[2024-01-24 14:39:02,790] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:02,792] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:02,792] [INFO] DQC Reference Directory: /var/lib/cwl/stg01d17d52-eb10-4d96-b6b5-a2300fc9f5fc/dqc_reference
[2024-01-24 14:39:04,241] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:04,243] [INFO] Task started: Prodigal
[2024-01-24 14:39:04,243] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbd14ebd-c809-4691-ba98-3163f0c1fb02/GCF_013166595.1_ASM1316659v1_genomic.fna.gz | prodigal -d GCF_013166595.1_ASM1316659v1_genomic.fna/cds.fna -a GCF_013166595.1_ASM1316659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:25,486] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:25,487] [INFO] Task started: HMMsearch
[2024-01-24 14:39:25,487] [INFO] Running command: hmmsearch --tblout GCF_013166595.1_ASM1316659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01d17d52-eb10-4d96-b6b5-a2300fc9f5fc/dqc_reference/reference_markers.hmm GCF_013166595.1_ASM1316659v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:25,776] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:25,780] [INFO] Found 6/6 markers.
[2024-01-24 14:39:25,812] [INFO] Query marker FASTA was written to GCF_013166595.1_ASM1316659v1_genomic.fna/markers.fasta
[2024-01-24 14:39:25,812] [INFO] Task started: Blastn
[2024-01-24 14:39:25,813] [INFO] Running command: blastn -query GCF_013166595.1_ASM1316659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01d17d52-eb10-4d96-b6b5-a2300fc9f5fc/dqc_reference/reference_markers.fasta -out GCF_013166595.1_ASM1316659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:26,427] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:26,430] [INFO] Selected 17 target genomes.
[2024-01-24 14:39:26,431] [INFO] Target genome list was writen to GCF_013166595.1_ASM1316659v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:26,437] [INFO] Task started: fastANI
[2024-01-24 14:39:26,438] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbd14ebd-c809-4691-ba98-3163f0c1fb02/GCF_013166595.1_ASM1316659v1_genomic.fna.gz --refList GCF_013166595.1_ASM1316659v1_genomic.fna/target_genomes.txt --output GCF_013166595.1_ASM1316659v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:37,368] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:37,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01d17d52-eb10-4d96-b6b5-a2300fc9f5fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:37,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01d17d52-eb10-4d96-b6b5-a2300fc9f5fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:37,379] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:37,380] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:37,380] [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
Palleniella intestinalis	strain=PINT	GCA_013166595.1	2736291	2736291	type	True	100.0	1161	1162	95	conclusive
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	79.6211	57	1162	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	79.6059	74	1162	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	79.4441	75	1162	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	78.836	90	1162	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	78.3169	63	1162	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	77.454	76	1162	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	77.3227	71	1162	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	76.9849	54	1162	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.6926	69	1162	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:37,382] [INFO] DFAST Taxonomy check result was written to GCF_013166595.1_ASM1316659v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:37,382] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:37,382] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:37,383] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01d17d52-eb10-4d96-b6b5-a2300fc9f5fc/dqc_reference/checkm_data
[2024-01-24 14:39:37,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:37,425] [INFO] Task started: CheckM
[2024-01-24 14:39:37,425] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013166595.1_ASM1316659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013166595.1_ASM1316659v1_genomic.fna/checkm_input GCF_013166595.1_ASM1316659v1_genomic.fna/checkm_result
[2024-01-24 14:40:39,431] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:39,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:39,450] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:39,450] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:39,450] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013166595.1_ASM1316659v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:39,450] [INFO] Task started: Blastn
[2024-01-24 14:40:39,451] [INFO] Running command: blastn -query GCF_013166595.1_ASM1316659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01d17d52-eb10-4d96-b6b5-a2300fc9f5fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_013166595.1_ASM1316659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:40,280] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:40,284] [INFO] Selected 13 target genomes.
[2024-01-24 14:40:40,284] [INFO] Target genome list was writen to GCF_013166595.1_ASM1316659v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:40,342] [INFO] Task started: fastANI
[2024-01-24 14:40:40,342] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbd14ebd-c809-4691-ba98-3163f0c1fb02/GCF_013166595.1_ASM1316659v1_genomic.fna.gz --refList GCF_013166595.1_ASM1316659v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013166595.1_ASM1316659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:47,721] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:47,730] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:47,730] [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_013166595.1	s__Prevotella sp002298815	100.0	1161	1162	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.88	99.76	0.99	0.99	4	conclusive
GCA_004792655.1	s__Prevotella sp004792655	91.9878	858	1162	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017462915.1	s__Prevotella sp017462915	80.9279	518	1162	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905372445.1	s__Prevotella sp905372445	79.5359	64	1162	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004555245.1	s__Prevotella sp004555245	77.6169	131	1162	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.26	98.55	0.94	0.92	3	-
GCA_017623655.1	s__Prevotella sp017623655	77.2711	64	1162	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017424205.1	s__Prevotella sp017424205	77.1345	74	1162	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004556065.1	s__Prevotella sp004556065	77.1244	125	1162	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.27	97.47	0.85	0.76	10	-
GCA_905233245.1	s__Prevotella sp905233245	76.9262	69	1162	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.87	97.81	0.80	0.79	3	-
GCA_902778265.1	s__Prevotella sp902778265	76.7251	78	1162	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:47,732] [INFO] GTDB search result was written to GCF_013166595.1_ASM1316659v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:47,733] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:47,737] [INFO] DFAST_QC result json was written to GCF_013166595.1_ASM1316659v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:47,737] [INFO] DFAST_QC completed!
[2024-01-24 14:40:47,738] [INFO] Total running time: 0h1m45s