[2024-01-24 13:27:31,899] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:31,901] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:31,901] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2ed039c-fc0f-4746-8aa2-60e5c746c516/dqc_reference
[2024-01-24 13:27:33,247] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:33,247] [INFO] Task started: Prodigal
[2024-01-24 13:27:33,248] [INFO] Running command: gunzip -c /var/lib/cwl/stg6336cf05-81dd-463d-b74f-a0cca16f6648/GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna.gz | prodigal -d GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna/cds.fna -a GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:39,960] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:39,961] [INFO] Task started: HMMsearch
[2024-01-24 13:27:39,961] [INFO] Running command: hmmsearch --tblout GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2ed039c-fc0f-4746-8aa2-60e5c746c516/dqc_reference/reference_markers.hmm GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:40,202] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:40,203] [INFO] Found 6/6 markers.
[2024-01-24 13:27:40,223] [INFO] Query marker FASTA was written to GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna/markers.fasta
[2024-01-24 13:27:40,223] [INFO] Task started: Blastn
[2024-01-24 13:27:40,223] [INFO] Running command: blastn -query GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2ed039c-fc0f-4746-8aa2-60e5c746c516/dqc_reference/reference_markers.fasta -out GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:40,824] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:40,828] [INFO] Selected 11 target genomes.
[2024-01-24 13:27:40,828] [INFO] Target genome list was writen to GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna/target_genomes.txt
[2024-01-24 13:27:40,860] [INFO] Task started: fastANI
[2024-01-24 13:27:40,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg6336cf05-81dd-463d-b74f-a0cca16f6648/GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna.gz --refList GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna/target_genomes.txt --output GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:27:45,772] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:45,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2ed039c-fc0f-4746-8aa2-60e5c746c516/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:27:45,773] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2ed039c-fc0f-4746-8aa2-60e5c746c516/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:27:45,785] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:27:45,785] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:27:45,785] [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
Slackia piriformis	strain=YIT 12062	GCA_000296445.1	626934	626934	type	True	99.9923	700	704	95	conclusive
Slackia faecicanis	strain=DSM 17537	GCA_003725295.1	255723	255723	type	True	80.5386	338	704	95	below_threshold
Slackia isoflavoniconvertens	strain=DSM 22006	GCA_014192995.1	572010	572010	type	True	78.8041	162	704	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	78.5672	56	704	95	below_threshold
Slackia isoflavoniconvertens	strain=DSM 22006	GCA_003725955.1	572010	572010	type	True	78.3391	163	704	95	below_threshold
Senegalimassilia anaerobia	strain=type strain: JC110	GCA_000236865.1	1473216	1473216	type	True	78.2871	125	704	95	below_threshold
Slackia equolifaciens	strain=DSM 24851	GCA_003725995.1	498718	498718	type	True	78.0603	208	704	95	below_threshold
Gordonibacter pamelaeae	strain=7-10-1-bT	GCA_000210055.1	471189	471189	type	True	77.6246	141	704	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003339815.1	242230	242230	type	True	77.3207	138	704	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003725965.1	242230	242230	type	True	77.2559	136	704	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:27:45,787] [INFO] DFAST Taxonomy check result was written to GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna/tc_result.tsv
[2024-01-24 13:27:45,787] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:27:45,787] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:27:45,788] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2ed039c-fc0f-4746-8aa2-60e5c746c516/dqc_reference/checkm_data
[2024-01-24 13:27:45,788] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:27:45,812] [INFO] Task started: CheckM
[2024-01-24 13:27:45,812] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna/checkm_input GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna/checkm_result
[2024-01-24 13:28:11,115] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:11,116] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:11,139] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:11,140] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:11,141] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna/markers.fasta)
[2024-01-24 13:28:11,141] [INFO] Task started: Blastn
[2024-01-24 13:28:11,141] [INFO] Running command: blastn -query GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2ed039c-fc0f-4746-8aa2-60e5c746c516/dqc_reference/reference_markers_gtdb.fasta -out GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:12,001] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:12,006] [INFO] Selected 11 target genomes.
[2024-01-24 13:28:12,006] [INFO] Target genome list was writen to GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:12,035] [INFO] Task started: fastANI
[2024-01-24 13:28:12,036] [INFO] Running command: fastANI --query /var/lib/cwl/stg6336cf05-81dd-463d-b74f-a0cca16f6648/GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna.gz --refList GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:17,330] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:17,344] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:17,344] [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
GCF_000296445.1	s__Slackia_A piriformis	99.9923	699	704	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	98.02	96.04	0.96	0.92	3	conclusive
GCA_900553655.1	s__Slackia_A sp900553655	90.6283	318	704	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	97.68	97.68	0.69	0.69	2	-
GCA_900553775.1	s__Slackia_A sp900553775	80.6109	280	704	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	98.24	98.24	0.77	0.77	2	-
GCF_003725295.1	s__Slackia_A faecicanis	80.4939	340	704	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555495.1	s__Slackia_A sp900555495	79.4902	211	704	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	100.00	100.00	0.96	0.96	2	-
GCF_004135645.1	s__Senegalimassilia faecalis	78.5453	130	704	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia	95.0	96.85	96.73	0.92	0.89	4	-
GCF_003725955.1	s__Slackia_A isoflavoniconvertens	78.3391	163	704	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	96.92	96.02	0.86	0.81	13	-
GCF_003725995.1	s__Slackia_A equolifaciens	78.0837	206	704	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008831035.1	s__Ellagibacter isourolithinifaciens	77.5342	100	704	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Ellagibacter	95.0	96.52	96.27	0.85	0.76	13	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:17,346] [INFO] GTDB search result was written to GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:17,346] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:17,349] [INFO] DFAST_QC result json was written to GCF_000296445.1_Slac_piri_YIT_12062_V1_genomic.fna/dqc_result.json
[2024-01-24 13:28:17,349] [INFO] DFAST_QC completed!
[2024-01-24 13:28:17,349] [INFO] Total running time: 0h0m45s