[2023-06-13 17:11:54,214] [INFO] DFAST_QC pipeline started.
[2023-06-13 17:11:54,216] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 17:11:54,217] [INFO] DQC Reference Directory: /var/lib/cwl/stg399d1e3c-65c5-4535-8d8b-fe067af469b9/dqc_reference
[2023-06-13 17:11:55,508] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 17:11:55,509] [INFO] Task started: Prodigal
[2023-06-13 17:11:55,509] [INFO] Running command: gunzip -c /var/lib/cwl/stg31c4366d-1bf6-4ea7-bb41-926fe8ceb942/GCA_022784915.1_ASM2278491v1_genomic.fna.gz | prodigal -d GCA_022784915.1_ASM2278491v1_genomic.fna/cds.fna -a GCA_022784915.1_ASM2278491v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 17:12:03,139] [INFO] Task succeeded: Prodigal
[2023-06-13 17:12:03,139] [INFO] Task started: HMMsearch
[2023-06-13 17:12:03,140] [INFO] Running command: hmmsearch --tblout GCA_022784915.1_ASM2278491v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg399d1e3c-65c5-4535-8d8b-fe067af469b9/dqc_reference/reference_markers.hmm GCA_022784915.1_ASM2278491v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 17:12:03,448] [INFO] Task succeeded: HMMsearch
[2023-06-13 17:12:03,450] [INFO] Found 6/6 markers.
[2023-06-13 17:12:03,486] [INFO] Query marker FASTA was written to GCA_022784915.1_ASM2278491v1_genomic.fna/markers.fasta
[2023-06-13 17:12:03,486] [INFO] Task started: Blastn
[2023-06-13 17:12:03,486] [INFO] Running command: blastn -query GCA_022784915.1_ASM2278491v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg399d1e3c-65c5-4535-8d8b-fe067af469b9/dqc_reference/reference_markers.fasta -out GCA_022784915.1_ASM2278491v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:12:04,098] [INFO] Task succeeded: Blastn
[2023-06-13 17:12:04,102] [INFO] Selected 18 target genomes.
[2023-06-13 17:12:04,102] [INFO] Target genome list was writen to GCA_022784915.1_ASM2278491v1_genomic.fna/target_genomes.txt
[2023-06-13 17:12:04,104] [INFO] Task started: fastANI
[2023-06-13 17:12:04,104] [INFO] Running command: fastANI --query /var/lib/cwl/stg31c4366d-1bf6-4ea7-bb41-926fe8ceb942/GCA_022784915.1_ASM2278491v1_genomic.fna.gz --refList GCA_022784915.1_ASM2278491v1_genomic.fna/target_genomes.txt --output GCA_022784915.1_ASM2278491v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 17:12:15,528] [INFO] Task succeeded: fastANI
[2023-06-13 17:12:15,529] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg399d1e3c-65c5-4535-8d8b-fe067af469b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 17:12:15,529] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg399d1e3c-65c5-4535-8d8b-fe067af469b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 17:12:15,544] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 17:12:15,545] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 17:12:15,545] [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
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	87.3178	707	1113	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	87.2206	758	1113	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	86.4903	646	1113	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	79.8676	292	1113	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	79.5379	304	1113	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	79.4242	296	1113	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	79.1316	66	1113	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	78.4457	231	1113	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	77.9471	146	1113	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	77.4093	96	1113	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	77.1379	82	1113	95	below_threshold
Coprococcus catus	strain=ATCC 27761	GCA_025289135.1	116085	116085	suspected-type	True	77.0279	75	1113	95	below_threshold
Blautia coccoides	strain=NCTC11035	GCA_900461125.1	1532	1532	type	True	76.7646	86	1113	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	76.75	88	1113	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 17:12:15,547] [INFO] DFAST Taxonomy check result was written to GCA_022784915.1_ASM2278491v1_genomic.fna/tc_result.tsv
[2023-06-13 17:12:15,547] [INFO] ===== Taxonomy check completed =====
[2023-06-13 17:12:15,547] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 17:12:15,548] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg399d1e3c-65c5-4535-8d8b-fe067af469b9/dqc_reference/checkm_data
[2023-06-13 17:12:15,549] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 17:12:15,590] [INFO] Task started: CheckM
[2023-06-13 17:12:15,590] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022784915.1_ASM2278491v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022784915.1_ASM2278491v1_genomic.fna/checkm_input GCA_022784915.1_ASM2278491v1_genomic.fna/checkm_result
[2023-06-13 17:12:45,745] [INFO] Task succeeded: CheckM
[2023-06-13 17:12:45,747] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.80%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 17:12:45,777] [INFO] ===== Completeness check finished =====
[2023-06-13 17:12:45,778] [INFO] ===== Start GTDB Search =====
[2023-06-13 17:12:45,778] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022784915.1_ASM2278491v1_genomic.fna/markers.fasta)
[2023-06-13 17:12:45,779] [INFO] Task started: Blastn
[2023-06-13 17:12:45,779] [INFO] Running command: blastn -query GCA_022784915.1_ASM2278491v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg399d1e3c-65c5-4535-8d8b-fe067af469b9/dqc_reference/reference_markers_gtdb.fasta -out GCA_022784915.1_ASM2278491v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:12:46,627] [INFO] Task succeeded: Blastn
[2023-06-13 17:12:46,631] [INFO] Selected 8 target genomes.
[2023-06-13 17:12:46,632] [INFO] Target genome list was writen to GCA_022784915.1_ASM2278491v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 17:12:46,635] [INFO] Task started: fastANI
[2023-06-13 17:12:46,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg31c4366d-1bf6-4ea7-bb41-926fe8ceb942/GCA_022784915.1_ASM2278491v1_genomic.fna.gz --refList GCA_022784915.1_ASM2278491v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022784915.1_ASM2278491v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 17:12:54,092] [INFO] Task succeeded: fastANI
[2023-06-13 17:12:54,108] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 17:12:54,109] [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
GCF_018919065.1	s__Blautia_A sp018919065	96.5825	785	1113	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905209435.1	s__Blautia_A sp905209435	87.4332	656	1113	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000484655.1	s__Blautia_A wexlerae	87.3182	707	1113	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.38	96.15	0.76	0.65	140	-
GCF_013300825.1	s__Blautia_A wexlerae_B	86.9534	713	1113	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.68	98.07	0.89	0.86	5	-
GCF_009707925.1	s__Blautia_A luti	86.4892	645	1113	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.33	97.04	0.87	0.84	5	-
GCF_003471165.1	s__Blautia_A sp003471165	86.2883	764	1113	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.40	97.74	0.83	0.79	20	-
GCF_003477525.1	s__Blautia_A sp003477525	85.91	729	1113	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.30	98.60	0.90	0.81	3	-
GCF_000210015.1	s__Blautia_A obeum_B	79.151	284	1113	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.64	98.44	0.85	0.84	7	-
--------------------------------------------------------------------------------
[2023-06-13 17:12:54,111] [INFO] GTDB search result was written to GCA_022784915.1_ASM2278491v1_genomic.fna/result_gtdb.tsv
[2023-06-13 17:12:54,112] [INFO] ===== GTDB Search completed =====
[2023-06-13 17:12:54,117] [INFO] DFAST_QC result json was written to GCA_022784915.1_ASM2278491v1_genomic.fna/dqc_result.json
[2023-06-13 17:12:54,117] [INFO] DFAST_QC completed!
[2023-06-13 17:12:54,117] [INFO] Total running time: 0h0m60s