[2023-06-28 18:41:22,137] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:41:22,142] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:41:22,143] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e08d038-f781-42e5-9f15-0bfce25c3a24/dqc_reference
[2023-06-28 18:41:23,857] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:41:23,858] [INFO] Task started: Prodigal
[2023-06-28 18:41:23,858] [INFO] Running command: gunzip -c /var/lib/cwl/stgaeaf01d6-f077-4b42-8b6d-f891b0491cb6/GCA_017474485.1_ASM1747448v1_genomic.fna.gz | prodigal -d GCA_017474485.1_ASM1747448v1_genomic.fna/cds.fna -a GCA_017474485.1_ASM1747448v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:41:39,487] [INFO] Task succeeded: Prodigal
[2023-06-28 18:41:39,488] [INFO] Task started: HMMsearch
[2023-06-28 18:41:39,488] [INFO] Running command: hmmsearch --tblout GCA_017474485.1_ASM1747448v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e08d038-f781-42e5-9f15-0bfce25c3a24/dqc_reference/reference_markers.hmm GCA_017474485.1_ASM1747448v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:41:39,725] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:41:39,727] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgaeaf01d6-f077-4b42-8b6d-f891b0491cb6/GCA_017474485.1_ASM1747448v1_genomic.fna.gz]
[2023-06-28 18:41:39,757] [INFO] Query marker FASTA was written to GCA_017474485.1_ASM1747448v1_genomic.fna/markers.fasta
[2023-06-28 18:41:39,758] [INFO] Task started: Blastn
[2023-06-28 18:41:39,758] [INFO] Running command: blastn -query GCA_017474485.1_ASM1747448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e08d038-f781-42e5-9f15-0bfce25c3a24/dqc_reference/reference_markers.fasta -out GCA_017474485.1_ASM1747448v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:41:40,278] [INFO] Task succeeded: Blastn
[2023-06-28 18:41:40,282] [INFO] Selected 17 target genomes.
[2023-06-28 18:41:40,282] [INFO] Target genome list was writen to GCA_017474485.1_ASM1747448v1_genomic.fna/target_genomes.txt
[2023-06-28 18:41:40,287] [INFO] Task started: fastANI
[2023-06-28 18:41:40,288] [INFO] Running command: fastANI --query /var/lib/cwl/stgaeaf01d6-f077-4b42-8b6d-f891b0491cb6/GCA_017474485.1_ASM1747448v1_genomic.fna.gz --refList GCA_017474485.1_ASM1747448v1_genomic.fna/target_genomes.txt --output GCA_017474485.1_ASM1747448v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:41:48,714] [INFO] Task succeeded: fastANI
[2023-06-28 18:41:48,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e08d038-f781-42e5-9f15-0bfce25c3a24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:41:48,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e08d038-f781-42e5-9f15-0bfce25c3a24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:41:48,727] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:41:48,728] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:41:48,728] [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
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	78.2781	189	873	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	78.1961	195	873	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	77.3341	152	873	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.2713	66	873	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	76.2123	68	873	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:41:48,734] [INFO] DFAST Taxonomy check result was written to GCA_017474485.1_ASM1747448v1_genomic.fna/tc_result.tsv
[2023-06-28 18:41:48,735] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:41:48,735] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:41:48,735] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e08d038-f781-42e5-9f15-0bfce25c3a24/dqc_reference/checkm_data
[2023-06-28 18:41:48,737] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:41:48,773] [INFO] Task started: CheckM
[2023-06-28 18:41:48,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017474485.1_ASM1747448v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017474485.1_ASM1747448v1_genomic.fna/checkm_input GCA_017474485.1_ASM1747448v1_genomic.fna/checkm_result
[2023-06-28 18:42:38,080] [INFO] Task succeeded: CheckM
[2023-06-28 18:42:38,081] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 40.62%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 18:42:38,104] [INFO] ===== Completeness check finished =====
[2023-06-28 18:42:38,104] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:42:38,104] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017474485.1_ASM1747448v1_genomic.fna/markers.fasta)
[2023-06-28 18:42:38,105] [INFO] Task started: Blastn
[2023-06-28 18:42:38,105] [INFO] Running command: blastn -query GCA_017474485.1_ASM1747448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e08d038-f781-42e5-9f15-0bfce25c3a24/dqc_reference/reference_markers_gtdb.fasta -out GCA_017474485.1_ASM1747448v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:42:38,607] [INFO] Task succeeded: Blastn
[2023-06-28 18:42:38,612] [INFO] Selected 11 target genomes.
[2023-06-28 18:42:38,612] [INFO] Target genome list was writen to GCA_017474485.1_ASM1747448v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:42:38,617] [INFO] Task started: fastANI
[2023-06-28 18:42:38,617] [INFO] Running command: fastANI --query /var/lib/cwl/stgaeaf01d6-f077-4b42-8b6d-f891b0491cb6/GCA_017474485.1_ASM1747448v1_genomic.fna.gz --refList GCA_017474485.1_ASM1747448v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017474485.1_ASM1747448v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:42:45,863] [INFO] Task succeeded: fastANI
[2023-06-28 18:42:45,874] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:42:45,874] [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_017474485.1	s__Prevotella sp017474485	100.0	860	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902762565.1	s__Prevotella sp902762565	82.9106	489	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.04	97.04	0.79	0.79	2	-
GCA_902772585.1	s__Prevotella sp902772585	79.795	307	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902782305.1	s__Prevotella sp902782305	79.573	261	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.21	96.08	0.74	0.67	4	-
GCA_902800925.1	s__Prevotella sp902800925	79.5694	304	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902764705.1	s__Prevotella sp902764705	79.5237	298	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016291085.1	s__Prevotella sp016291085	79.2502	343	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316265.1	s__Prevotella sp900316265	79.0228	291	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.64	96.94	0.80	0.66	12	-
GCA_900314985.1	s__Prevotella sp900314985	78.9858	302	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.71	97.24	0.86	0.81	12	-
GCA_002371715.1	s__Prevotella sp002371715	78.5998	316	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318795.1	s__Prevotella sp900318795	78.2953	252	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.54	96.27	0.80	0.72	18	-
--------------------------------------------------------------------------------
[2023-06-28 18:42:45,876] [INFO] GTDB search result was written to GCA_017474485.1_ASM1747448v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:42:45,877] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:42:45,880] [INFO] DFAST_QC result json was written to GCA_017474485.1_ASM1747448v1_genomic.fna/dqc_result.json
[2023-06-28 18:42:45,880] [INFO] DFAST_QC completed!
[2023-06-28 18:42:45,880] [INFO] Total running time: 0h1m24s