[2023-06-28 12:49:03,213] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:49:03,216] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:49:03,216] [INFO] DQC Reference Directory: /var/lib/cwl/stgd243f792-fd10-407e-a1a9-c523354a30cb/dqc_reference
[2023-06-28 12:49:04,453] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:49:04,454] [INFO] Task started: Prodigal
[2023-06-28 12:49:04,454] [INFO] Running command: gunzip -c /var/lib/cwl/stg0380d6dd-0c5f-48bd-8eb8-f9870a22a070/GCA_017960585.1_ASM1796058v1_genomic.fna.gz | prodigal -d GCA_017960585.1_ASM1796058v1_genomic.fna/cds.fna -a GCA_017960585.1_ASM1796058v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:49:15,639] [INFO] Task succeeded: Prodigal
[2023-06-28 12:49:15,640] [INFO] Task started: HMMsearch
[2023-06-28 12:49:15,640] [INFO] Running command: hmmsearch --tblout GCA_017960585.1_ASM1796058v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd243f792-fd10-407e-a1a9-c523354a30cb/dqc_reference/reference_markers.hmm GCA_017960585.1_ASM1796058v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:49:15,878] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:49:15,880] [INFO] Found 6/6 markers.
[2023-06-28 12:49:15,905] [INFO] Query marker FASTA was written to GCA_017960585.1_ASM1796058v1_genomic.fna/markers.fasta
[2023-06-28 12:49:15,905] [INFO] Task started: Blastn
[2023-06-28 12:49:15,905] [INFO] Running command: blastn -query GCA_017960585.1_ASM1796058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd243f792-fd10-407e-a1a9-c523354a30cb/dqc_reference/reference_markers.fasta -out GCA_017960585.1_ASM1796058v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:49:16,590] [INFO] Task succeeded: Blastn
[2023-06-28 12:49:16,595] [INFO] Selected 30 target genomes.
[2023-06-28 12:49:16,596] [INFO] Target genome list was writen to GCA_017960585.1_ASM1796058v1_genomic.fna/target_genomes.txt
[2023-06-28 12:49:16,600] [INFO] Task started: fastANI
[2023-06-28 12:49:16,601] [INFO] Running command: fastANI --query /var/lib/cwl/stg0380d6dd-0c5f-48bd-8eb8-f9870a22a070/GCA_017960585.1_ASM1796058v1_genomic.fna.gz --refList GCA_017960585.1_ASM1796058v1_genomic.fna/target_genomes.txt --output GCA_017960585.1_ASM1796058v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:49:35,357] [INFO] Task succeeded: fastANI
[2023-06-28 12:49:35,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd243f792-fd10-407e-a1a9-c523354a30cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:49:35,358] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd243f792-fd10-407e-a1a9-c523354a30cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:49:35,374] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:49:35,375] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:49:35,375] [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
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	76.565	53	630	95	below_threshold
Alistipes dispar	strain=5CPEGH6	GCA_006542685.1	2585119	2585119	type	True	76.5519	65	630	95	below_threshold
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	76.5242	54	630	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	76.4921	55	630	95	below_threshold
Alistipes megaguti	strain=Marseille-P5997	GCA_900604385.1	2364787	2364787	type	True	76.4319	57	630	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	76.3113	52	630	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	76.2754	53	630	95	below_threshold
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	76.1945	56	630	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	74.8442	57	630	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:49:35,377] [INFO] DFAST Taxonomy check result was written to GCA_017960585.1_ASM1796058v1_genomic.fna/tc_result.tsv
[2023-06-28 12:49:35,378] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:49:35,378] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:49:35,379] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd243f792-fd10-407e-a1a9-c523354a30cb/dqc_reference/checkm_data
[2023-06-28 12:49:35,380] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:49:35,410] [INFO] Task started: CheckM
[2023-06-28 12:49:35,411] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017960585.1_ASM1796058v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017960585.1_ASM1796058v1_genomic.fna/checkm_input GCA_017960585.1_ASM1796058v1_genomic.fna/checkm_result
[2023-06-28 12:50:09,629] [INFO] Task succeeded: CheckM
[2023-06-28 12:50:09,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.91%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 12:50:09,653] [INFO] ===== Completeness check finished =====
[2023-06-28 12:50:09,654] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:50:09,654] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017960585.1_ASM1796058v1_genomic.fna/markers.fasta)
[2023-06-28 12:50:09,655] [INFO] Task started: Blastn
[2023-06-28 12:50:09,655] [INFO] Running command: blastn -query GCA_017960585.1_ASM1796058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd243f792-fd10-407e-a1a9-c523354a30cb/dqc_reference/reference_markers_gtdb.fasta -out GCA_017960585.1_ASM1796058v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:50:10,697] [INFO] Task succeeded: Blastn
[2023-06-28 12:50:10,703] [INFO] Selected 12 target genomes.
[2023-06-28 12:50:10,703] [INFO] Target genome list was writen to GCA_017960585.1_ASM1796058v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:50:10,711] [INFO] Task started: fastANI
[2023-06-28 12:50:10,711] [INFO] Running command: fastANI --query /var/lib/cwl/stg0380d6dd-0c5f-48bd-8eb8-f9870a22a070/GCA_017960585.1_ASM1796058v1_genomic.fna.gz --refList GCA_017960585.1_ASM1796058v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017960585.1_ASM1796058v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:50:16,501] [INFO] Task succeeded: fastANI
[2023-06-28 12:50:16,516] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:50:16,516] [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_017960585.1	s__Cryptobacteroides sp017960585	100.0	617	630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017535125.1	s__Cryptobacteroides sp017535125	87.7792	427	630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902768985.1	s__Cryptobacteroides sp902768985	87.3242	481	630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.65	98.07	0.93	0.92	5	-
GCA_017651225.1	s__Cryptobacteroides sp017651225	87.3084	414	630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902798975.1	s__Cryptobacteroides sp902798975	87.2708	417	630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902789245.1	s__Cryptobacteroides sp902789245	86.9154	477	630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.35	96.71	0.87	0.86	3	-
GCA_016291185.1	s__Cryptobacteroides sp016291185	86.1621	419	630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235775.1	s__Cryptobacteroides sp905235775	85.6821	360	630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017561865.1	s__Cryptobacteroides sp017561865	84.8313	338	630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902762435.1	s__Cryptobacteroides sp902762435	84.589	432	630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.59	98.59	0.91	0.91	2	-
GCA_017428725.1	s__Cryptobacteroides sp017428725	83.8307	422	630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.64	97.64	0.87	0.87	2	-
GCA_012744435.1	s__Cryptobacteroides sp012744435	83.6048	382	630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:50:16,519] [INFO] GTDB search result was written to GCA_017960585.1_ASM1796058v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:50:16,519] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:50:16,523] [INFO] DFAST_QC result json was written to GCA_017960585.1_ASM1796058v1_genomic.fna/dqc_result.json
[2023-06-28 12:50:16,523] [INFO] DFAST_QC completed!
[2023-06-28 12:50:16,523] [INFO] Total running time: 0h1m13s