[2023-06-29 19:54:41,310] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:54:41,312] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:54:41,312] [INFO] DQC Reference Directory: /var/lib/cwl/stga8c52c20-9103-4101-8c79-47500c03b9cf/dqc_reference
[2023-06-29 19:54:42,748] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:54:42,749] [INFO] Task started: Prodigal
[2023-06-29 19:54:42,750] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d00b7fa-b3df-4641-b736-c73d2bab586c/GCA_023439265.1_ASM2343926v1_genomic.fna.gz | prodigal -d GCA_023439265.1_ASM2343926v1_genomic.fna/cds.fna -a GCA_023439265.1_ASM2343926v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:54:47,692] [INFO] Task succeeded: Prodigal
[2023-06-29 19:54:47,692] [INFO] Task started: HMMsearch
[2023-06-29 19:54:47,692] [INFO] Running command: hmmsearch --tblout GCA_023439265.1_ASM2343926v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8c52c20-9103-4101-8c79-47500c03b9cf/dqc_reference/reference_markers.hmm GCA_023439265.1_ASM2343926v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:54:47,942] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:54:47,943] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3d00b7fa-b3df-4641-b736-c73d2bab586c/GCA_023439265.1_ASM2343926v1_genomic.fna.gz]
[2023-06-29 19:54:47,966] [INFO] Query marker FASTA was written to GCA_023439265.1_ASM2343926v1_genomic.fna/markers.fasta
[2023-06-29 19:54:47,967] [INFO] Task started: Blastn
[2023-06-29 19:54:47,967] [INFO] Running command: blastn -query GCA_023439265.1_ASM2343926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8c52c20-9103-4101-8c79-47500c03b9cf/dqc_reference/reference_markers.fasta -out GCA_023439265.1_ASM2343926v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:54:48,595] [INFO] Task succeeded: Blastn
[2023-06-29 19:54:48,599] [INFO] Selected 14 target genomes.
[2023-06-29 19:54:48,599] [INFO] Target genome list was writen to GCA_023439265.1_ASM2343926v1_genomic.fna/target_genomes.txt
[2023-06-29 19:54:48,601] [INFO] Task started: fastANI
[2023-06-29 19:54:48,601] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d00b7fa-b3df-4641-b736-c73d2bab586c/GCA_023439265.1_ASM2343926v1_genomic.fna.gz --refList GCA_023439265.1_ASM2343926v1_genomic.fna/target_genomes.txt --output GCA_023439265.1_ASM2343926v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:54:55,550] [INFO] Task succeeded: fastANI
[2023-06-29 19:54:55,550] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8c52c20-9103-4101-8c79-47500c03b9cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:54:55,551] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8c52c20-9103-4101-8c79-47500c03b9cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:54:55,563] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2023-06-29 19:54:55,563] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 19:54:55,563] [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
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	98.9992	599	648	95	conclusive
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	98.9702	610	648	95	conclusive
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	78.6512	209	648	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	78.6462	209	648	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	77.9957	147	648	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	77.9649	199	648	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	77.7826	128	648	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	77.6765	124	648	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	77.6688	126	648	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	77.5964	127	648	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	77.4955	123	648	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	77.4527	143	648	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	77.3895	133	648	95	below_threshold
Aequitasia blattaphilus	strain=PAL113	GCA_024160205.1	2949332	2949332	type	True	76.5342	53	648	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 19:54:55,565] [INFO] DFAST Taxonomy check result was written to GCA_023439265.1_ASM2343926v1_genomic.fna/tc_result.tsv
[2023-06-29 19:54:55,566] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:54:55,566] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:54:55,566] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8c52c20-9103-4101-8c79-47500c03b9cf/dqc_reference/checkm_data
[2023-06-29 19:54:55,567] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:54:55,593] [INFO] Task started: CheckM
[2023-06-29 19:54:55,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023439265.1_ASM2343926v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023439265.1_ASM2343926v1_genomic.fna/checkm_input GCA_023439265.1_ASM2343926v1_genomic.fna/checkm_result
[2023-06-29 19:55:18,044] [INFO] Task succeeded: CheckM
[2023-06-29 19:55:18,045] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.73%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 19:55:18,071] [INFO] ===== Completeness check finished =====
[2023-06-29 19:55:18,071] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:55:18,072] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023439265.1_ASM2343926v1_genomic.fna/markers.fasta)
[2023-06-29 19:55:18,072] [INFO] Task started: Blastn
[2023-06-29 19:55:18,072] [INFO] Running command: blastn -query GCA_023439265.1_ASM2343926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8c52c20-9103-4101-8c79-47500c03b9cf/dqc_reference/reference_markers_gtdb.fasta -out GCA_023439265.1_ASM2343926v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:55:19,043] [INFO] Task succeeded: Blastn
[2023-06-29 19:55:19,047] [INFO] Selected 10 target genomes.
[2023-06-29 19:55:19,047] [INFO] Target genome list was writen to GCA_023439265.1_ASM2343926v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:55:19,048] [INFO] Task started: fastANI
[2023-06-29 19:55:19,048] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d00b7fa-b3df-4641-b736-c73d2bab586c/GCA_023439265.1_ASM2343926v1_genomic.fna.gz --refList GCA_023439265.1_ASM2343926v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023439265.1_ASM2343926v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:55:24,443] [INFO] Task succeeded: fastANI
[2023-06-29 19:55:24,458] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 19:55:24,459] [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_000154065.1	s__Dorea_A longicatena	98.9992	599	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	98.55	97.61	0.85	0.69	49	conclusive
GCF_001404875.1	s__Dorea_A longicatena_B	89.8921	528	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	97.75	96.72	0.80	0.69	20	-
GCA_900550865.1	s__Dorea_A sp900550865	89.5107	489	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003435815.1	s__CAG-317 sp000433215	79.1372	233	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	98.71	98.41	0.89	0.86	9	-
GCA_016295505.1	s__Dorea_A sp016295505	78.7248	201	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169235.1	s__Dorea formicigenerans	78.6259	210	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea	95.0	97.68	96.97	0.80	0.73	43	-
GCF_003477705.1	s__Lachnoclostridium_B sp900066555	78.4939	170	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	97.98	96.92	0.87	0.81	6	-
GCA_900554415.1	s__Bariatricus sp900554415	77.5017	79	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	99.94	99.94	0.94	0.94	2	-
GCF_001754075.1	s__Merdimonas faecis	77.4527	143	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdimonas	95.0	98.52	97.96	0.90	0.84	10	-
GCA_910574285.1	s__Sporofaciens sp009774295	77.2883	138	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	98.51	98.02	0.91	0.84	4	-
--------------------------------------------------------------------------------
[2023-06-29 19:55:24,461] [INFO] GTDB search result was written to GCA_023439265.1_ASM2343926v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:55:24,461] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:55:24,465] [INFO] DFAST_QC result json was written to GCA_023439265.1_ASM2343926v1_genomic.fna/dqc_result.json
[2023-06-29 19:55:24,465] [INFO] DFAST_QC completed!
[2023-06-29 19:55:24,465] [INFO] Total running time: 0h0m43s