[2023-06-05 11:30:15,449] [INFO] DFAST_QC pipeline started.
[2023-06-05 11:30:15,451] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 11:30:15,452] [INFO] DQC Reference Directory: /var/lib/cwl/stgf51c9668-a92f-4e10-83e5-0eb9261e635a/dqc_reference
[2023-06-05 11:30:18,607] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 11:30:18,608] [INFO] Task started: Prodigal
[2023-06-05 11:30:18,609] [INFO] Running command: gunzip -c /var/lib/cwl/stg10303724-b01f-490a-985b-5907fbbd09a3/GCA_934192035.1_ERR7745831_bin.74_genomic.fna.gz | prodigal -d GCA_934192035.1_ERR7745831_bin.74_genomic.fna/cds.fna -a GCA_934192035.1_ERR7745831_bin.74_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 11:30:33,872] [INFO] Task succeeded: Prodigal
[2023-06-05 11:30:33,873] [INFO] Task started: HMMsearch
[2023-06-05 11:30:33,873] [INFO] Running command: hmmsearch --tblout GCA_934192035.1_ERR7745831_bin.74_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf51c9668-a92f-4e10-83e5-0eb9261e635a/dqc_reference/reference_markers.hmm GCA_934192035.1_ERR7745831_bin.74_genomic.fna/protein.faa > /dev/null
[2023-06-05 11:30:34,154] [INFO] Task succeeded: HMMsearch
[2023-06-05 11:30:34,155] [INFO] Found 6/6 markers.
[2023-06-05 11:30:34,193] [INFO] Query marker FASTA was written to GCA_934192035.1_ERR7745831_bin.74_genomic.fna/markers.fasta
[2023-06-05 11:30:34,193] [INFO] Task started: Blastn
[2023-06-05 11:30:34,193] [INFO] Running command: blastn -query GCA_934192035.1_ERR7745831_bin.74_genomic.fna/markers.fasta -db /var/lib/cwl/stgf51c9668-a92f-4e10-83e5-0eb9261e635a/dqc_reference/reference_markers.fasta -out GCA_934192035.1_ERR7745831_bin.74_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 11:30:34,815] [INFO] Task succeeded: Blastn
[2023-06-05 11:30:34,820] [INFO] Selected 20 target genomes.
[2023-06-05 11:30:34,820] [INFO] Target genome list was writen to GCA_934192035.1_ERR7745831_bin.74_genomic.fna/target_genomes.txt
[2023-06-05 11:30:34,827] [INFO] Task started: fastANI
[2023-06-05 11:30:34,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg10303724-b01f-490a-985b-5907fbbd09a3/GCA_934192035.1_ERR7745831_bin.74_genomic.fna.gz --refList GCA_934192035.1_ERR7745831_bin.74_genomic.fna/target_genomes.txt --output GCA_934192035.1_ERR7745831_bin.74_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 11:30:45,338] [INFO] Task succeeded: fastANI
[2023-06-05 11:30:45,339] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf51c9668-a92f-4e10-83e5-0eb9261e635a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 11:30:45,340] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf51c9668-a92f-4e10-83e5-0eb9261e635a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 11:30:45,359] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 11:30:45,359] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 11:30:45,359] [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 hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	82.6008	398	882	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	81.617	439	882	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	81.5073	445	882	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	81.4815	434	882	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	78.0609	146	882	95	below_threshold
Prevotella herbatica	strain=WR041	GCA_017347605.1	2801997	2801997	type	True	77.3786	76	882	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.2742	148	882	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	77.2065	96	882	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.9436	121	882	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.8637	95	882	95	below_threshold
Prevotella oris	strain=DSM 18711	GCA_000377685.1	28135	28135	type	True	76.6863	93	882	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	76.6756	101	882	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.5878	99	882	95	below_threshold
Prevotella intermedia	strain=DSM 20706	GCA_000439065.1	28131	28131	type	True	76.5868	60	882	95	below_threshold
Prevotella intermedia	strain=ATCC 25611	GCA_000519165.1	28131	28131	type	True	76.5868	60	882	95	below_threshold
Prevotella timonensis	strain=4401737	GCA_000455445.1	386414	386414	type	True	76.4789	50	882	95	below_threshold
Prevotella falsenii	strain=JCM 15124	GCA_000613945.1	515414	515414	type	True	76.271	57	882	95	below_threshold
Prevotella cerevisiae	strain=DSM 100619	GCA_024054555.1	2053716	2053716	type	True	76.0628	54	882	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 11:30:45,362] [INFO] DFAST Taxonomy check result was written to GCA_934192035.1_ERR7745831_bin.74_genomic.fna/tc_result.tsv
[2023-06-05 11:30:45,363] [INFO] ===== Taxonomy check completed =====
[2023-06-05 11:30:45,363] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 11:30:45,363] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf51c9668-a92f-4e10-83e5-0eb9261e635a/dqc_reference/checkm_data
[2023-06-05 11:30:45,365] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 11:30:45,398] [INFO] Task started: CheckM
[2023-06-05 11:30:45,398] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934192035.1_ERR7745831_bin.74_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934192035.1_ERR7745831_bin.74_genomic.fna/checkm_input GCA_934192035.1_ERR7745831_bin.74_genomic.fna/checkm_result
[2023-06-05 11:31:31,528] [INFO] Task succeeded: CheckM
[2023-06-05 11:31:31,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.21%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 11:31:31,550] [INFO] ===== Completeness check finished =====
[2023-06-05 11:31:31,550] [INFO] ===== Start GTDB Search =====
[2023-06-05 11:31:31,550] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934192035.1_ERR7745831_bin.74_genomic.fna/markers.fasta)
[2023-06-05 11:31:31,551] [INFO] Task started: Blastn
[2023-06-05 11:31:31,551] [INFO] Running command: blastn -query GCA_934192035.1_ERR7745831_bin.74_genomic.fna/markers.fasta -db /var/lib/cwl/stgf51c9668-a92f-4e10-83e5-0eb9261e635a/dqc_reference/reference_markers_gtdb.fasta -out GCA_934192035.1_ERR7745831_bin.74_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 11:31:32,436] [INFO] Task succeeded: Blastn
[2023-06-05 11:31:32,440] [INFO] Selected 16 target genomes.
[2023-06-05 11:31:32,440] [INFO] Target genome list was writen to GCA_934192035.1_ERR7745831_bin.74_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 11:31:32,447] [INFO] Task started: fastANI
[2023-06-05 11:31:32,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg10303724-b01f-490a-985b-5907fbbd09a3/GCA_934192035.1_ERR7745831_bin.74_genomic.fna.gz --refList GCA_934192035.1_ERR7745831_bin.74_genomic.fna/target_genomes_gtdb.txt --output GCA_934192035.1_ERR7745831_bin.74_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 11:31:43,257] [INFO] Task succeeded: fastANI
[2023-06-05 11:31:43,277] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 11:31:43,278] [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_009495355.1	s__Prevotella sp900313215	97.439	755	882	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.34	96.92	0.81	0.74	15	conclusive
GCA_900556395.1	s__Prevotella sp900556395	86.3667	516	882	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.82	97.81	0.83	0.82	3	-
GCA_002439605.1	s__Prevotella sp002439605	84.7193	516	882	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.57	99.57	0.81	0.81	2	-
GCA_019249655.1	s__Prevotella sp900767615	81.8423	438	882	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.47	95.77	0.82	0.75	7	-
GCF_019127135.1	s__Prevotella sp900551275	81.7995	441	882	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0063	98.12	96.96	0.86	0.77	7	-
GCF_015074785.1	s__Prevotella sp015074785	81.7715	437	882	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.50	95.88	0.80	0.71	45	-
GCA_900557255.1	s__Prevotella sp900557255	81.7508	232	882	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551985.1	s__Prevotella sp900551985	81.6736	354	882	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.28	99.28	0.87	0.87	2	-
GCA_900544825.1	s__Prevotella sp900544825	81.5962	385	882	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.36	98.76	0.90	0.84	3	-
GCF_000157935.1	s__Prevotella copri	81.5806	441	882	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	-
GCA_900555035.1	s__Prevotella sp900555035	80.8241	342	882	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002297965.1	s__Prevotella sp002297965	80.4266	324	882	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.14	99.14	0.78	0.78	2	-
GCA_002451555.1	s__Prevotella sp002451555	80.3517	364	882	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.47	99.47	0.85	0.85	2	-
GCA_000436035.1	s__Prevotella sp000436035	80.3371	367	882	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.58	97.92	0.86	0.81	4	-
GCA_900548535.1	s__Prevotella sp900548535	80.2065	375	882	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900765465.1	s__Prevotella sp900765465	78.9372	206	882	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 11:31:43,280] [INFO] GTDB search result was written to GCA_934192035.1_ERR7745831_bin.74_genomic.fna/result_gtdb.tsv
[2023-06-05 11:31:43,281] [INFO] ===== GTDB Search completed =====
[2023-06-05 11:31:43,288] [INFO] DFAST_QC result json was written to GCA_934192035.1_ERR7745831_bin.74_genomic.fna/dqc_result.json
[2023-06-05 11:31:43,289] [INFO] DFAST_QC completed!
[2023-06-05 11:31:43,289] [INFO] Total running time: 0h1m28s