[2024-01-24 13:25:45,650] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:45,652] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:45,652] [INFO] DQC Reference Directory: /var/lib/cwl/stg3282d569-8d11-46cc-bc70-75bf99405cde/dqc_reference
[2024-01-24 13:25:46,884] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:46,884] [INFO] Task started: Prodigal
[2024-01-24 13:25:46,885] [INFO] Running command: gunzip -c /var/lib/cwl/stg79e69e29-dcb5-47d0-818c-186888948872/GCF_020687045.1_ASM2068704v1_genomic.fna.gz | prodigal -d GCF_020687045.1_ASM2068704v1_genomic.fna/cds.fna -a GCF_020687045.1_ASM2068704v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:56,349] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:56,350] [INFO] Task started: HMMsearch
[2024-01-24 13:25:56,350] [INFO] Running command: hmmsearch --tblout GCF_020687045.1_ASM2068704v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3282d569-8d11-46cc-bc70-75bf99405cde/dqc_reference/reference_markers.hmm GCF_020687045.1_ASM2068704v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:56,637] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:56,638] [INFO] Found 6/6 markers.
[2024-01-24 13:25:56,672] [INFO] Query marker FASTA was written to GCF_020687045.1_ASM2068704v1_genomic.fna/markers.fasta
[2024-01-24 13:25:56,673] [INFO] Task started: Blastn
[2024-01-24 13:25:56,673] [INFO] Running command: blastn -query GCF_020687045.1_ASM2068704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3282d569-8d11-46cc-bc70-75bf99405cde/dqc_reference/reference_markers.fasta -out GCF_020687045.1_ASM2068704v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:57,385] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:57,387] [INFO] Selected 14 target genomes.
[2024-01-24 13:25:57,388] [INFO] Target genome list was writen to GCF_020687045.1_ASM2068704v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:57,442] [INFO] Task started: fastANI
[2024-01-24 13:25:57,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg79e69e29-dcb5-47d0-818c-186888948872/GCF_020687045.1_ASM2068704v1_genomic.fna.gz --refList GCF_020687045.1_ASM2068704v1_genomic.fna/target_genomes.txt --output GCF_020687045.1_ASM2068704v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:06,311] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:06,312] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3282d569-8d11-46cc-bc70-75bf99405cde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:06,313] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3282d569-8d11-46cc-bc70-75bf99405cde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:06,330] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:26:06,330] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:26:06,331] [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
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	84.5524	439	1037	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	83.0678	356	1037	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	80.9741	293	1037	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	80.9507	198	1037	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	80.5856	114	1037	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	80.3518	176	1037	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	79.1083	207	1037	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.6377	198	1037	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	78.6027	192	1037	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.7909	129	1037	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	77.7533	143	1037	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	77.6593	121	1037	95	below_threshold
Sporobacter termitidis	strain=DSM 10068	GCA_900130065.1	44749	44749	type	True	76.3334	69	1037	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:06,333] [INFO] DFAST Taxonomy check result was written to GCF_020687045.1_ASM2068704v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:06,335] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:06,336] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:06,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3282d569-8d11-46cc-bc70-75bf99405cde/dqc_reference/checkm_data
[2024-01-24 13:26:06,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:06,376] [INFO] Task started: CheckM
[2024-01-24 13:26:06,376] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020687045.1_ASM2068704v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020687045.1_ASM2068704v1_genomic.fna/checkm_input GCF_020687045.1_ASM2068704v1_genomic.fna/checkm_result
[2024-01-24 13:26:37,563] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:37,565] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:37,582] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:37,582] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:37,583] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020687045.1_ASM2068704v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:37,583] [INFO] Task started: Blastn
[2024-01-24 13:26:37,584] [INFO] Running command: blastn -query GCF_020687045.1_ASM2068704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3282d569-8d11-46cc-bc70-75bf99405cde/dqc_reference/reference_markers_gtdb.fasta -out GCF_020687045.1_ASM2068704v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:38,853] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:38,857] [INFO] Selected 15 target genomes.
[2024-01-24 13:26:38,857] [INFO] Target genome list was writen to GCF_020687045.1_ASM2068704v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:38,873] [INFO] Task started: fastANI
[2024-01-24 13:26:38,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg79e69e29-dcb5-47d0-818c-186888948872/GCF_020687045.1_ASM2068704v1_genomic.fna.gz --refList GCF_020687045.1_ASM2068704v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020687045.1_ASM2068704v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:45,693] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:45,705] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:45,706] [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_018228685.1	s__CAG-83 sp001916855	96.8351	714	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	96.79	95.43	0.86	0.74	11	conclusive
GCA_000435975.1	s__CAG-83 sp000435975	90.6774	465	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.04	97.67	0.83	0.76	8	-
GCF_018408575.1	s__CAG-83 sp000431575	84.5463	439	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.84	97.37	0.92	0.86	9	-
GCA_900551355.1	s__CAG-83 sp900551355	82.8015	263	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.94	98.90	0.93	0.92	3	-
GCA_900554275.1	s__CAG-83 sp900554275	82.1612	278	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.46	96.91	0.80	0.75	4	-
GCA_902388735.1	s__CAG-83 sp902388735	82.125	291	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.86	98.86	0.87	0.87	2	-
GCA_900545495.1	s__CAG-83 sp900545495	82.1058	355	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.95	95.34	0.89	0.84	5	-
GCA_900547745.1	s__CAG-83 sp900547745	82.0924	325	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.22	99.21	0.93	0.91	3	-
GCA_900545585.1	s__CAG-83 sp900545585	82.0065	347	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.41	98.11	0.88	0.81	5	-
GCA_900550585.1	s__CAG-83 sp900550585	81.4912	304	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.85	99.85	0.92	0.92	2	-
GCA_002392625.1	s__CAG-83 sp002392625	81.0612	243	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.65	99.65	0.89	0.89	2	-
GCA_015068325.1	s__CAG-83 sp015068325	80.499	261	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552475.1	s__CAG-83 sp900552475	79.9204	261	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.74	98.42	0.88	0.85	4	-
GCA_017415775.1	s__CAG-83 sp017415775	79.7824	199	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905210385.1	s__Enterenecus sp905210385	78.2903	87	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:45,707] [INFO] GTDB search result was written to GCF_020687045.1_ASM2068704v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:45,708] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:45,711] [INFO] DFAST_QC result json was written to GCF_020687045.1_ASM2068704v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:45,711] [INFO] DFAST_QC completed!
[2024-01-24 13:26:45,711] [INFO] Total running time: 0h1m0s