[2024-01-24 13:25:46,669] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:46,671] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:46,671] [INFO] DQC Reference Directory: /var/lib/cwl/stg2040c514-cd52-4cc2-8912-c1da87ad0cf3/dqc_reference
[2024-01-24 13:25:48,027] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:48,028] [INFO] Task started: Prodigal
[2024-01-24 13:25:48,028] [INFO] Running command: gunzip -c /var/lib/cwl/stg9dc7b79c-70f7-44c2-ad51-6e90cd9cae43/GCF_025150085.1_ASM2515008v1_genomic.fna.gz | prodigal -d GCF_025150085.1_ASM2515008v1_genomic.fna/cds.fna -a GCF_025150085.1_ASM2515008v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:55,327] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:55,328] [INFO] Task started: HMMsearch
[2024-01-24 13:25:55,328] [INFO] Running command: hmmsearch --tblout GCF_025150085.1_ASM2515008v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2040c514-cd52-4cc2-8912-c1da87ad0cf3/dqc_reference/reference_markers.hmm GCF_025150085.1_ASM2515008v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:55,588] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:55,589] [INFO] Found 6/6 markers.
[2024-01-24 13:25:55,621] [INFO] Query marker FASTA was written to GCF_025150085.1_ASM2515008v1_genomic.fna/markers.fasta
[2024-01-24 13:25:55,621] [INFO] Task started: Blastn
[2024-01-24 13:25:55,621] [INFO] Running command: blastn -query GCF_025150085.1_ASM2515008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2040c514-cd52-4cc2-8912-c1da87ad0cf3/dqc_reference/reference_markers.fasta -out GCF_025150085.1_ASM2515008v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:56,300] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:56,303] [INFO] Selected 18 target genomes.
[2024-01-24 13:25:56,304] [INFO] Target genome list was writen to GCF_025150085.1_ASM2515008v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:56,312] [INFO] Task started: fastANI
[2024-01-24 13:25:56,312] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dc7b79c-70f7-44c2-ad51-6e90cd9cae43/GCF_025150085.1_ASM2515008v1_genomic.fna.gz --refList GCF_025150085.1_ASM2515008v1_genomic.fna/target_genomes.txt --output GCF_025150085.1_ASM2515008v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:06,417] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:06,417] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2040c514-cd52-4cc2-8912-c1da87ad0cf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:06,417] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2040c514-cd52-4cc2-8912-c1da87ad0cf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:06,430] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:26:06,431] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:06,431] [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_025150085.1	88431	88431	type	True	100.0	973	973	95	conclusive
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	99.9658	945	973	95	conclusive
Wujia chipingensis	strain=NSJ-4	GCA_014337155.1	2763670	2763670	type	True	81.5901	73	973	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	81.2342	216	973	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	80.8608	308	973	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	80.6937	309	973	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	80.4759	248	973	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	80.0443	177	973	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	79.1375	179	973	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	79.056	177	973	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	79.0409	197	973	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	79.0143	207	973	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	78.8644	172	973	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	78.7544	154	973	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_025151995.1	438033	438033	type	True	78.2612	54	973	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	78.1208	70	973	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	77.8984	180	973	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:06,433] [INFO] DFAST Taxonomy check result was written to GCF_025150085.1_ASM2515008v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:06,433] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:06,433] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:06,433] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2040c514-cd52-4cc2-8912-c1da87ad0cf3/dqc_reference/checkm_data
[2024-01-24 13:26:06,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:06,464] [INFO] Task started: CheckM
[2024-01-24 13:26:06,465] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025150085.1_ASM2515008v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025150085.1_ASM2515008v1_genomic.fna/checkm_input GCF_025150085.1_ASM2515008v1_genomic.fna/checkm_result
[2024-01-24 13:26:33,745] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:33,746] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:33,762] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:33,762] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:33,763] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025150085.1_ASM2515008v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:33,763] [INFO] Task started: Blastn
[2024-01-24 13:26:33,764] [INFO] Running command: blastn -query GCF_025150085.1_ASM2515008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2040c514-cd52-4cc2-8912-c1da87ad0cf3/dqc_reference/reference_markers_gtdb.fasta -out GCF_025150085.1_ASM2515008v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:34,820] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:34,824] [INFO] Selected 12 target genomes.
[2024-01-24 13:26:34,824] [INFO] Target genome list was writen to GCF_025150085.1_ASM2515008v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:34,847] [INFO] Task started: fastANI
[2024-01-24 13:26:34,847] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dc7b79c-70f7-44c2-ad51-6e90cd9cae43/GCF_025150085.1_ASM2515008v1_genomic.fna.gz --refList GCF_025150085.1_ASM2515008v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025150085.1_ASM2515008v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:42,047] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:42,057] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:42,057] [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	99.9658	945	973	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	91.0276	723	973	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	89.6918	603	973	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	81.1582	335	973	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	-
GCF_000169235.1	s__Dorea formicigenerans	80.6937	309	973	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	79.6248	225	973	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	79.4083	100	973	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	99.94	99.94	0.94	0.94	2	-
GCA_016295505.1	s__Dorea_A sp016295505	79.019	220	973	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	-
GCA_000433535.1	s__CAG-317 sp000433535	78.8247	208	973	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	98.49	98.19	0.84	0.83	3	-
GCA_900543415.1	s__CAG-317 sp900543415	78.6136	199	973	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	97.35	95.87	0.87	0.78	4	-
GCA_910574285.1	s__Sporofaciens sp009774295	78.249	168	973	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	98.51	98.02	0.91	0.84	4	-
GCF_001754075.1	s__Merdimonas faecis	77.8984	180	973	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdimonas	95.0	98.52	97.96	0.90	0.84	10	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:42,059] [INFO] GTDB search result was written to GCF_025150085.1_ASM2515008v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:42,060] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:42,065] [INFO] DFAST_QC result json was written to GCF_025150085.1_ASM2515008v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:42,066] [INFO] DFAST_QC completed!
[2024-01-24 13:26:42,066] [INFO] Total running time: 0h0m55s