[2024-01-24 15:32:05,860] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:32:05,870] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:32:05,870] [INFO] DQC Reference Directory: /var/lib/cwl/stg34295c44-b01f-44f8-b1ef-28b7ca1b9924/dqc_reference
[2024-01-24 15:32:07,107] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:32:07,107] [INFO] Task started: Prodigal
[2024-01-24 15:32:07,108] [INFO] Running command: gunzip -c /var/lib/cwl/stge8faa392-582b-43b4-b049-1d1ff5539707/GCF_014287675.1_ASM1428767v1_genomic.fna.gz | prodigal -d GCF_014287675.1_ASM1428767v1_genomic.fna/cds.fna -a GCF_014287675.1_ASM1428767v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:32:18,684] [INFO] Task succeeded: Prodigal
[2024-01-24 15:32:18,685] [INFO] Task started: HMMsearch
[2024-01-24 15:32:18,685] [INFO] Running command: hmmsearch --tblout GCF_014287675.1_ASM1428767v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34295c44-b01f-44f8-b1ef-28b7ca1b9924/dqc_reference/reference_markers.hmm GCF_014287675.1_ASM1428767v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:32:18,955] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:32:18,956] [INFO] Found 6/6 markers.
[2024-01-24 15:32:18,995] [INFO] Query marker FASTA was written to GCF_014287675.1_ASM1428767v1_genomic.fna/markers.fasta
[2024-01-24 15:32:18,995] [INFO] Task started: Blastn
[2024-01-24 15:32:18,995] [INFO] Running command: blastn -query GCF_014287675.1_ASM1428767v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34295c44-b01f-44f8-b1ef-28b7ca1b9924/dqc_reference/reference_markers.fasta -out GCF_014287675.1_ASM1428767v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:32:19,677] [INFO] Task succeeded: Blastn
[2024-01-24 15:32:19,680] [INFO] Selected 16 target genomes.
[2024-01-24 15:32:19,680] [INFO] Target genome list was writen to GCF_014287675.1_ASM1428767v1_genomic.fna/target_genomes.txt
[2024-01-24 15:32:19,692] [INFO] Task started: fastANI
[2024-01-24 15:32:19,693] [INFO] Running command: fastANI --query /var/lib/cwl/stge8faa392-582b-43b4-b049-1d1ff5539707/GCF_014287675.1_ASM1428767v1_genomic.fna.gz --refList GCF_014287675.1_ASM1428767v1_genomic.fna/target_genomes.txt --output GCF_014287675.1_ASM1428767v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:32:27,292] [INFO] Task succeeded: fastANI
[2024-01-24 15:32:27,293] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34295c44-b01f-44f8-b1ef-28b7ca1b9924/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:32:27,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34295c44-b01f-44f8-b1ef-28b7ca1b9924/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:32:27,307] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:32:27,307] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:32:27,307] [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
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	80.1735	442	1334	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	80.164	464	1334	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	79.5613	379	1334	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	78.8913	128	1334	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	78.6156	318	1334	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	78.5413	283	1334	95	below_threshold
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	78.4836	319	1334	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	78.4767	310	1334	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.7854	218	1334	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.777	190	1334	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	77.5452	148	1334	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_008121455.1	2211183	2211183	type	True	77.5412	149	1334	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:32:27,309] [INFO] DFAST Taxonomy check result was written to GCF_014287675.1_ASM1428767v1_genomic.fna/tc_result.tsv
[2024-01-24 15:32:27,310] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:32:27,310] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:32:27,310] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34295c44-b01f-44f8-b1ef-28b7ca1b9924/dqc_reference/checkm_data
[2024-01-24 15:32:27,311] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:32:27,350] [INFO] Task started: CheckM
[2024-01-24 15:32:27,350] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014287675.1_ASM1428767v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014287675.1_ASM1428767v1_genomic.fna/checkm_input GCF_014287675.1_ASM1428767v1_genomic.fna/checkm_result
[2024-01-24 15:33:03,594] [INFO] Task succeeded: CheckM
[2024-01-24 15:33:03,595] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:33:03,615] [INFO] ===== Completeness check finished =====
[2024-01-24 15:33:03,615] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:33:03,615] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014287675.1_ASM1428767v1_genomic.fna/markers.fasta)
[2024-01-24 15:33:03,616] [INFO] Task started: Blastn
[2024-01-24 15:33:03,616] [INFO] Running command: blastn -query GCF_014287675.1_ASM1428767v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34295c44-b01f-44f8-b1ef-28b7ca1b9924/dqc_reference/reference_markers_gtdb.fasta -out GCF_014287675.1_ASM1428767v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:33:04,854] [INFO] Task succeeded: Blastn
[2024-01-24 15:33:04,857] [INFO] Selected 15 target genomes.
[2024-01-24 15:33:04,857] [INFO] Target genome list was writen to GCF_014287675.1_ASM1428767v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:33:04,903] [INFO] Task started: fastANI
[2024-01-24 15:33:04,904] [INFO] Running command: fastANI --query /var/lib/cwl/stge8faa392-582b-43b4-b049-1d1ff5539707/GCF_014287675.1_ASM1428767v1_genomic.fna.gz --refList GCF_014287675.1_ASM1428767v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014287675.1_ASM1428767v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:33:15,628] [INFO] Task succeeded: fastANI
[2024-01-24 15:33:15,653] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:33:15,653] [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_014287675.1	s__Pseudoflavonifractor sp014287675	100.0	1333	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pseudoflavonifractor	95.0	99.22	99.20	0.93	0.92	18	conclusive
GCA_904419835.1	s__Pseudoflavonifractor sp904419835	81.5305	524	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pseudoflavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169255.2	s__Pseudoflavonifractor capillosus	81.2609	600	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pseudoflavonifractor	95.0	95.82	95.81	0.78	0.78	3	-
GCA_900549565.1	s__UMGS1202 sp900549565	81.1017	545	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UMGS1202	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540545.1	s__Intestinimonas sp900540545	80.6345	455	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161215.1	s__Flavonifractor avistercoris	80.1994	480	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	96.82	96.45	0.91	0.89	7	-
GCF_000239295.1	s__Flavonifractor plautii	80.1987	440	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	98.23	97.77	0.83	0.59	43	-
GCF_017811815.1	s__Flavonifractor sp017811815	80.1216	407	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159175.1	s__An92 sp002159175	79.7653	427	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.91	98.91	0.91	0.91	2	-
GCA_019119335.1	s__Flavonifractor merdavium	79.7475	367	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199495.1	s__An92 sp900199495	79.6005	380	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.28	97.84	0.85	0.79	7	-
GCA_900079765.1	s__Pseudoflavonifractor sp900079765	79.5649	432	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pseudoflavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014287895.1	s__NSJ-51 sp900549795	79.409	395	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NSJ-51	95.0	99.27	99.06	0.90	0.89	3	-
GCA_018374635.1	s__An92 sp018374635	79.3881	358	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585415.1	s__NSJ-51 sp910585415	78.3319	279	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NSJ-51	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:33:15,655] [INFO] GTDB search result was written to GCF_014287675.1_ASM1428767v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:33:15,655] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:33:15,659] [INFO] DFAST_QC result json was written to GCF_014287675.1_ASM1428767v1_genomic.fna/dqc_result.json
[2024-01-24 15:33:15,659] [INFO] DFAST_QC completed!
[2024-01-24 15:33:15,659] [INFO] Total running time: 0h1m10s