[2024-01-24 13:45:46,529] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:46,532] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:46,532] [INFO] DQC Reference Directory: /var/lib/cwl/stg84c8af76-8279-4d1c-abb6-8fc9ca95c5ae/dqc_reference
[2024-01-24 13:45:47,964] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:47,965] [INFO] Task started: Prodigal
[2024-01-24 13:45:47,966] [INFO] Running command: gunzip -c /var/lib/cwl/stgad09ef6c-4d37-48e2-9145-76e88eca2528/GCF_022024115.1_ASM2202411v1_genomic.fna.gz | prodigal -d GCF_022024115.1_ASM2202411v1_genomic.fna/cds.fna -a GCF_022024115.1_ASM2202411v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:08,879] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:08,880] [INFO] Task started: HMMsearch
[2024-01-24 13:46:08,880] [INFO] Running command: hmmsearch --tblout GCF_022024115.1_ASM2202411v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84c8af76-8279-4d1c-abb6-8fc9ca95c5ae/dqc_reference/reference_markers.hmm GCF_022024115.1_ASM2202411v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:09,245] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:09,247] [INFO] Found 6/6 markers.
[2024-01-24 13:46:09,289] [INFO] Query marker FASTA was written to GCF_022024115.1_ASM2202411v1_genomic.fna/markers.fasta
[2024-01-24 13:46:09,289] [INFO] Task started: Blastn
[2024-01-24 13:46:09,289] [INFO] Running command: blastn -query GCF_022024115.1_ASM2202411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84c8af76-8279-4d1c-abb6-8fc9ca95c5ae/dqc_reference/reference_markers.fasta -out GCF_022024115.1_ASM2202411v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:09,958] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:09,962] [INFO] Selected 21 target genomes.
[2024-01-24 13:46:09,962] [INFO] Target genome list was writen to GCF_022024115.1_ASM2202411v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:10,000] [INFO] Task started: fastANI
[2024-01-24 13:46:10,000] [INFO] Running command: fastANI --query /var/lib/cwl/stgad09ef6c-4d37-48e2-9145-76e88eca2528/GCF_022024115.1_ASM2202411v1_genomic.fna.gz --refList GCF_022024115.1_ASM2202411v1_genomic.fna/target_genomes.txt --output GCF_022024115.1_ASM2202411v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:20,665] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:20,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84c8af76-8279-4d1c-abb6-8fc9ca95c5ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:20,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84c8af76-8279-4d1c-abb6-8fc9ca95c5ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:20,678] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:46:20,679] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:46:20,679] [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 brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	80.0978	361	1189	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	79.6785	293	1189	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	79.6033	293	1189	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	78.3438	70	1189	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	78.1538	85	1189	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	78.1402	85	1189	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	78.055	127	1189	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	78.0046	128	1189	95	below_threshold
Prevotella multisaccharivorax	strain=DSM 17128	GCA_000218235.1	310514	310514	type	True	77.9796	58	1189	95	below_threshold
Prevotella multisaccharivorax	strain=JCM 12954	GCA_019973315.1	310514	310514	type	True	77.589	56	1189	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	77.5218	122	1189	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	77.3834	92	1189	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	77.3699	79	1189	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	77.2917	80	1189	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.22	91	1189	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.5712	76	1189	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:20,681] [INFO] DFAST Taxonomy check result was written to GCF_022024115.1_ASM2202411v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:20,681] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:20,681] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:20,682] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84c8af76-8279-4d1c-abb6-8fc9ca95c5ae/dqc_reference/checkm_data
[2024-01-24 13:46:20,683] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:20,720] [INFO] Task started: CheckM
[2024-01-24 13:46:20,720] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022024115.1_ASM2202411v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022024115.1_ASM2202411v1_genomic.fna/checkm_input GCF_022024115.1_ASM2202411v1_genomic.fna/checkm_result
[2024-01-24 13:47:23,601] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:23,602] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:23,628] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:23,629] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:23,629] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022024115.1_ASM2202411v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:23,630] [INFO] Task started: Blastn
[2024-01-24 13:47:23,630] [INFO] Running command: blastn -query GCF_022024115.1_ASM2202411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84c8af76-8279-4d1c-abb6-8fc9ca95c5ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_022024115.1_ASM2202411v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:24,578] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:24,581] [INFO] Selected 10 target genomes.
[2024-01-24 13:47:24,582] [INFO] Target genome list was writen to GCF_022024115.1_ASM2202411v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:24,607] [INFO] Task started: fastANI
[2024-01-24 13:47:24,607] [INFO] Running command: fastANI --query /var/lib/cwl/stgad09ef6c-4d37-48e2-9145-76e88eca2528/GCF_022024115.1_ASM2202411v1_genomic.fna.gz --refList GCF_022024115.1_ASM2202411v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022024115.1_ASM2202411v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:33,028] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:33,040] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:33,040] [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_900100635.1	s__Prevotella sp900100635	97.4451	1001	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	96.60	0.86	0.83	10	conclusive
GCA_902799975.1	s__Prevotella sp902799975	82.592	611	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902778255.1	s__Prevotella sp902778255	82.4959	588	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.79	98.79	0.87	0.87	2	-
GCA_902788605.1	s__Prevotella sp902788605	81.5592	497	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.22	98.10	0.87	0.84	7	-
GCA_902785695.1	s__Prevotella sp902785695	80.8607	396	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775605.1	s__Prevotella sp902775605	80.7677	417	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621725.1	s__Prevotella brevis	80.0842	361	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.58	97.58	0.89	0.89	2	-
GCA_902799905.1	s__Prevotella sp902799905	79.4291	394	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.33	98.29	0.89	0.87	3	-
GCA_900199555.1	s__Prevotella sp900199555	79.337	251	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.82	97.80	0.89	0.85	3	-
GCA_017474925.1	s__Prevotella sp017474925	78.5905	132	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.19	98.19	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:33,041] [INFO] GTDB search result was written to GCF_022024115.1_ASM2202411v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:33,042] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:33,045] [INFO] DFAST_QC result json was written to GCF_022024115.1_ASM2202411v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:33,046] [INFO] DFAST_QC completed!
[2024-01-24 13:47:33,046] [INFO] Total running time: 0h1m47s