target_genomes.txt --output GCA_017561085.1_ASM1756108v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:57:23,359] [INFO] Task succeeded: fastANI
[2023-06-28 17:57:23,360] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7537bc53-1283-45e2-b68d-1a1638ccff24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:57:23,360] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7537bc53-1283-45e2-b68d-1a1638ccff24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:57:23,371] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:57:23,371] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 17:57:23,372] [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=DSM 100556	GCA_004345255.1	1469948	1469948	type	True	77.2288	80	921	95	below_threshold
Kineothrix alysoides	strain=KNHs209	GCA_000732725.1	1469948	1469948	type	True	77.2228	81	921	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	77.1457	82	921	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	77.0166	89	921	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.9226	94	921	95	below_threshold
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	76.221	53	921	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 17:57:23,374] [INFO] DFAST Taxonomy check result was written to GCA_017561085.1_ASM1756108v1_genomic.fna/tc_result.tsv
[2023-06-28 17:57:23,375] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:57:23,375] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:57:23,375] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7537bc53-1283-45e2-b68d-1a1638ccff24/dqc_reference/checkm_data
[2023-06-28 17:57:23,376] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:57:23,412] [INFO] Task started: CheckM
[2023-06-28 17:57:23,412] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017561085.1_ASM1756108v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017561085.1_ASM1756108v1_genomic.fna/checkm_input GCA_017561085.1_ASM1756108v1_genomic.fna/checkm_result
[2023-06-28 17:57:49,556] [INFO] Task succeeded: CheckM
[2023-06-28 17:57:49,558] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 17:57:49,590] [INFO] ===== Completeness check finished =====
[2023-06-28 17:57:49,591] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:57:49,591] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017561085.1_ASM1756108v1_genomic.fna/markers.fasta)
[2023-06-28 17:57:49,591] [INFO] Task started: Blastn
[2023-06-28 17:57:49,592] [INFO] Running command: blastn -query GCA_017561085.1_ASM1756108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7537bc53-1283-45e2-b68d-1a1638ccff24/dqc_reference/reference_markers_gtdb.fasta -out GCA_017561085.1_ASM1756108v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:57:50,642] [INFO] Task succeeded: Blastn
[2023-06-28 17:57:50,648] [INFO] Selected 17 target genomes.
[2023-06-28 17:57:50,648] [INFO] Target genome list was writen to GCA_017561085.1_ASM1756108v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:57:50,663] [INFO] Task started: fastANI
[2023-06-28 17:57:50,663] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9f72ada-220a-45d9-b9b9-5eb6ef5464fc/GCA_017561085.1_ASM1756108v1_genomic.fna.gz --refList GCA_017561085.1_ASM1756108v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017561085.1_ASM1756108v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:57:59,525] [INFO] Task succeeded: fastANI
[2023-06-28 17:57:59,551] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 17:57:59,551] [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_017561085.1	s__CAG-95 sp017561085	100.0	915	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017411305.1	s__CAG-95 sp017411305	79.8005	249	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017434885.1	s__CAG-95 sp017434885	79.6739	280	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017938315.1	s__CAG-95 sp017938315	79.602	274	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553305.1	s__CAG-95 sp900553305	78.3797	97	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	99.81	99.81	0.85	0.85	2	-
GCA_017621815.1	s__CAG-95 sp017621815	78.3486	225	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014803415.1	s__CAG-95 sp014803415	78.3079	178	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	97.80	97.80	0.82	0.82	2	-
GCA_017622575.1	s__CAG-95 sp017622575	78.2754	203	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000403495.2	s__CAG-95 sp000403495	77.8448	131	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.68	98.68	0.87	0.87	2	-
GCA_000438155.1	s__CAG-95 sp000438155	77.8415	127	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.06	97.32	0.83	0.81	5	-
GCA_017624835.1	s__Acetatifactor sp017624835	77.7568	124	921	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_001916965.1	s__COE1 sp001916965	77.5264	69	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	98.52	98.34	0.88	0.83	8	-
GCA_002490775.1	s__CAG-95 sp002490775	77.4975	113	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003612395.1	s__CAG-95 sp003612395	77.4189	135	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017465095.1	s__CAG-194 sp017465095	77.1725	83	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-194	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017473445.1	s__Acetatifactor sp017473445	76.9773	88	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 17:57:59,554] [INFO] GTDB search result was written to GCA_017561085.1_ASM1756108v1_genomic.fna/result_gtdb.tsv
[2023-06-28 17:57:59,555] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:57:59,558] [INFO] DFAST_QC result json was written to GCA_017561085.1_ASM1756108v1_genomic.fna/dqc_result.json
[2023-06-28 17:57:59,559] [INFO] DFAST_QC completed!
[2023-06-28 17:57:59,559] [INFO] Total running time: 0h1m3s