[2023-06-17 09:20:56,164] [INFO] DFAST_QC pipeline started.
[2023-06-17 09:20:56,180] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 09:20:56,180] [INFO] DQC Reference Directory: /var/lib/cwl/stg7558fd7d-1d34-4b46-87b5-3ab93475d82c/dqc_reference
[2023-06-17 09:20:58,174] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 09:20:58,175] [INFO] Task started: Prodigal
[2023-06-17 09:20:58,175] [INFO] Running command: gunzip -c /var/lib/cwl/stgba298811-4132-4417-a149-60122bbd7e2d/GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna.gz | prodigal -d GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna/cds.fna -a GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 09:21:18,428] [INFO] Task succeeded: Prodigal
[2023-06-17 09:21:18,429] [INFO] Task started: HMMsearch
[2023-06-17 09:21:18,429] [INFO] Running command: hmmsearch --tblout GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7558fd7d-1d34-4b46-87b5-3ab93475d82c/dqc_reference/reference_markers.hmm GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna/protein.faa > /dev/null
[2023-06-17 09:21:18,667] [INFO] Task succeeded: HMMsearch
[2023-06-17 09:21:18,669] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgba298811-4132-4417-a149-60122bbd7e2d/GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna.gz]
[2023-06-17 09:21:18,699] [INFO] Query marker FASTA was written to GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna/markers.fasta
[2023-06-17 09:21:18,699] [INFO] Task started: Blastn
[2023-06-17 09:21:18,699] [INFO] Running command: blastn -query GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna/markers.fasta -db /var/lib/cwl/stg7558fd7d-1d34-4b46-87b5-3ab93475d82c/dqc_reference/reference_markers.fasta -out GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:21:19,291] [INFO] Task succeeded: Blastn
[2023-06-17 09:21:19,296] [INFO] Selected 21 target genomes.
[2023-06-17 09:21:19,297] [INFO] Target genome list was writen to GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna/target_genomes.txt
[2023-06-17 09:21:19,301] [INFO] Task started: fastANI
[2023-06-17 09:21:19,302] [INFO] Running command: fastANI --query /var/lib/cwl/stgba298811-4132-4417-a149-60122bbd7e2d/GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna.gz --refList GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna/target_genomes.txt --output GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 09:21:30,889] [INFO] Task succeeded: fastANI
[2023-06-17 09:21:30,889] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7558fd7d-1d34-4b46-87b5-3ab93475d82c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 09:21:30,890] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7558fd7d-1d34-4b46-87b5-3ab93475d82c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 09:21:30,904] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 09:21:30,905] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 09:21:30,905] [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
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	81.3026	577	1036	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	77.1981	147	1036	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.9095	130	1036	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.824	131	1036	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.7165	156	1036	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.7038	119	1036	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.6827	158	1036	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.6001	164	1036	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	76.4905	117	1036	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.2734	59	1036	95	below_threshold
Xylanibacter muris	strain=PMUR	GCA_013166605.1	2736290	2736290	type	True	76.2436	139	1036	95	below_threshold
Palleniella intestinalis	strain=PINT	GCA_013166595.1	2736291	2736291	type	True	76.1575	88	1036	95	below_threshold
Prevotella bergensis	strain=DSM 17361	GCA_000160535.1	242750	242750	type	True	76.0464	60	1036	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	75.9477	103	1036	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 09:21:30,907] [INFO] DFAST Taxonomy check result was written to GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna/tc_result.tsv
[2023-06-17 09:21:30,907] [INFO] ===== Taxonomy check completed =====
[2023-06-17 09:21:30,908] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 09:21:30,908] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7558fd7d-1d34-4b46-87b5-3ab93475d82c/dqc_reference/checkm_data
[2023-06-17 09:21:30,909] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 09:21:30,951] [INFO] Task started: CheckM
[2023-06-17 09:21:30,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna/checkm_input GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna/checkm_result
[2023-06-17 09:22:27,825] [INFO] Task succeeded: CheckM
[2023-06-17 09:22:27,827] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 09:22:27,845] [INFO] ===== Completeness check finished =====
[2023-06-17 09:22:27,845] [INFO] ===== Start GTDB Search =====
[2023-06-17 09:22:27,846] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna/markers.fasta)
[2023-06-17 09:22:27,846] [INFO] Task started: Blastn
[2023-06-17 09:22:27,846] [INFO] Running command: blastn -query GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna/markers.fasta -db /var/lib/cwl/stg7558fd7d-1d34-4b46-87b5-3ab93475d82c/dqc_reference/reference_markers_gtdb.fasta -out GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:22:28,707] [INFO] Task succeeded: Blastn
[2023-06-17 09:22:28,712] [INFO] Selected 13 target genomes.
[2023-06-17 09:22:28,712] [INFO] Target genome list was writen to GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 09:22:28,721] [INFO] Task started: fastANI
[2023-06-17 09:22:28,721] [INFO] Running command: fastANI --query /var/lib/cwl/stgba298811-4132-4417-a149-60122bbd7e2d/GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna.gz --refList GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna/target_genomes_gtdb.txt --output GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 09:22:36,285] [INFO] Task succeeded: fastANI
[2023-06-17 09:22:36,301] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 09:22:36,302] [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_900549175.1	s__Prevotella sp900549175	99.7302	836	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.84	99.84	0.89	0.89	2	conclusive
GCF_013166545.1	s__Prevotella sp013166545	81.3941	584	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.93	99.88	0.98	0.97	6	-
GCA_900553965.1	s__Prevotella sp900553965	81.3612	320	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.57	97.60	0.86	0.85	3	-
GCA_017483185.1	s__Prevotella sp017483185	80.8633	334	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905216025.1	s__Prevotella sp905216025	80.0166	403	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.83	95.83	0.83	0.83	2	-
GCA_017623155.1	s__Prevotella sp017623155	78.418	240	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016899955.1	s__Prevotella sp900540415	77.7668	295	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.44	98.08	0.94	0.91	6	-
GCA_016302965.1	s__Prevotella sp016302965	77.6757	179	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933775.1	s__Prevotella sp002933775	77.5771	201	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.87	97.52	0.85	0.83	11	-
GCA_002353205.1	s__Prevotella sp002353205	77.216	150	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.92	99.92	0.98	0.98	2	-
GCA_017476785.1	s__Prevotella sp017476785	76.9501	175	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315095.1	s__Prevotella sp900315095	76.7787	112	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.59	96.16	0.90	0.86	18	-
GCA_017471245.1	s__Prevotella sp017471245	76.5527	98	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.04	98.04	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-06-17 09:22:36,304] [INFO] GTDB search result was written to GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna/result_gtdb.tsv
[2023-06-17 09:22:36,304] [INFO] ===== GTDB Search completed =====
[2023-06-17 09:22:36,308] [INFO] DFAST_QC result json was written to GCA_905193405.1_ERR1190945-mag-bin.46_genomic.fna/dqc_result.json
[2023-06-17 09:22:36,308] [INFO] DFAST_QC completed!
[2023-06-17 09:22:36,308] [INFO] Total running time: 0h1m40s