[2023-06-05 18:50:28,494] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:50:28,496] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:50:28,496] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a59549d-5387-428e-b775-750ceb25941a/dqc_reference
[2023-06-05 18:50:29,603] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:50:29,604] [INFO] Task started: Prodigal
[2023-06-05 18:50:29,604] [INFO] Running command: gunzip -c /var/lib/cwl/stg135e79e1-e313-4e5c-ac51-7bc7d1106bbd/GCA_004554545.1_ASM455454v1_genomic.fna.gz | prodigal -d GCA_004554545.1_ASM455454v1_genomic.fna/cds.fna -a GCA_004554545.1_ASM455454v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:50:42,213] [INFO] Task succeeded: Prodigal
[2023-06-05 18:50:42,213] [INFO] Task started: HMMsearch
[2023-06-05 18:50:42,213] [INFO] Running command: hmmsearch --tblout GCA_004554545.1_ASM455454v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a59549d-5387-428e-b775-750ceb25941a/dqc_reference/reference_markers.hmm GCA_004554545.1_ASM455454v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:50:42,499] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:50:42,500] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg135e79e1-e313-4e5c-ac51-7bc7d1106bbd/GCA_004554545.1_ASM455454v1_genomic.fna.gz]
[2023-06-05 18:50:42,526] [INFO] Query marker FASTA was written to GCA_004554545.1_ASM455454v1_genomic.fna/markers.fasta
[2023-06-05 18:50:42,526] [INFO] Task started: Blastn
[2023-06-05 18:50:42,526] [INFO] Running command: blastn -query GCA_004554545.1_ASM455454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a59549d-5387-428e-b775-750ceb25941a/dqc_reference/reference_markers.fasta -out GCA_004554545.1_ASM455454v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:50:43,278] [INFO] Task succeeded: Blastn
[2023-06-05 18:50:43,281] [INFO] Selected 19 target genomes.
[2023-06-05 18:50:43,282] [INFO] Target genome list was writen to GCA_004554545.1_ASM455454v1_genomic.fna/target_genomes.txt
[2023-06-05 18:50:43,284] [INFO] Task started: fastANI
[2023-06-05 18:50:43,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg135e79e1-e313-4e5c-ac51-7bc7d1106bbd/GCA_004554545.1_ASM455454v1_genomic.fna.gz --refList GCA_004554545.1_ASM455454v1_genomic.fna/target_genomes.txt --output GCA_004554545.1_ASM455454v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:50:56,283] [INFO] Task succeeded: fastANI
[2023-06-05 18:50:56,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a59549d-5387-428e-b775-750ceb25941a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:50:56,283] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a59549d-5387-428e-b775-750ceb25941a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:50:56,293] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:50:56,293] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:50:56,294] [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	89.4504	572	813	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	78.0062	199	813	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	77.8929	127	813	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.5394	185	813	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	77.4242	150	813	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	76.8554	93	813	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.8343	124	813	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.678	98	813	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.6463	128	813	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	76.6362	102	813	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.5816	80	813	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.577	107	813	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.576	99	813	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.5094	124	813	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	76.4684	93	813	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:50:56,296] [INFO] DFAST Taxonomy check result was written to GCA_004554545.1_ASM455454v1_genomic.fna/tc_result.tsv
[2023-06-05 18:50:56,296] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:50:56,296] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:50:56,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a59549d-5387-428e-b775-750ceb25941a/dqc_reference/checkm_data
[2023-06-05 18:50:56,297] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:50:56,325] [INFO] Task started: CheckM
[2023-06-05 18:50:56,325] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004554545.1_ASM455454v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004554545.1_ASM455454v1_genomic.fna/checkm_input GCA_004554545.1_ASM455454v1_genomic.fna/checkm_result
[2023-06-05 18:51:33,756] [INFO] Task succeeded: CheckM
[2023-06-05 18:51:33,757] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.30%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:51:33,775] [INFO] ===== Completeness check finished =====
[2023-06-05 18:51:33,776] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:51:33,777] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004554545.1_ASM455454v1_genomic.fna/markers.fasta)
[2023-06-05 18:51:33,777] [INFO] Task started: Blastn
[2023-06-05 18:51:33,777] [INFO] Running command: blastn -query GCA_004554545.1_ASM455454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a59549d-5387-428e-b775-750ceb25941a/dqc_reference/reference_markers_gtdb.fasta -out GCA_004554545.1_ASM455454v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:51:34,612] [INFO] Task succeeded: Blastn
[2023-06-05 18:51:34,616] [INFO] Selected 10 target genomes.
[2023-06-05 18:51:34,616] [INFO] Target genome list was writen to GCA_004554545.1_ASM455454v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:51:34,616] [INFO] Task started: fastANI
[2023-06-05 18:51:34,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg135e79e1-e313-4e5c-ac51-7bc7d1106bbd/GCA_004554545.1_ASM455454v1_genomic.fna.gz --refList GCA_004554545.1_ASM455454v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004554545.1_ASM455454v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:51:41,361] [INFO] Task succeeded: fastANI
[2023-06-05 18:51:41,368] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:51:41,369] [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_019052365.1	s__Prevotella sp000434975	96.7552	599	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.59	0.82	0.74	11	conclusive
GCF_000235885.1	s__Prevotella stercorea	89.4239	572	813	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	80.7719	411	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.90	96.80	0.88	0.86	4	-
GCA_002490315.1	s__Prevotella sp002490315	80.659	314	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544495.1	s__Prevotella sp900544495	80.5776	346	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.45	98.42	0.86	0.82	3	-
GCA_900550035.1	s__Prevotella sp900550035	80.4695	357	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.97	99.93	0.97	0.97	3	-
GCA_900552515.1	s__Prevotella sp900552515	80.3741	308	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.61	97.50	0.85	0.85	3	-
GCA_900546575.1	s__Prevotella sp900546575	80.1883	353	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.21	95.49	0.86	0.86	4	-
GCA_900553155.1	s__Prevotella sp900553155	80.1289	246	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.04	96.93	0.80	0.75	3	-
--------------------------------------------------------------------------------
[2023-06-05 18:51:41,371] [INFO] GTDB search result was written to GCA_004554545.1_ASM455454v1_genomic.fna/result_gtdb.tsv
[2023-06-05 18:51:41,371] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:51:41,374] [INFO] DFAST_QC result json was written to GCA_004554545.1_ASM455454v1_genomic.fna/dqc_result.json
[2023-06-05 18:51:41,374] [INFO] DFAST_QC completed!
[2023-06-05 18:51:41,374] [INFO] Total running time: 0h1m13s