[2023-06-13 15:45:08,134] [INFO] DFAST_QC pipeline started.
[2023-06-13 15:45:08,136] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 15:45:08,136] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b60d7a6-e227-47f5-a511-aafc8cd5cef0/dqc_reference
[2023-06-13 15:45:09,447] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 15:45:09,448] [INFO] Task started: Prodigal
[2023-06-13 15:45:09,448] [INFO] Running command: gunzip -c /var/lib/cwl/stg17dea958-f797-43b8-b254-6e1d544f0f6d/GCA_022744805.1_ASM2274480v1_genomic.fna.gz | prodigal -d GCA_022744805.1_ASM2274480v1_genomic.fna/cds.fna -a GCA_022744805.1_ASM2274480v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 15:45:26,072] [INFO] Task succeeded: Prodigal
[2023-06-13 15:45:26,072] [INFO] Task started: HMMsearch
[2023-06-13 15:45:26,073] [INFO] Running command: hmmsearch --tblout GCA_022744805.1_ASM2274480v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b60d7a6-e227-47f5-a511-aafc8cd5cef0/dqc_reference/reference_markers.hmm GCA_022744805.1_ASM2274480v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 15:45:26,323] [INFO] Task succeeded: HMMsearch
[2023-06-13 15:45:26,325] [INFO] Found 6/6 markers.
[2023-06-13 15:45:26,352] [INFO] Query marker FASTA was written to GCA_022744805.1_ASM2274480v1_genomic.fna/markers.fasta
[2023-06-13 15:45:26,353] [INFO] Task started: Blastn
[2023-06-13 15:45:26,353] [INFO] Running command: blastn -query GCA_022744805.1_ASM2274480v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b60d7a6-e227-47f5-a511-aafc8cd5cef0/dqc_reference/reference_markers.fasta -out GCA_022744805.1_ASM2274480v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:45:26,991] [INFO] Task succeeded: Blastn
[2023-06-13 15:45:26,995] [INFO] Selected 25 target genomes.
[2023-06-13 15:45:26,995] [INFO] Target genome list was writen to GCA_022744805.1_ASM2274480v1_genomic.fna/target_genomes.txt
[2023-06-13 15:45:26,997] [INFO] Task started: fastANI
[2023-06-13 15:45:26,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg17dea958-f797-43b8-b254-6e1d544f0f6d/GCA_022744805.1_ASM2274480v1_genomic.fna.gz --refList GCA_022744805.1_ASM2274480v1_genomic.fna/target_genomes.txt --output GCA_022744805.1_ASM2274480v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 15:45:39,585] [INFO] Task succeeded: fastANI
[2023-06-13 15:45:39,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b60d7a6-e227-47f5-a511-aafc8cd5cef0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 15:45:39,586] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b60d7a6-e227-47f5-a511-aafc8cd5cef0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 15:45:39,608] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 15:45:39,608] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 15:45:39,608] [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 stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	80.2599	312	865	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	78.3781	159	865	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	77.8541	141	865	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	77.7237	150	865	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	77.3559	86	865	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	77.176	98	865	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	77.174	94	865	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	77.1231	118	865	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.03	136	865	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	76.9609	101	865	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.7869	94	865	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.729	90	865	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.6717	98	865	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.6701	98	865	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.588	99	865	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	76.5628	87	865	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	76.5302	89	865	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.3893	79	865	95	below_threshold
Prevotella maculosa	strain=JCM 15638	GCA_000613965.1	439703	439703	type	True	76.3402	50	865	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.2988	84	865	95	below_threshold
Prevotella maculosa	strain=DSM 19339	GCA_000382385.1	439703	439703	type	True	76.2806	55	865	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	76.2781	85	865	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 15:45:39,612] [INFO] DFAST Taxonomy check result was written to GCA_022744805.1_ASM2274480v1_genomic.fna/tc_result.tsv
[2023-06-13 15:45:39,612] [INFO] ===== Taxonomy check completed =====
[2023-06-13 15:45:39,612] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 15:45:39,613] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b60d7a6-e227-47f5-a511-aafc8cd5cef0/dqc_reference/checkm_data
[2023-06-13 15:45:39,613] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 15:45:39,649] [INFO] Task started: CheckM
[2023-06-13 15:45:39,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022744805.1_ASM2274480v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022744805.1_ASM2274480v1_genomic.fna/checkm_input GCA_022744805.1_ASM2274480v1_genomic.fna/checkm_result
[2023-06-13 15:46:29,010] [INFO] Task succeeded: CheckM
[2023-06-13 15:46:29,012] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 15:46:29,041] [INFO] ===== Completeness check finished =====
[2023-06-13 15:46:29,042] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:46:29,042] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022744805.1_ASM2274480v1_genomic.fna/markers.fasta)
[2023-06-13 15:46:29,042] [INFO] Task started: Blastn
[2023-06-13 15:46:29,043] [INFO] Running command: blastn -query GCA_022744805.1_ASM2274480v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b60d7a6-e227-47f5-a511-aafc8cd5cef0/dqc_reference/reference_markers_gtdb.fasta -out GCA_022744805.1_ASM2274480v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:46:29,958] [INFO] Task succeeded: Blastn
[2023-06-13 15:46:29,963] [INFO] Selected 8 target genomes.
[2023-06-13 15:46:29,963] [INFO] Target genome list was writen to GCA_022744805.1_ASM2274480v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:46:29,964] [INFO] Task started: fastANI
[2023-06-13 15:46:29,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg17dea958-f797-43b8-b254-6e1d544f0f6d/GCA_022744805.1_ASM2274480v1_genomic.fna.gz --refList GCA_022744805.1_ASM2274480v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022744805.1_ASM2274480v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:46:34,969] [INFO] Task succeeded: fastANI
[2023-06-13 15:46:34,981] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 15:46:34,981] [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_900546575.1	s__Prevotella sp900546575	95.1791	656	865	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.21	95.49	0.86	0.86	4	conclusive
GCA_900544495.1	s__Prevotella sp900544495	92.7226	596	865	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.45	98.42	0.86	0.82	3	-
GCA_900552515.1	s__Prevotella sp900552515	90.781	484	865	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.61	97.50	0.85	0.85	3	-
GCA_900550035.1	s__Prevotella sp900550035	90.6706	632	865	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.97	99.93	0.97	0.97	3	-
GCF_900290275.1	s__Prevotella sp900290275	81.1004	366	865	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.80	97.71	0.90	0.86	4	-
GCF_002265625.1	s__Prevotella sp002265625	80.7041	375	865	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.90	96.80	0.88	0.86	4	-
GCF_019052365.1	s__Prevotella sp000434975	80.4865	362	865	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.59	0.82	0.74	11	-
GCA_900553155.1	s__Prevotella sp900553155	80.4577	258	865	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.04	96.93	0.80	0.75	3	-
--------------------------------------------------------------------------------
[2023-06-13 15:46:34,984] [INFO] GTDB search result was written to GCA_022744805.1_ASM2274480v1_genomic.fna/result_gtdb.tsv
[2023-06-13 15:46:34,984] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:46:34,988] [INFO] DFAST_QC result json was written to GCA_022744805.1_ASM2274480v1_genomic.fna/dqc_result.json
[2023-06-13 15:46:34,988] [INFO] DFAST_QC completed!
[2023-06-13 15:46:34,988] [INFO] Total running time: 0h1m27s