[2023-06-16 21:53:33,299] [INFO] DFAST_QC pipeline started.
[2023-06-16 21:53:33,304] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 21:53:33,304] [INFO] DQC Reference Directory: /var/lib/cwl/stg4aef3a99-09ac-4708-ada1-72fc280b9364/dqc_reference
[2023-06-16 21:53:35,664] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 21:53:35,667] [INFO] Task started: Prodigal
[2023-06-16 21:53:35,667] [INFO] Running command: gunzip -c /var/lib/cwl/stg770108b1-4de6-49e3-a9e9-33175fa94c25/GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna.gz | prodigal -d GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna/cds.fna -a GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 21:53:54,062] [INFO] Task succeeded: Prodigal
[2023-06-16 21:53:54,062] [INFO] Task started: HMMsearch
[2023-06-16 21:53:54,062] [INFO] Running command: hmmsearch --tblout GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4aef3a99-09ac-4708-ada1-72fc280b9364/dqc_reference/reference_markers.hmm GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna/protein.faa > /dev/null
[2023-06-16 21:53:54,343] [INFO] Task succeeded: HMMsearch
[2023-06-16 21:53:54,345] [INFO] Found 6/6 markers.
[2023-06-16 21:53:54,377] [INFO] Query marker FASTA was written to GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna/markers.fasta
[2023-06-16 21:53:54,378] [INFO] Task started: Blastn
[2023-06-16 21:53:54,378] [INFO] Running command: blastn -query GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna/markers.fasta -db /var/lib/cwl/stg4aef3a99-09ac-4708-ada1-72fc280b9364/dqc_reference/reference_markers.fasta -out GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:53:55,065] [INFO] Task succeeded: Blastn
[2023-06-16 21:53:55,071] [INFO] Selected 22 target genomes.
[2023-06-16 21:53:55,072] [INFO] Target genome list was writen to GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna/target_genomes.txt
[2023-06-16 21:53:55,097] [INFO] Task started: fastANI
[2023-06-16 21:53:55,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg770108b1-4de6-49e3-a9e9-33175fa94c25/GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna.gz --refList GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna/target_genomes.txt --output GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 21:54:09,388] [INFO] Task succeeded: fastANI
[2023-06-16 21:54:09,388] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4aef3a99-09ac-4708-ada1-72fc280b9364/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 21:54:09,389] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4aef3a99-09ac-4708-ada1-72fc280b9364/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 21:54:09,406] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 21:54:09,407] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 21:54:09,407] [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	81.1749	435	1053	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	80.6903	179	1053	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	79.0494	204	1053	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	78.4921	159	1053	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	78.2675	147	1053	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.929	201	1053	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	77.2963	114	1053	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	77.1407	92	1053	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	77.0699	92	1053	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	76.954	100	1053	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	76.9505	98	1053	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	76.924	102	1053	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	76.8871	103	1053	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.5969	110	1053	95	below_threshold
Prevotella oulorum	strain=ATCC 43324	GCA_900167385.1	28136	28136	type	True	76.5759	53	1053	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.5175	122	1053	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.459	126	1053	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 21:54:09,410] [INFO] DFAST Taxonomy check result was written to GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna/tc_result.tsv
[2023-06-16 21:54:09,410] [INFO] ===== Taxonomy check completed =====
[2023-06-16 21:54:09,411] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 21:54:09,411] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4aef3a99-09ac-4708-ada1-72fc280b9364/dqc_reference/checkm_data
[2023-06-16 21:54:09,413] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 21:54:09,451] [INFO] Task started: CheckM
[2023-06-16 21:54:09,451] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna/checkm_input GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna/checkm_result
[2023-06-16 21:55:03,110] [INFO] Task succeeded: CheckM
[2023-06-16 21:55:03,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 21:55:03,133] [INFO] ===== Completeness check finished =====
[2023-06-16 21:55:03,133] [INFO] ===== Start GTDB Search =====
[2023-06-16 21:55:03,133] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna/markers.fasta)
[2023-06-16 21:55:03,134] [INFO] Task started: Blastn
[2023-06-16 21:55:03,134] [INFO] Running command: blastn -query GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna/markers.fasta -db /var/lib/cwl/stg4aef3a99-09ac-4708-ada1-72fc280b9364/dqc_reference/reference_markers_gtdb.fasta -out GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:55:04,012] [INFO] Task succeeded: Blastn
[2023-06-16 21:55:04,016] [INFO] Selected 12 target genomes.
[2023-06-16 21:55:04,016] [INFO] Target genome list was writen to GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 21:55:04,028] [INFO] Task started: fastANI
[2023-06-16 21:55:04,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg770108b1-4de6-49e3-a9e9-33175fa94c25/GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna.gz --refList GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna/target_genomes_gtdb.txt --output GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 21:55:12,313] [INFO] Task succeeded: fastANI
[2023-06-16 21:55:12,324] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 21:55:12,324] [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_002265625.1	s__Prevotella sp002265625	96.812	907	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.90	96.80	0.88	0.86	4	conclusive
GCF_019052365.1	s__Prevotella sp000434975	81.6449	440	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.59	0.82	0.74	11	-
GCF_900290275.1	s__Prevotella sp900290275	81.6107	398	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.80	97.71	0.90	0.86	4	-
GCA_900552515.1	s__Prevotella sp900552515	81.354	332	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.61	97.50	0.85	0.85	3	-
GCF_000235885.1	s__Prevotella stercorea	81.2048	433	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.02	96.84	0.81	0.69	8	-
GCA_900544495.1	s__Prevotella sp900544495	81.0198	396	1053	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	80.951	421	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.97	99.93	0.97	0.97	3	-
GCA_900546575.1	s__Prevotella sp900546575	80.4713	399	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.21	95.49	0.86	0.86	4	-
GCA_002490315.1	s__Prevotella sp002490315	79.9716	288	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553155.1	s__Prevotella sp900553155	79.8986	253	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.04	96.93	0.80	0.75	3	-
GCA_900543975.1	s__Prevotella sp900543975	78.7978	234	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.48	97.34	0.84	0.79	5	-
--------------------------------------------------------------------------------
[2023-06-16 21:55:12,326] [INFO] GTDB search result was written to GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna/result_gtdb.tsv
[2023-06-16 21:55:12,327] [INFO] ===== GTDB Search completed =====
[2023-06-16 21:55:12,331] [INFO] DFAST_QC result json was written to GCA_905207445.1_ERR321647-mag-bin.3_genomic.fna/dqc_result.json
[2023-06-16 21:55:12,332] [INFO] DFAST_QC completed!
[2023-06-16 21:55:12,332] [INFO] Total running time: 0h1m39s