[2023-06-13 00:45:05,485] [INFO] DFAST_QC pipeline started.
[2023-06-13 00:45:05,489] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 00:45:05,490] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b6a05e3-12db-46ad-9c5d-d0fac071901e/dqc_reference
[2023-06-13 00:45:06,899] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 00:45:06,908] [INFO] Task started: Prodigal
[2023-06-13 00:45:06,908] [INFO] Running command: gunzip -c /var/lib/cwl/stgf06f58c6-c777-4ac5-bdac-1a59a2aeb735/GCA_022787705.1_ASM2278770v1_genomic.fna.gz | prodigal -d GCA_022787705.1_ASM2278770v1_genomic.fna/cds.fna -a GCA_022787705.1_ASM2278770v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 00:45:21,099] [INFO] Task succeeded: Prodigal
[2023-06-13 00:45:21,099] [INFO] Task started: HMMsearch
[2023-06-13 00:45:21,099] [INFO] Running command: hmmsearch --tblout GCA_022787705.1_ASM2278770v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b6a05e3-12db-46ad-9c5d-d0fac071901e/dqc_reference/reference_markers.hmm GCA_022787705.1_ASM2278770v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 00:45:21,332] [INFO] Task succeeded: HMMsearch
[2023-06-13 00:45:21,333] [INFO] Found 6/6 markers.
[2023-06-13 00:45:21,360] [INFO] Query marker FASTA was written to GCA_022787705.1_ASM2278770v1_genomic.fna/markers.fasta
[2023-06-13 00:45:21,361] [INFO] Task started: Blastn
[2023-06-13 00:45:21,361] [INFO] Running command: blastn -query GCA_022787705.1_ASM2278770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b6a05e3-12db-46ad-9c5d-d0fac071901e/dqc_reference/reference_markers.fasta -out GCA_022787705.1_ASM2278770v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:45:21,964] [INFO] Task succeeded: Blastn
[2023-06-13 00:45:21,968] [INFO] Selected 28 target genomes.
[2023-06-13 00:45:21,968] [INFO] Target genome list was writen to GCA_022787705.1_ASM2278770v1_genomic.fna/target_genomes.txt
[2023-06-13 00:45:21,969] [INFO] Task started: fastANI
[2023-06-13 00:45:21,969] [INFO] Running command: fastANI --query /var/lib/cwl/stgf06f58c6-c777-4ac5-bdac-1a59a2aeb735/GCA_022787705.1_ASM2278770v1_genomic.fna.gz --refList GCA_022787705.1_ASM2278770v1_genomic.fna/target_genomes.txt --output GCA_022787705.1_ASM2278770v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 00:45:35,522] [INFO] Task succeeded: fastANI
[2023-06-13 00:45:35,523] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b6a05e3-12db-46ad-9c5d-d0fac071901e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 00:45:35,523] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b6a05e3-12db-46ad-9c5d-d0fac071901e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 00:45:35,538] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 00:45:35,538] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 00:45:35,539] [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 illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	77.3714	52	715	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	77.1821	109	715	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	77.1253	119	715	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	77.0005	89	715	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.9652	88	715	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	76.9566	89	715	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	76.918	89	715	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	76.8292	87	715	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	76.8142	81	715	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.8142	81	715	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.7384	101	715	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.6727	84	715	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	76.6484	64	715	95	below_threshold
Prevotella maculosa	strain=DSM 19339	GCA_000382385.1	439703	439703	type	True	76.6152	61	715	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	76.5985	88	715	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.5865	106	715	95	below_threshold
Prevotella maculosa	strain=JCM 15638	GCA_000613965.1	439703	439703	type	True	76.5257	59	715	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.5219	105	715	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.3126	85	715	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 00:45:35,541] [INFO] DFAST Taxonomy check result was written to GCA_022787705.1_ASM2278770v1_genomic.fna/tc_result.tsv
[2023-06-13 00:45:35,542] [INFO] ===== Taxonomy check completed =====
[2023-06-13 00:45:35,542] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 00:45:35,542] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b6a05e3-12db-46ad-9c5d-d0fac071901e/dqc_reference/checkm_data
[2023-06-13 00:45:35,543] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 00:45:35,575] [INFO] Task started: CheckM
[2023-06-13 00:45:35,575] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022787705.1_ASM2278770v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022787705.1_ASM2278770v1_genomic.fna/checkm_input GCA_022787705.1_ASM2278770v1_genomic.fna/checkm_result
[2023-06-13 00:46:19,171] [INFO] Task succeeded: CheckM
[2023-06-13 00:46:19,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 00:46:19,193] [INFO] ===== Completeness check finished =====
[2023-06-13 00:46:19,194] [INFO] ===== Start GTDB Search =====
[2023-06-13 00:46:19,194] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022787705.1_ASM2278770v1_genomic.fna/markers.fasta)
[2023-06-13 00:46:19,195] [INFO] Task started: Blastn
[2023-06-13 00:46:19,195] [INFO] Running command: blastn -query GCA_022787705.1_ASM2278770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b6a05e3-12db-46ad-9c5d-d0fac071901e/dqc_reference/reference_markers_gtdb.fasta -out GCA_022787705.1_ASM2278770v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:46:20,048] [INFO] Task succeeded: Blastn
[2023-06-13 00:46:20,053] [INFO] Selected 21 target genomes.
[2023-06-13 00:46:20,054] [INFO] Target genome list was writen to GCA_022787705.1_ASM2278770v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 00:46:20,059] [INFO] Task started: fastANI
[2023-06-13 00:46:20,060] [INFO] Running command: fastANI --query /var/lib/cwl/stgf06f58c6-c777-4ac5-bdac-1a59a2aeb735/GCA_022787705.1_ASM2278770v1_genomic.fna.gz --refList GCA_022787705.1_ASM2278770v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022787705.1_ASM2278770v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 00:46:30,936] [INFO] Task succeeded: fastANI
[2023-06-13 00:46:30,953] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 00:46:30,954] [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_002251365.1	s__Prevotella sp002251365	98.4357	677	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.20	97.97	0.85	0.80	5	conclusive
GCA_900769055.1	s__Prevotella sp900769055	87.1793	470	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000436915.1	s__Prevotella sp000436915	78.4542	192	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.18	97.08	0.77	0.76	4	-
GCF_019052365.1	s__Prevotella sp000434975	77.2599	114	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.59	0.82	0.74	11	-
GCF_000834015.1	s__Prevotella pectinovora	77.1821	109	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.37	97.34	0.86	0.79	12	-
GCF_000235885.1	s__Prevotella stercorea	77.1253	119	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.02	96.84	0.81	0.69	8	-
GCF_002265625.1	s__Prevotella sp002265625	77.1125	128	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.90	96.80	0.88	0.86	4	-
GCA_900544495.1	s__Prevotella sp900544495	77.0503	106	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.45	98.42	0.86	0.82	3	-
GCA_900546345.1	s__Prevotella sp900546345	77.0276	75	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902762325.1	s__Prevotella sp902762325	76.9735	79	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.14	98.03	0.81	0.79	4	-
GCA_900553155.1	s__Prevotella sp900553155	76.8691	69	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.04	96.93	0.80	0.75	3	-
GCA_900546575.1	s__Prevotella sp900546575	76.8206	117	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.21	95.49	0.86	0.86	4	-
GCF_009695775.1	s__Prevotella mizrahii	76.7156	102	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	96.87	0.87	0.84	6	-
GCA_900318915.1	s__Prevotella sp900318915	76.6561	98	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.05	95.26	0.87	0.81	11	-
GCA_002481295.1	s__Prevotella sp002481295	76.5658	89	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.83	96.70	0.87	0.78	4	-
GCA_900548535.1	s__Prevotella sp900548535	76.5588	91	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113305.1	s__Prevotella sp900113305	76.5441	86	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900557405.1	s__Prevotella sp900557405	76.4673	81	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.88	97.88	0.76	0.76	2	-
GCA_900318815.1	s__Prevotella sp900318815	76.3789	97	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.58	97.15	0.91	0.81	3	-
GCF_003043945.1	s__Prevotella sp003043945	76.3552	81	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.81	99.81	0.99	0.99	2	-
GCA_002317385.1	s__Prevotella sp002317385	76.3475	103	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 00:46:30,956] [INFO] GTDB search result was written to GCA_022787705.1_ASM2278770v1_genomic.fna/result_gtdb.tsv
[2023-06-13 00:46:30,956] [INFO] ===== GTDB Search completed =====
[2023-06-13 00:46:30,960] [INFO] DFAST_QC result json was written to GCA_022787705.1_ASM2278770v1_genomic.fna/dqc_result.json
[2023-06-13 00:46:30,961] [INFO] DFAST_QC completed!
[2023-06-13 00:46:30,961] [INFO] Total running time: 0h1m25s