[2023-06-28 12:49:33,842] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:49:33,844] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:49:33,844] [INFO] DQC Reference Directory: /var/lib/cwl/stg23623948-6f8a-4d2a-b061-04d31d754783/dqc_reference
[2023-06-28 12:49:35,106] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:49:35,107] [INFO] Task started: Prodigal
[2023-06-28 12:49:35,107] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d4503e6-435f-4a58-a9dc-a82e55302b41/GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:49:49,635] [INFO] Task succeeded: Prodigal
[2023-06-28 12:49:49,636] [INFO] Task started: HMMsearch
[2023-06-28 12:49:49,636] [INFO] Running command: hmmsearch --tblout GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23623948-6f8a-4d2a-b061-04d31d754783/dqc_reference/reference_markers.hmm GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:49:49,821] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:49:49,822] [INFO] Found 6/6 markers.
[2023-06-28 12:49:49,847] [INFO] Query marker FASTA was written to GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-28 12:49:49,847] [INFO] Task started: Blastn
[2023-06-28 12:49:49,848] [INFO] Running command: blastn -query GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg23623948-6f8a-4d2a-b061-04d31d754783/dqc_reference/reference_markers.fasta -out GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:49:50,443] [INFO] Task succeeded: Blastn
[2023-06-28 12:49:50,449] [INFO] Selected 28 target genomes.
[2023-06-28 12:49:50,449] [INFO] Target genome list was writen to GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-28 12:49:50,451] [INFO] Task started: fastANI
[2023-06-28 12:49:50,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d4503e6-435f-4a58-a9dc-a82e55302b41/GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:50:03,465] [INFO] Task succeeded: fastANI
[2023-06-28 12:50:03,465] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23623948-6f8a-4d2a-b061-04d31d754783/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:50:03,466] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23623948-6f8a-4d2a-b061-04d31d754783/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:50:03,475] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:50:03,475] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:50:03,475] [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	76.9984	124	779	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.8543	95	779	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.7461	86	779	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	76.3329	67	779	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	76.3286	80	779	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	76.324	76	779	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	76.1191	57	779	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	76.0818	59	779	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.0667	61	779	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:50:03,477] [INFO] DFAST Taxonomy check result was written to GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-28 12:50:03,477] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:50:03,477] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:50:03,478] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23623948-6f8a-4d2a-b061-04d31d754783/dqc_reference/checkm_data
[2023-06-28 12:50:03,479] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:50:03,508] [INFO] Task started: CheckM
[2023-06-28 12:50:03,509] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-28 12:50:46,225] [INFO] Task succeeded: CheckM
[2023-06-28 12:50:46,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.64%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:50:46,247] [INFO] ===== Completeness check finished =====
[2023-06-28 12:50:46,248] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:50:46,248] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-28 12:50:46,248] [INFO] Task started: Blastn
[2023-06-28 12:50:46,248] [INFO] Running command: blastn -query GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg23623948-6f8a-4d2a-b061-04d31d754783/dqc_reference/reference_markers_gtdb.fasta -out GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:50:47,069] [INFO] Task succeeded: Blastn
[2023-06-28 12:50:47,073] [INFO] Selected 28 target genomes.
[2023-06-28 12:50:47,073] [INFO] Target genome list was writen to GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:50:47,078] [INFO] Task started: fastANI
[2023-06-28 12:50:47,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d4503e6-435f-4a58-a9dc-a82e55302b41/GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:50:59,613] [INFO] Task succeeded: fastANI
[2023-06-28 12:50:59,629] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:50:59,630] [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_900552675.1	s__Prevotella sp900552675	96.9725	532	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.55	95.81	0.80	0.75	5	conclusive
GCA_900543975.1	s__Prevotella sp900543975	79.2113	282	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.48	97.34	0.84	0.79	5	-
GCA_900553155.1	s__Prevotella sp900553155	77.3627	107	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.04	96.93	0.80	0.75	3	-
GCA_900552515.1	s__Prevotella sp900552515	77.3384	116	779	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	77.1831	162	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.97	99.93	0.97	0.97	3	-
GCF_019052365.1	s__Prevotella sp000434975	77.1627	124	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.59	0.82	0.74	11	-
GCF_002265625.1	s__Prevotella sp002265625	77.1057	109	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.90	96.80	0.88	0.86	4	-
GCA_900546575.1	s__Prevotella sp900546575	77.0418	125	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.21	95.49	0.86	0.86	4	-
GCF_000235885.1	s__Prevotella stercorea	77.0197	123	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.02	96.84	0.81	0.69	8	-
GCA_905198745.1	s__Prevotella sp905198745	76.8251	69	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550365.1	s__Prevotella sp900550365	76.6728	50	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902776685.1	s__Prevotella sp902776685	76.4927	82	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002317385.1	s__Prevotella sp002317385	76.3628	66	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002353485.1	s__Prevotella sp002353485	76.3055	50	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.45	97.45	0.90	0.90	2	-
GCA_017509155.1	s__Prevotella sp017509155	76.2892	72	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100635.1	s__Prevotella sp900100635	76.2207	51	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	96.60	0.86	0.83	10	-
GCA_900315095.1	s__Prevotella sp900315095	76.1704	54	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.59	96.16	0.90	0.86	18	-
GCA_017442765.1	s__Prevotella sp017442765	76.143	58	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902771445.1	s__Prevotella sp902771445	75.828	61	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.22	99.22	0.83	0.83	2	-
GCA_017458125.1	s__Prevotella sp017458125	75.7346	55	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.42	97.42	0.81	0.81	2	-
GCA_017478085.1	s__Prevotella sp017478085	75.7145	64	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:50:59,635] [INFO] GTDB search result was written to GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 12:50:59,635] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:50:59,642] [INFO] DFAST_QC result json was written to GCA_948467175.1_SRR17622767_bin.95_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-28 12:50:59,642] [INFO] DFAST_QC completed!
[2023-06-28 12:50:59,643] [INFO] Total running time: 0h1m26s