[2023-06-08 20:21:59,386] [INFO] DFAST_QC pipeline started.
[2023-06-08 20:21:59,388] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 20:21:59,388] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ad6edce-2062-4292-80c5-51c7a8eaf3af/dqc_reference
[2023-06-08 20:22:00,642] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 20:22:00,643] [INFO] Task started: Prodigal
[2023-06-08 20:22:00,643] [INFO] Running command: gunzip -c /var/lib/cwl/stg69617023-ee04-4223-94ce-25be9fbcde16/GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna.gz | prodigal -d GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna/cds.fna -a GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 20:22:14,374] [INFO] Task succeeded: Prodigal
[2023-06-08 20:22:14,375] [INFO] Task started: HMMsearch
[2023-06-08 20:22:14,375] [INFO] Running command: hmmsearch --tblout GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ad6edce-2062-4292-80c5-51c7a8eaf3af/dqc_reference/reference_markers.hmm GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna/protein.faa > /dev/null
[2023-06-08 20:22:14,637] [INFO] Task succeeded: HMMsearch
[2023-06-08 20:22:14,639] [INFO] Found 6/6 markers.
[2023-06-08 20:22:14,669] [INFO] Query marker FASTA was written to GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna/markers.fasta
[2023-06-08 20:22:14,669] [INFO] Task started: Blastn
[2023-06-08 20:22:14,670] [INFO] Running command: blastn -query GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ad6edce-2062-4292-80c5-51c7a8eaf3af/dqc_reference/reference_markers.fasta -out GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:22:15,318] [INFO] Task succeeded: Blastn
[2023-06-08 20:22:15,324] [INFO] Selected 22 target genomes.
[2023-06-08 20:22:15,325] [INFO] Target genome list was writen to GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna/target_genomes.txt
[2023-06-08 20:22:15,326] [INFO] Task started: fastANI
[2023-06-08 20:22:15,327] [INFO] Running command: fastANI --query /var/lib/cwl/stg69617023-ee04-4223-94ce-25be9fbcde16/GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna.gz --refList GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna/target_genomes.txt --output GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 20:22:26,785] [INFO] Task succeeded: fastANI
[2023-06-08 20:22:26,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ad6edce-2062-4292-80c5-51c7a8eaf3af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 20:22:26,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ad6edce-2062-4292-80c5-51c7a8eaf3af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 20:22:26,798] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 20:22:26,798] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 20:22:26,798] [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 ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	78.1537	164	715	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	78.0625	168	715	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	78.0457	138	715	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.6194	62	715	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.4347	61	715	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.4318	64	715	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	76.3642	74	715	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 20:22:26,801] [INFO] DFAST Taxonomy check result was written to GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna/tc_result.tsv
[2023-06-08 20:22:26,801] [INFO] ===== Taxonomy check completed =====
[2023-06-08 20:22:26,802] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 20:22:26,802] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ad6edce-2062-4292-80c5-51c7a8eaf3af/dqc_reference/checkm_data
[2023-06-08 20:22:26,803] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 20:22:26,831] [INFO] Task started: CheckM
[2023-06-08 20:22:26,832] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna/checkm_input GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna/checkm_result
[2023-06-08 20:23:09,929] [INFO] Task succeeded: CheckM
[2023-06-08 20:23:09,931] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.09%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 20:23:09,950] [INFO] ===== Completeness check finished =====
[2023-06-08 20:23:09,951] [INFO] ===== Start GTDB Search =====
[2023-06-08 20:23:09,951] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna/markers.fasta)
[2023-06-08 20:23:09,952] [INFO] Task started: Blastn
[2023-06-08 20:23:09,952] [INFO] Running command: blastn -query GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ad6edce-2062-4292-80c5-51c7a8eaf3af/dqc_reference/reference_markers_gtdb.fasta -out GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:23:11,026] [INFO] Task succeeded: Blastn
[2023-06-08 20:23:11,032] [INFO] Selected 23 target genomes.
[2023-06-08 20:23:11,032] [INFO] Target genome list was writen to GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 20:23:11,035] [INFO] Task started: fastANI
[2023-06-08 20:23:11,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg69617023-ee04-4223-94ce-25be9fbcde16/GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna.gz --refList GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna/target_genomes_gtdb.txt --output GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 20:23:22,853] [INFO] Task succeeded: fastANI
[2023-06-08 20:23:22,871] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 20:23:22,872] [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_900316645.1	s__Prevotella sp900316645	98.0658	584	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.95	97.51	0.83	0.71	20	conclusive
GCA_002354095.1	s__Prevotella sp002354095	82.0007	405	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.88	96.42	0.77	0.68	6	-
GCA_002353295.1	s__Prevotella sp002353295	80.292	369	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.89	97.89	0.87	0.87	2	-
GCA_905235835.1	s__Prevotella sp905235835	79.8525	300	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.69	98.69	0.87	0.87	2	-
GCA_002353225.1	s__Prevotella sp002353225	79.6147	353	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.18	97.50	0.85	0.76	6	-
GCF_900115435.1	s__Prevotella sp900115435	79.4582	348	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.38	96.23	0.89	0.86	8	-
GCA_017470055.1	s__Prevotella sp017470055	79.4372	312	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017645645.1	s__Prevotella sp017645645	79.2393	238	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017554145.1	s__Prevotella sp017554145	79.139	266	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017449675.1	s__Prevotella sp017449675	79.0031	172	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800585.1	s__Prevotella sp902800585	78.9547	277	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.25	98.25	0.85	0.85	2	-
GCF_900107705.1	s__Prevotella sp900107705	78.7792	242	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.93	97.93	0.92	0.92	2	-
GCA_902799355.1	s__Prevotella sp902799355	78.6662	208	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.80	96.48	0.80	0.78	3	-
GCA_015060535.1	s__Prevotella sp015060535	78.6037	235	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.13	96.66	0.74	0.70	4	-
GCA_902770635.1	s__Prevotella sp902770635	78.5601	243	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.83	96.83	0.78	0.78	2	-
GCA_902772585.1	s__Prevotella sp902772585	78.4828	206	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902762565.1	s__Prevotella sp902762565	78.4458	205	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.04	97.04	0.79	0.79	2	-
GCA_902782305.1	s__Prevotella sp902782305	78.3518	235	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.21	96.08	0.74	0.67	4	-
GCA_900119285.1	s__Prevotella sp900119285	78.2669	196	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.20	98.20	0.84	0.84	2	-
GCF_900109055.1	s__Prevotella sp900109055	78.0819	164	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.78	98.70	0.94	0.92	3	-
GCF_000621725.1	s__Prevotella brevis	78.0191	139	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.58	97.58	0.89	0.89	2	-
GCA_902798285.1	s__Prevotella sp902798285	77.8464	170	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.28	98.28	0.87	0.87	2	-
GCA_902775475.1	s__Prevotella sp902775475	77.3744	131	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.69	98.51	0.89	0.87	7	-
--------------------------------------------------------------------------------
[2023-06-08 20:23:22,874] [INFO] GTDB search result was written to GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna/result_gtdb.tsv
[2023-06-08 20:23:22,874] [INFO] ===== GTDB Search completed =====
[2023-06-08 20:23:22,878] [INFO] DFAST_QC result json was written to GCA_902755795.1_Rumen_uncultured_genome_RUG10090_genomic.fna/dqc_result.json
[2023-06-08 20:23:22,878] [INFO] DFAST_QC completed!
[2023-06-08 20:23:22,878] [INFO] Total running time: 0h1m23s