[2023-06-05 18:10:15,784] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:10:15,799] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:10:15,800] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b0d13b0-88e3-4881-87e3-30e66376b99b/dqc_reference
[2023-06-05 18:10:17,022] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:10:17,023] [INFO] Task started: Prodigal
[2023-06-05 18:10:17,023] [INFO] Running command: gunzip -c /var/lib/cwl/stg41b9a1d4-de97-4ab3-9c2f-85f219c7a243/GCA_934201545.1_ERR7738580_bin.131_genomic.fna.gz | prodigal -d GCA_934201545.1_ERR7738580_bin.131_genomic.fna/cds.fna -a GCA_934201545.1_ERR7738580_bin.131_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:10:30,217] [INFO] Task succeeded: Prodigal
[2023-06-05 18:10:30,217] [INFO] Task started: HMMsearch
[2023-06-05 18:10:30,217] [INFO] Running command: hmmsearch --tblout GCA_934201545.1_ERR7738580_bin.131_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b0d13b0-88e3-4881-87e3-30e66376b99b/dqc_reference/reference_markers.hmm GCA_934201545.1_ERR7738580_bin.131_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:10:30,571] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:10:30,572] [INFO] Found 6/6 markers.
[2023-06-05 18:10:30,594] [INFO] Query marker FASTA was written to GCA_934201545.1_ERR7738580_bin.131_genomic.fna/markers.fasta
[2023-06-05 18:10:30,594] [INFO] Task started: Blastn
[2023-06-05 18:10:30,594] [INFO] Running command: blastn -query GCA_934201545.1_ERR7738580_bin.131_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b0d13b0-88e3-4881-87e3-30e66376b99b/dqc_reference/reference_markers.fasta -out GCA_934201545.1_ERR7738580_bin.131_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:10:31,372] [INFO] Task succeeded: Blastn
[2023-06-05 18:10:31,376] [INFO] Selected 22 target genomes.
[2023-06-05 18:10:31,376] [INFO] Target genome list was writen to GCA_934201545.1_ERR7738580_bin.131_genomic.fna/target_genomes.txt
[2023-06-05 18:10:31,379] [INFO] Task started: fastANI
[2023-06-05 18:10:31,379] [INFO] Running command: fastANI --query /var/lib/cwl/stg41b9a1d4-de97-4ab3-9c2f-85f219c7a243/GCA_934201545.1_ERR7738580_bin.131_genomic.fna.gz --refList GCA_934201545.1_ERR7738580_bin.131_genomic.fna/target_genomes.txt --output GCA_934201545.1_ERR7738580_bin.131_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:10:42,897] [INFO] Task succeeded: fastANI
[2023-06-05 18:10:42,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b0d13b0-88e3-4881-87e3-30e66376b99b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:10:42,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b0d13b0-88e3-4881-87e3-30e66376b99b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:10:42,910] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:10:42,910] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:10:42,910] [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	80.1289	317	808	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.8899	140	808	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	77.7722	127	808	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	77.7245	126	808	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	77.6271	135	808	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	77.4065	140	808	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	77.0703	100	808	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	76.9558	88	808	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	76.9467	90	808	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.1315	79	808	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	76.1282	59	808	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	76.1062	60	808	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.076	93	808	95	below_threshold
Prevotella dentasini	strain=JCM 15908	GCA_000614065.1	589537	589537	type	True	76.0029	82	808	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	75.9999	92	808	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	75.9814	67	808	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	75.8976	97	808	95	below_threshold
Prevotella oris	strain=DSM 18711	GCA_000377685.1	28135	28135	type	True	75.8705	50	808	95	below_threshold
Prevotella intermedia	strain=ATCC 25611	GCA_000519165.1	28131	28131	type	True	75.8147	55	808	95	below_threshold
Prevotella intermedia	strain=DSM 20706	GCA_000439065.1	28131	28131	type	True	75.7942	54	808	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:10:42,912] [INFO] DFAST Taxonomy check result was written to GCA_934201545.1_ERR7738580_bin.131_genomic.fna/tc_result.tsv
[2023-06-05 18:10:42,912] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:10:42,912] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:10:42,913] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b0d13b0-88e3-4881-87e3-30e66376b99b/dqc_reference/checkm_data
[2023-06-05 18:10:42,913] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:10:42,941] [INFO] Task started: CheckM
[2023-06-05 18:10:42,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934201545.1_ERR7738580_bin.131_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934201545.1_ERR7738580_bin.131_genomic.fna/checkm_input GCA_934201545.1_ERR7738580_bin.131_genomic.fna/checkm_result
[2023-06-05 18:11:20,445] [INFO] Task succeeded: CheckM
[2023-06-05 18:11:20,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:11:20,506] [INFO] ===== Completeness check finished =====
[2023-06-05 18:11:20,506] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:11:20,508] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934201545.1_ERR7738580_bin.131_genomic.fna/markers.fasta)
[2023-06-05 18:11:20,508] [INFO] Task started: Blastn
[2023-06-05 18:11:20,508] [INFO] Running command: blastn -query GCA_934201545.1_ERR7738580_bin.131_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b0d13b0-88e3-4881-87e3-30e66376b99b/dqc_reference/reference_markers_gtdb.fasta -out GCA_934201545.1_ERR7738580_bin.131_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:11:21,478] [INFO] Task succeeded: Blastn
[2023-06-05 18:11:21,482] [INFO] Selected 10 target genomes.
[2023-06-05 18:11:21,482] [INFO] Target genome list was writen to GCA_934201545.1_ERR7738580_bin.131_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:11:21,492] [INFO] Task started: fastANI
[2023-06-05 18:11:21,492] [INFO] Running command: fastANI --query /var/lib/cwl/stg41b9a1d4-de97-4ab3-9c2f-85f219c7a243/GCA_934201545.1_ERR7738580_bin.131_genomic.fna.gz --refList GCA_934201545.1_ERR7738580_bin.131_genomic.fna/target_genomes_gtdb.txt --output GCA_934201545.1_ERR7738580_bin.131_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:11:27,984] [INFO] Task succeeded: fastANI
[2023-06-05 18:11:27,990] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:11:27,991] [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_900553155.1	s__Prevotella sp900553155	96.9094	420	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.04	96.93	0.80	0.75	3	conclusive
GCF_900290275.1	s__Prevotella sp900290275	85.8244	618	808	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	81.0282	312	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.61	97.50	0.85	0.85	3	-
GCA_900544495.1	s__Prevotella sp900544495	80.8561	355	808	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	80.7122	400	808	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	80.6149	382	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.21	95.49	0.86	0.86	4	-
GCF_019052365.1	s__Prevotella sp000434975	80.4018	326	808	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	80.2594	348	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.90	96.80	0.88	0.86	4	-
GCF_000235885.1	s__Prevotella stercorea	80.1292	317	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.02	96.84	0.81	0.69	8	-
--------------------------------------------------------------------------------
[2023-06-05 18:11:27,993] [INFO] GTDB search result was written to GCA_934201545.1_ERR7738580_bin.131_genomic.fna/result_gtdb.tsv
[2023-06-05 18:11:27,993] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:11:27,996] [INFO] DFAST_QC result json was written to GCA_934201545.1_ERR7738580_bin.131_genomic.fna/dqc_result.json
[2023-06-05 18:11:27,997] [INFO] DFAST_QC completed!
[2023-06-05 18:11:27,997] [INFO] Total running time: 0h1m12s