[2024-01-24 11:12:38,994] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:38,996] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:38,997] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ac74bff-c5a4-4f0b-9d91-6e767996f6be/dqc_reference
[2024-01-24 11:12:40,378] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:40,379] [INFO] Task started: Prodigal
[2024-01-24 11:12:40,379] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2c7f1b9-ac3b-4377-82a4-5cac3c1a320b/GCF_003725995.1_ASM372599v1_genomic.fna.gz | prodigal -d GCF_003725995.1_ASM372599v1_genomic.fna/cds.fna -a GCF_003725995.1_ASM372599v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:49,525] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:49,525] [INFO] Task started: HMMsearch
[2024-01-24 11:12:49,525] [INFO] Running command: hmmsearch --tblout GCF_003725995.1_ASM372599v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ac74bff-c5a4-4f0b-9d91-6e767996f6be/dqc_reference/reference_markers.hmm GCF_003725995.1_ASM372599v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:49,789] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:49,790] [INFO] Found 6/6 markers.
[2024-01-24 11:12:49,820] [INFO] Query marker FASTA was written to GCF_003725995.1_ASM372599v1_genomic.fna/markers.fasta
[2024-01-24 11:12:49,820] [INFO] Task started: Blastn
[2024-01-24 11:12:49,821] [INFO] Running command: blastn -query GCF_003725995.1_ASM372599v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ac74bff-c5a4-4f0b-9d91-6e767996f6be/dqc_reference/reference_markers.fasta -out GCF_003725995.1_ASM372599v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:50,436] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:50,441] [INFO] Selected 21 target genomes.
[2024-01-24 11:12:50,441] [INFO] Target genome list was writen to GCF_003725995.1_ASM372599v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:50,464] [INFO] Task started: fastANI
[2024-01-24 11:12:50,464] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2c7f1b9-ac3b-4377-82a4-5cac3c1a320b/GCF_003725995.1_ASM372599v1_genomic.fna.gz --refList GCF_003725995.1_ASM372599v1_genomic.fna/target_genomes.txt --output GCF_003725995.1_ASM372599v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:00,984] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:00,985] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ac74bff-c5a4-4f0b-9d91-6e767996f6be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:00,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ac74bff-c5a4-4f0b-9d91-6e767996f6be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:01,002] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:01,002] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:01,003] [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 equolifaciens	strain=DSM 24851	GCA_003725995.1	498718	498718	type	True	100.0	890	892	95	conclusive
Slackia faecicanis	strain=DSM 17537	GCA_003725295.1	255723	255723	type	True	79.4527	272	892	95	below_threshold
Slackia isoflavoniconvertens	strain=DSM 22006	GCA_014192995.1	572010	572010	type	True	78.3867	180	892	95	below_threshold
Slackia isoflavoniconvertens	strain=DSM 22006	GCA_003725955.1	572010	572010	type	True	78.3427	178	892	95	below_threshold
Slackia piriformis	strain=YIT 12062	GCA_000296445.1	626934	626934	type	True	78.2777	192	892	95	below_threshold
Eggerthella timonensis	strain=Marseille-P3135	GCA_900184265.1	1871008	1871008	type	True	78.2576	189	892	95	below_threshold
Xiamenia xianingshaonis	strain=zg-886	GCA_011392455.1	2682776	2682776	type	True	77.7761	104	892	95	below_threshold
Xiamenia xianingshaonis	strain=zg-886	GCA_017945865.1	2682776	2682776	type	True	77.7657	97	892	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	77.7371	95	892	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	77.6465	197	892	95	below_threshold
Adlercreutzia caecimuris	strain=B7	GCA_000403355.2	671266	671266	type	True	77.6216	148	892	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	77.5964	198	892	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	77.2417	87	892	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:01,004] [INFO] DFAST Taxonomy check result was written to GCF_003725995.1_ASM372599v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:01,005] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:01,005] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:01,005] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ac74bff-c5a4-4f0b-9d91-6e767996f6be/dqc_reference/checkm_data
[2024-01-24 11:13:01,007] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:01,038] [INFO] Task started: CheckM
[2024-01-24 11:13:01,038] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003725995.1_ASM372599v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003725995.1_ASM372599v1_genomic.fna/checkm_input GCF_003725995.1_ASM372599v1_genomic.fna/checkm_result
[2024-01-24 11:13:32,396] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:32,397] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:32,418] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:32,418] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:32,419] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003725995.1_ASM372599v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:32,419] [INFO] Task started: Blastn
[2024-01-24 11:13:32,420] [INFO] Running command: blastn -query GCF_003725995.1_ASM372599v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ac74bff-c5a4-4f0b-9d91-6e767996f6be/dqc_reference/reference_markers_gtdb.fasta -out GCF_003725995.1_ASM372599v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:33,378] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:33,381] [INFO] Selected 20 target genomes.
[2024-01-24 11:13:33,381] [INFO] Target genome list was writen to GCF_003725995.1_ASM372599v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:33,418] [INFO] Task started: fastANI
[2024-01-24 11:13:33,419] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2c7f1b9-ac3b-4377-82a4-5cac3c1a320b/GCF_003725995.1_ASM372599v1_genomic.fna.gz --refList GCF_003725995.1_ASM372599v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003725995.1_ASM372599v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:41,543] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:41,567] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:41,567] [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_003725995.1	s__Slackia_A equolifaciens	100.0	890	892	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003725295.1	s__Slackia_A faecicanis	79.444	273	892	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_900553775.1	s__Slackia_A sp900553775	78.7514	216	892	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	98.24	98.24	0.77	0.77	2	-
GCA_905215325.1	s__Senegalimassilia sp905215325	78.4434	144	892	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135645.1	s__Senegalimassilia faecalis	78.4128	169	892	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia	95.0	96.85	96.73	0.92	0.89	4	-
GCA_900555495.1	s__Slackia_A sp900555495	78.3561	162	892	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_003725955.1	s__Slackia_A isoflavoniconvertens	78.3427	178	892	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_000296445.1	s__Slackia_A piriformis	78.2777	192	892	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	98.02	96.04	0.96	0.92	3	-
GCA_900754495.1	s__Aphodovivens avicola	78.2709	175	892	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aphodovivens	95.0	96.28	95.91	0.79	0.73	3	-
GCA_900550055.1	s__Senegalimassilia sp900550055	78.2629	130	892	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia	95.0	97.04	96.58	0.76	0.72	3	-
GCA_900550385.1	s__Aphodovivens sp900550385	78.1799	165	892	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aphodovivens	95.0	99.66	99.66	0.86	0.86	2	-
GCA_018715725.1	s__Aveggerthella excrementigallinarum	77.9084	154	892	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aveggerthella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715935.1	s__Aphodovivens excrementavium	77.9039	101	892	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aphodovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588095.1	s__D16-63 sp910588095	77.775	123	892	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__D16-63	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553655.1	s__Slackia_A sp900553655	77.7048	110	892	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_019113915.1	s__Gordonibacter avicola	77.6876	140	892	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003612475.1	s__D16-63 sp003612475	77.6363	116	892	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__D16-63	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589695.1	s__QWKK01 sp910589695	77.6189	136	892	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__QWKK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001486445.1	s__RUG013 sp001486445	77.4757	96	892	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__RUG013	95.0	98.36	97.63	0.92	0.89	7	-
GCA_900758075.1	s__CACZQA01 sp900758075	77.0915	52	892	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__QAMH01;g__CACZQA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:41,569] [INFO] GTDB search result was written to GCF_003725995.1_ASM372599v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:41,570] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:41,574] [INFO] DFAST_QC result json was written to GCF_003725995.1_ASM372599v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:41,574] [INFO] DFAST_QC completed!
[2024-01-24 11:13:41,574] [INFO] Total running time: 0h1m3s