[2024-01-24 11:34:38,683] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:38,686] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:38,686] [INFO] DQC Reference Directory: /var/lib/cwl/stg514ce130-04f1-4c1a-a4af-b6dcf1772523/dqc_reference
[2024-01-24 11:34:41,321] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:41,324] [INFO] Task started: Prodigal
[2024-01-24 11:34:41,324] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3027e96-e264-4495-8850-ab41ee4fd68c/GCF_008121455.1_ASM812145v1_genomic.fna.gz | prodigal -d GCF_008121455.1_ASM812145v1_genomic.fna/cds.fna -a GCF_008121455.1_ASM812145v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:48,836] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:48,837] [INFO] Task started: HMMsearch
[2024-01-24 11:34:48,837] [INFO] Running command: hmmsearch --tblout GCF_008121455.1_ASM812145v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg514ce130-04f1-4c1a-a4af-b6dcf1772523/dqc_reference/reference_markers.hmm GCF_008121455.1_ASM812145v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:49,130] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:49,131] [INFO] Found 6/6 markers.
[2024-01-24 11:34:49,167] [INFO] Query marker FASTA was written to GCF_008121455.1_ASM812145v1_genomic.fna/markers.fasta
[2024-01-24 11:34:49,167] [INFO] Task started: Blastn
[2024-01-24 11:34:49,167] [INFO] Running command: blastn -query GCF_008121455.1_ASM812145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg514ce130-04f1-4c1a-a4af-b6dcf1772523/dqc_reference/reference_markers.fasta -out GCF_008121455.1_ASM812145v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:49,835] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:49,841] [INFO] Selected 13 target genomes.
[2024-01-24 11:34:49,842] [INFO] Target genome list was writen to GCF_008121455.1_ASM812145v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:49,902] [INFO] Task started: fastANI
[2024-01-24 11:34:49,902] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3027e96-e264-4495-8850-ab41ee4fd68c/GCF_008121455.1_ASM812145v1_genomic.fna.gz --refList GCF_008121455.1_ASM812145v1_genomic.fna/target_genomes.txt --output GCF_008121455.1_ASM812145v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:34:57,367] [INFO] Task succeeded: fastANI
[2024-01-24 11:34:57,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg514ce130-04f1-4c1a-a4af-b6dcf1772523/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:34:57,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg514ce130-04f1-4c1a-a4af-b6dcf1772523/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:34:57,379] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:34:57,379] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:34:57,379] [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
Evtepia gabavorous	strain=KLE1738	GCA_008121455.1	2211183	2211183	type	True	100.0	799	803	95	conclusive
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	100.0	799	803	95	conclusive
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	82.5411	54	803	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	82.2284	52	803	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	78.8658	169	803	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	78.7526	90	803	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.543	160	803	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	78.4942	150	803	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	78.1953	137	803	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.8869	101	803	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.8842	158	803	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:34:57,381] [INFO] DFAST Taxonomy check result was written to GCF_008121455.1_ASM812145v1_genomic.fna/tc_result.tsv
[2024-01-24 11:34:57,381] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:34:57,381] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:34:57,382] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg514ce130-04f1-4c1a-a4af-b6dcf1772523/dqc_reference/checkm_data
[2024-01-24 11:34:57,383] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:34:57,411] [INFO] Task started: CheckM
[2024-01-24 11:34:57,411] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008121455.1_ASM812145v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008121455.1_ASM812145v1_genomic.fna/checkm_input GCF_008121455.1_ASM812145v1_genomic.fna/checkm_result
[2024-01-24 11:35:24,479] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:24,480] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:24,499] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:24,500] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:24,500] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008121455.1_ASM812145v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:24,501] [INFO] Task started: Blastn
[2024-01-24 11:35:24,501] [INFO] Running command: blastn -query GCF_008121455.1_ASM812145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg514ce130-04f1-4c1a-a4af-b6dcf1772523/dqc_reference/reference_markers_gtdb.fasta -out GCF_008121455.1_ASM812145v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:25,720] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:25,723] [INFO] Selected 11 target genomes.
[2024-01-24 11:35:25,723] [INFO] Target genome list was writen to GCF_008121455.1_ASM812145v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:25,763] [INFO] Task started: fastANI
[2024-01-24 11:35:25,763] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3027e96-e264-4495-8850-ab41ee4fd68c/GCF_008121455.1_ASM812145v1_genomic.fna.gz --refList GCF_008121455.1_ASM812145v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008121455.1_ASM812145v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:31,566] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:31,578] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:31,578] [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_003425665.1	s__Evtepia gabavorous	100.0	799	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	99.51	98.88	0.95	0.87	8	conclusive
GCA_004554585.1	s__Evtepia sp004554585	82.722	461	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.56	98.47	0.94	0.93	3	-
GCA_019115545.1	s__Evtepia faecavium	82.6315	404	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115225.1	s__Evtepia faecigallinarum	82.3965	425	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546255.1	s__Evtepia excrementipullorum	82.3912	422	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.07	97.85	0.89	0.87	5	-
GCA_004551945.1	s__Evtepia sp004551945	81.556	404	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.68	98.58	0.91	0.88	5	-
GCA_004556345.1	s__Evtepia sp004556345	81.3419	328	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.03	97.32	0.86	0.79	7	-
GCA_016296565.1	s__Evtepia sp016296565	81.3364	339	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902781745.1	s__Evtepia sp902781745	80.919	294	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.13	97.74	0.85	0.79	11	-
GCA_016295225.1	s__Evtepia sp016295225	80.4787	293	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017435425.1	s__Evtepia sp017435425	79.9962	312	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.49	98.49	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:31,579] [INFO] GTDB search result was written to GCF_008121455.1_ASM812145v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:31,580] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:31,583] [INFO] DFAST_QC result json was written to GCF_008121455.1_ASM812145v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:31,583] [INFO] DFAST_QC completed!
[2024-01-24 11:35:31,583] [INFO] Total running time: 0h0m53s