[2024-01-24 13:57:25,740] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:25,743] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:25,743] [INFO] DQC Reference Directory: /var/lib/cwl/stg77029775-2513-415e-a781-2f7bf3e47532/dqc_reference
[2024-01-24 13:57:27,213] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:27,214] [INFO] Task started: Prodigal
[2024-01-24 13:57:27,214] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0fb074b-a023-4543-85de-446d2cb7df57/GCF_000156515.1_ASM15651v1_genomic.fna.gz | prodigal -d GCF_000156515.1_ASM15651v1_genomic.fna/cds.fna -a GCF_000156515.1_ASM15651v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:38,083] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:38,084] [INFO] Task started: HMMsearch
[2024-01-24 13:57:38,084] [INFO] Running command: hmmsearch --tblout GCF_000156515.1_ASM15651v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77029775-2513-415e-a781-2f7bf3e47532/dqc_reference/reference_markers.hmm GCF_000156515.1_ASM15651v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:38,382] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:38,383] [INFO] Found 6/6 markers.
[2024-01-24 13:57:38,424] [INFO] Query marker FASTA was written to GCF_000156515.1_ASM15651v1_genomic.fna/markers.fasta
[2024-01-24 13:57:38,424] [INFO] Task started: Blastn
[2024-01-24 13:57:38,424] [INFO] Running command: blastn -query GCF_000156515.1_ASM15651v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77029775-2513-415e-a781-2f7bf3e47532/dqc_reference/reference_markers.fasta -out GCF_000156515.1_ASM15651v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:39,125] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:39,130] [INFO] Selected 22 target genomes.
[2024-01-24 13:57:39,130] [INFO] Target genome list was writen to GCF_000156515.1_ASM15651v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:39,152] [INFO] Task started: fastANI
[2024-01-24 13:57:39,152] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0fb074b-a023-4543-85de-446d2cb7df57/GCF_000156515.1_ASM15651v1_genomic.fna.gz --refList GCF_000156515.1_ASM15651v1_genomic.fna/target_genomes.txt --output GCF_000156515.1_ASM15651v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:53,130] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:53,131] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77029775-2513-415e-a781-2f7bf3e47532/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:53,131] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77029775-2513-415e-a781-2f7bf3e47532/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:53,145] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:53,145] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:53,145] [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
[Clostridium] hylemonae	strain=DSM 15053	GCA_000156515.1	89153	89153	type	True	100.0	1270	1270	95	conclusive
[Clostridium] hylemonae	strain=DSM 15053	GCA_008281175.1	89153	89153	type	True	99.9503	1263	1270	95	conclusive
[Clostridium] scindens	strain=ATCC 35704	GCA_004295125.1	29347	29347	suspected-type	True	78.3099	270	1270	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	78.2822	268	1270	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	77.9653	106	1270	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	77.897	150	1270	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	77.8796	143	1270	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	77.7118	142	1270	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	77.5684	91	1270	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	77.4573	82	1270	95	below_threshold
Blautia coccoides	strain=NCTC11035	GCA_900461125.1	1532	1532	type	True	77.4051	78	1270	95	below_threshold
Muricomes intestini	strain=DSM 29489	GCA_004346165.1	1796634	1796634	type	True	77.2309	76	1270	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	77.1986	74	1270	95	below_threshold
Sellimonas caecigallum	strain=SW451	GCA_019754295.1	2592333	2592333	type	True	77.0267	101	1270	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	76.6763	73	1270	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	76.4268	56	1270	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:53,148] [INFO] DFAST Taxonomy check result was written to GCF_000156515.1_ASM15651v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:53,149] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:53,149] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:53,149] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77029775-2513-415e-a781-2f7bf3e47532/dqc_reference/checkm_data
[2024-01-24 13:57:53,150] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:53,190] [INFO] Task started: CheckM
[2024-01-24 13:57:53,191] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000156515.1_ASM15651v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000156515.1_ASM15651v1_genomic.fna/checkm_input GCF_000156515.1_ASM15651v1_genomic.fna/checkm_result
[2024-01-24 13:58:31,323] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:31,324] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:31,343] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:31,344] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:31,344] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000156515.1_ASM15651v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:31,345] [INFO] Task started: Blastn
[2024-01-24 13:58:31,345] [INFO] Running command: blastn -query GCF_000156515.1_ASM15651v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77029775-2513-415e-a781-2f7bf3e47532/dqc_reference/reference_markers_gtdb.fasta -out GCF_000156515.1_ASM15651v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:32,505] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:32,509] [INFO] Selected 13 target genomes.
[2024-01-24 13:58:32,510] [INFO] Target genome list was writen to GCF_000156515.1_ASM15651v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:33,199] [INFO] Task started: fastANI
[2024-01-24 13:58:33,200] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0fb074b-a023-4543-85de-446d2cb7df57/GCF_000156515.1_ASM15651v1_genomic.fna.gz --refList GCF_000156515.1_ASM15651v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000156515.1_ASM15651v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:42,259] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:42,276] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:42,276] [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_008281175.1	s__Extibacter hylemonae	99.9503	1263	1270	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Extibacter	95.0	99.20	98.44	0.97	0.93	5	conclusive
GCF_004345005.1	s__Extibacter muris	82.6929	738	1270	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Extibacter	95.0	95.70	95.67	0.77	0.77	4	-
GCF_017566055.1	s__Extibacter sp017566055	82.4657	802	1270	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Extibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001185345.1	s__Extibacter sp001185345	82.2345	832	1270	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Extibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000509125.1	s__Clostridium_AP sp000509125	78.3297	292	1270	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_AP	95.0	99.12	98.62	0.95	0.91	5	-
GCF_004295125.1	s__Clostridium_AP scindens	78.3079	269	1270	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_AP	95.0	99.44	99.12	0.90	0.78	13	-
GCA_900543415.1	s__CAG-317 sp900543415	77.908	152	1270	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_000433535.1	s__CAG-317 sp000433535	77.9049	162	1270	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_011960625.1	s__Sporofaciens sp011960625	77.6421	57	1270	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900461125.1	s__Blautia coccoides	77.4051	78	1270	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.33	97.47	0.84	0.79	11	-
GCF_016901695.1	s__Lachnoclostridium_B massiliensis_A	77.3968	132	1270	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004560705.1	s__Bariatricus sp004560705	77.3554	79	1270	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	99.19	99.19	0.81	0.81	2	-
GCA_900553355.1	s__Merdimonas sp900553355	77.111	160	1270	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:42,278] [INFO] GTDB search result was written to GCF_000156515.1_ASM15651v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:42,279] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:42,286] [INFO] DFAST_QC result json was written to GCF_000156515.1_ASM15651v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:42,287] [INFO] DFAST_QC completed!
[2024-01-24 13:58:42,287] [INFO] Total running time: 0h1m17s