[2024-01-25 20:04:50,557] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:04:50,558] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:04:50,558] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c126ccf-c9d1-4552-b508-f44c6ee9443c/dqc_reference
[2024-01-25 20:04:51,667] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:04:51,667] [INFO] Task started: Prodigal
[2024-01-25 20:04:51,668] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ce7e196-449e-4a2b-8bb0-ad25b7f7f9fd/GCF_025567405.1_ASM2556740v1_genomic.fna.gz | prodigal -d GCF_025567405.1_ASM2556740v1_genomic.fna/cds.fna -a GCF_025567405.1_ASM2556740v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:04:58,786] [INFO] Task succeeded: Prodigal
[2024-01-25 20:04:58,786] [INFO] Task started: HMMsearch
[2024-01-25 20:04:58,786] [INFO] Running command: hmmsearch --tblout GCF_025567405.1_ASM2556740v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c126ccf-c9d1-4552-b508-f44c6ee9443c/dqc_reference/reference_markers.hmm GCF_025567405.1_ASM2556740v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:04:59,006] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:04:59,007] [INFO] Found 6/6 markers.
[2024-01-25 20:04:59,035] [INFO] Query marker FASTA was written to GCF_025567405.1_ASM2556740v1_genomic.fna/markers.fasta
[2024-01-25 20:04:59,036] [INFO] Task started: Blastn
[2024-01-25 20:04:59,036] [INFO] Running command: blastn -query GCF_025567405.1_ASM2556740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c126ccf-c9d1-4552-b508-f44c6ee9443c/dqc_reference/reference_markers.fasta -out GCF_025567405.1_ASM2556740v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:59,632] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:59,635] [INFO] Selected 29 target genomes.
[2024-01-25 20:04:59,636] [INFO] Target genome list was writen to GCF_025567405.1_ASM2556740v1_genomic.fna/target_genomes.txt
[2024-01-25 20:04:59,648] [INFO] Task started: fastANI
[2024-01-25 20:04:59,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ce7e196-449e-4a2b-8bb0-ad25b7f7f9fd/GCF_025567405.1_ASM2556740v1_genomic.fna.gz --refList GCF_025567405.1_ASM2556740v1_genomic.fna/target_genomes.txt --output GCF_025567405.1_ASM2556740v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:05:17,802] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:17,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c126ccf-c9d1-4552-b508-f44c6ee9443c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:05:17,802] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c126ccf-c9d1-4552-b508-f44c6ee9443c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:05:17,815] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:05:17,815] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:05:17,815] [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
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	83.0852	153	1090	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	82.0862	130	1090	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	81.635	121	1090	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	81.2191	64	1090	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	80.0673	135	1090	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	79.4301	145	1090	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	79.2925	91	1090	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_004295125.1	29347	29347	suspected-type	True	79.0155	62	1090	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	78.9264	62	1090	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	78.7486	60	1090	95	below_threshold
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	78.2333	77	1090	95	below_threshold
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	77.7504	59	1090	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	77.5511	78	1090	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	77.3823	125	1090	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_016696745.1	1796616	1796616	type	True	77.1813	65	1090	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	77.167	65	1090	95	below_threshold
Kineothrix alysoides	strain=KNHs209	GCA_000732725.1	1469948	1469948	type	True	77.1598	89	1090	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	77.1297	68	1090	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_002221555.2	1796616	1796616	type	True	77.1214	64	1090	95	below_threshold
Butyrivibrio hungatei	strain=DSM 14810	GCA_900143205.1	185008	185008	type	True	77.1121	63	1090	95	below_threshold
Kineothrix alysoides	strain=DSM 100556	GCA_004345255.1	1469948	1469948	type	True	76.7754	87	1090	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	76.4461	61	1090	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:05:17,817] [INFO] DFAST Taxonomy check result was written to GCF_025567405.1_ASM2556740v1_genomic.fna/tc_result.tsv
[2024-01-25 20:05:17,817] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:05:17,817] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:05:17,817] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c126ccf-c9d1-4552-b508-f44c6ee9443c/dqc_reference/checkm_data
[2024-01-25 20:05:17,818] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:05:17,853] [INFO] Task started: CheckM
[2024-01-25 20:05:17,853] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025567405.1_ASM2556740v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025567405.1_ASM2556740v1_genomic.fna/checkm_input GCF_025567405.1_ASM2556740v1_genomic.fna/checkm_result
[2024-01-25 20:05:43,815] [INFO] Task succeeded: CheckM
[2024-01-25 20:05:43,816] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:05:43,839] [INFO] ===== Completeness check finished =====
[2024-01-25 20:05:43,839] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:05:43,840] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025567405.1_ASM2556740v1_genomic.fna/markers.fasta)
[2024-01-25 20:05:43,840] [INFO] Task started: Blastn
[2024-01-25 20:05:43,840] [INFO] Running command: blastn -query GCF_025567405.1_ASM2556740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c126ccf-c9d1-4552-b508-f44c6ee9443c/dqc_reference/reference_markers_gtdb.fasta -out GCF_025567405.1_ASM2556740v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:44,895] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:44,897] [INFO] Selected 18 target genomes.
[2024-01-25 20:05:44,898] [INFO] Target genome list was writen to GCF_025567405.1_ASM2556740v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:05:44,912] [INFO] Task started: fastANI
[2024-01-25 20:05:44,912] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ce7e196-449e-4a2b-8bb0-ad25b7f7f9fd/GCF_025567405.1_ASM2556740v1_genomic.fna.gz --refList GCF_025567405.1_ASM2556740v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025567405.1_ASM2556740v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:05:54,979] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:54,990] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:05:54,990] [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_003490145.1	s__CAG-95 sp900066375	97.5742	888	1090	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.74	97.55	0.91	0.82	5	conclusive
GCA_902766365.1	s__CAG-95 sp902766365	90.3046	641	1090	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000438155.1	s__CAG-95 sp000438155	78.9641	228	1090	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.06	97.32	0.83	0.81	5	-
GCA_017622575.1	s__CAG-95 sp017622575	78.9409	296	1090	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000403495.2	s__CAG-95 sp000403495	78.5834	174	1090	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.68	98.68	0.87	0.87	2	-
GCA_900553305.1	s__CAG-95 sp900553305	78.4127	168	1090	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	99.81	99.81	0.85	0.85	2	-
GCA_017411305.1	s__CAG-95 sp017411305	78.2696	168	1090	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014803415.1	s__CAG-95 sp014803415	78.2634	238	1090	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	97.80	97.80	0.82	0.82	2	-
GCA_000436115.1	s__CAG-95 sp000436115	78.0264	246	1090	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	99.37	99.32	0.91	0.90	3	-
GCA_018384375.1	s__CAG-95 sp018384375	77.8539	225	1090	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.73	98.22	0.80	0.77	3	-
GCA_017621815.1	s__CAG-95 sp017621815	77.7048	223	1090	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057005.1	s__Acetatifactor sp015057005	77.6348	63	1090	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009695765.1	s__VUNI01 sp009695765	77.5107	79	1090	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__VUNI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579495.1	s__CAG-95 sp910579495	77.0946	127	1090	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017465845.1	s__Acetatifactor sp017465845	77.0115	94	1090	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017476765.1	s__RGIG3040 sp017476765	76.226	54	1090	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG3040	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:05:54,991] [INFO] GTDB search result was written to GCF_025567405.1_ASM2556740v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:05:54,992] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:05:54,995] [INFO] DFAST_QC result json was written to GCF_025567405.1_ASM2556740v1_genomic.fna/dqc_result.json
[2024-01-25 20:05:54,995] [INFO] DFAST_QC completed!
[2024-01-25 20:05:54,995] [INFO] Total running time: 0h1m4s