[2023-06-08 04:00:12,613] [INFO] DFAST_QC pipeline started.
[2023-06-08 04:00:12,616] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 04:00:12,616] [INFO] DQC Reference Directory: /var/lib/cwl/stgee20549f-ef5c-424d-a747-5b944bb9c7ec/dqc_reference
[2023-06-08 04:00:14,552] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 04:00:14,553] [INFO] Task started: Prodigal
[2023-06-08 04:00:14,553] [INFO] Running command: gunzip -c /var/lib/cwl/stg8045e00a-637b-47aa-bfb5-042b2e02b56f/GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna.gz | prodigal -d GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna/cds.fna -a GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 04:00:33,049] [INFO] Task succeeded: Prodigal
[2023-06-08 04:00:33,050] [INFO] Task started: HMMsearch
[2023-06-08 04:00:33,050] [INFO] Running command: hmmsearch --tblout GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee20549f-ef5c-424d-a747-5b944bb9c7ec/dqc_reference/reference_markers.hmm GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna/protein.faa > /dev/null
[2023-06-08 04:00:33,380] [INFO] Task succeeded: HMMsearch
[2023-06-08 04:00:33,381] [INFO] Found 6/6 markers.
[2023-06-08 04:00:33,424] [INFO] Query marker FASTA was written to GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna/markers.fasta
[2023-06-08 04:00:33,424] [INFO] Task started: Blastn
[2023-06-08 04:00:33,424] [INFO] Running command: blastn -query GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna/markers.fasta -db /var/lib/cwl/stgee20549f-ef5c-424d-a747-5b944bb9c7ec/dqc_reference/reference_markers.fasta -out GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:00:34,121] [INFO] Task succeeded: Blastn
[2023-06-08 04:00:34,125] [INFO] Selected 25 target genomes.
[2023-06-08 04:00:34,126] [INFO] Target genome list was writen to GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna/target_genomes.txt
[2023-06-08 04:00:34,128] [INFO] Task started: fastANI
[2023-06-08 04:00:34,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg8045e00a-637b-47aa-bfb5-042b2e02b56f/GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna.gz --refList GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna/target_genomes.txt --output GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 04:00:45,997] [INFO] Task succeeded: fastANI
[2023-06-08 04:00:45,998] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee20549f-ef5c-424d-a747-5b944bb9c7ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 04:00:45,998] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee20549f-ef5c-424d-a747-5b944bb9c7ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 04:00:46,013] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 04:00:46,013] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 04:00:46,013] [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 albensis	strain=DSM 11370	GCA_000426565.1	77768	77768	type	True	77.5034	55	1052	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	77.4706	173	1052	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	77.4497	56	1052	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	77.4468	170	1052	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	77.0473	132	1052	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.9824	98	1052	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.9352	95	1052	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	76.8349	108	1052	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.8018	114	1052	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	76.7854	108	1052	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.7301	110	1052	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.6985	51	1052	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.6804	123	1052	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.6679	123	1052	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.6208	122	1052	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 04:00:46,016] [INFO] DFAST Taxonomy check result was written to GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna/tc_result.tsv
[2023-06-08 04:00:46,017] [INFO] ===== Taxonomy check completed =====
[2023-06-08 04:00:46,017] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 04:00:46,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee20549f-ef5c-424d-a747-5b944bb9c7ec/dqc_reference/checkm_data
[2023-06-08 04:00:46,019] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 04:00:46,070] [INFO] Task started: CheckM
[2023-06-08 04:00:46,070] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna/checkm_input GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna/checkm_result
[2023-06-08 04:01:40,879] [INFO] Task succeeded: CheckM
[2023-06-08 04:01:40,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.87%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 04:01:40,902] [INFO] ===== Completeness check finished =====
[2023-06-08 04:01:40,903] [INFO] ===== Start GTDB Search =====
[2023-06-08 04:01:40,903] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna/markers.fasta)
[2023-06-08 04:01:40,903] [INFO] Task started: Blastn
[2023-06-08 04:01:40,904] [INFO] Running command: blastn -query GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna/markers.fasta -db /var/lib/cwl/stgee20549f-ef5c-424d-a747-5b944bb9c7ec/dqc_reference/reference_markers_gtdb.fasta -out GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:01:41,757] [INFO] Task succeeded: Blastn
[2023-06-08 04:01:41,762] [INFO] Selected 16 target genomes.
[2023-06-08 04:01:41,762] [INFO] Target genome list was writen to GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 04:01:41,772] [INFO] Task started: fastANI
[2023-06-08 04:01:41,772] [INFO] Running command: fastANI --query /var/lib/cwl/stg8045e00a-637b-47aa-bfb5-042b2e02b56f/GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna.gz --refList GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna/target_genomes_gtdb.txt --output GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 04:01:50,553] [INFO] Task succeeded: fastANI
[2023-06-08 04:01:50,572] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 04:01:50,572] [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_900316985.1	s__Prevotella sp900316985	96.3177	854	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.90	96.04	0.81	0.71	7	conclusive
GCA_900314655.1	s__Prevotella sp900314655	85.8811	772	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	95.82	0.85	0.71	9	-
GCA_902784755.1	s__Prevotella sp902784755	83.1084	519	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.59	97.59	0.83	0.83	2	-
GCA_017508965.1	s__Prevotella sp017508965	83.0725	384	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.39	95.39	0.73	0.73	2	-
GCA_017428925.1	s__Prevotella sp017428925	80.8398	409	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002394385.1	s__Prevotella sp002394385	78.7466	221	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.28	97.06	0.88	0.86	9	-
GCA_017509155.1	s__Prevotella sp017509155	77.652	213	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107705.1	s__Prevotella sp900107705	77.6036	166	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.93	97.93	0.92	0.92	2	-
GCA_017557405.1	s__Prevotella sp017557405	77.3925	191	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902768105.1	s__Prevotella sp902768105	77.3765	168	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785695.1	s__Prevotella sp902785695	77.2219	138	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017471245.1	s__Prevotella sp017471245	77.1535	187	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.04	98.04	0.83	0.83	2	-
GCA_017400455.1	s__Prevotella sp017400455	77.0394	133	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783165.1	s__Prevotella sp902783165	76.7373	131	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002353975.1	s__Prevotella sp002353975	76.4069	56	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.61	96.48	0.79	0.75	4	-
--------------------------------------------------------------------------------
[2023-06-08 04:01:50,574] [INFO] GTDB search result was written to GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna/result_gtdb.tsv
[2023-06-08 04:01:50,574] [INFO] ===== GTDB Search completed =====
[2023-06-08 04:01:50,578] [INFO] DFAST_QC result json was written to GCA_902778005.1_Rumen_uncultured_genome_RUG12325_genomic.fna/dqc_result.json
[2023-06-08 04:01:50,578] [INFO] DFAST_QC completed!
[2023-06-08 04:01:50,578] [INFO] Total running time: 0h1m38s