[2024-01-24 12:44:53,651] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:53,656] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:53,657] [INFO] DQC Reference Directory: /var/lib/cwl/stg46708488-d911-4eda-8f76-e42ec3afdcd7/dqc_reference
[2024-01-24 12:44:55,026] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:55,027] [INFO] Task started: Prodigal
[2024-01-24 12:44:55,028] [INFO] Running command: gunzip -c /var/lib/cwl/stg69229edf-b6e1-42ff-aed0-0c0fb929c423/GCF_015159595.1_ASM1515959v1_genomic.fna.gz | prodigal -d GCF_015159595.1_ASM1515959v1_genomic.fna/cds.fna -a GCF_015159595.1_ASM1515959v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:03,741] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:03,742] [INFO] Task started: HMMsearch
[2024-01-24 12:45:03,742] [INFO] Running command: hmmsearch --tblout GCF_015159595.1_ASM1515959v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46708488-d911-4eda-8f76-e42ec3afdcd7/dqc_reference/reference_markers.hmm GCF_015159595.1_ASM1515959v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:04,002] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:04,004] [INFO] Found 6/6 markers.
[2024-01-24 12:45:04,038] [INFO] Query marker FASTA was written to GCF_015159595.1_ASM1515959v1_genomic.fna/markers.fasta
[2024-01-24 12:45:04,039] [INFO] Task started: Blastn
[2024-01-24 12:45:04,039] [INFO] Running command: blastn -query GCF_015159595.1_ASM1515959v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46708488-d911-4eda-8f76-e42ec3afdcd7/dqc_reference/reference_markers.fasta -out GCF_015159595.1_ASM1515959v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:04,662] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:04,665] [INFO] Selected 27 target genomes.
[2024-01-24 12:45:04,665] [INFO] Target genome list was writen to GCF_015159595.1_ASM1515959v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:04,679] [INFO] Task started: fastANI
[2024-01-24 12:45:04,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg69229edf-b6e1-42ff-aed0-0c0fb929c423/GCF_015159595.1_ASM1515959v1_genomic.fna.gz --refList GCF_015159595.1_ASM1515959v1_genomic.fna/target_genomes.txt --output GCF_015159595.1_ASM1515959v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:19,805] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:19,806] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46708488-d911-4eda-8f76-e42ec3afdcd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:19,806] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46708488-d911-4eda-8f76-e42ec3afdcd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:19,823] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:19,823] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:19,824] [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
Blautia liquoris	strain=LZLJ-3	GCA_015159595.1	2779518	2779518	type	True	100.0	1171	1172	95	conclusive
Novisyntrophococcus fermenticellae	strain=JN500902	GCA_018866245.1	2068655	2068655	type	True	80.6824	257	1172	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	79.2849	56	1172	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	78.1571	52	1172	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	77.9518	52	1172	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	77.9458	63	1172	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_025151995.1	438033	438033	type	True	77.8586	63	1172	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_000425525.1	438033	438033	type	True	76.5391	56	1172	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	76.398	57	1172	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	76.3429	54	1172	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	76.133	57	1172	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:19,825] [INFO] DFAST Taxonomy check result was written to GCF_015159595.1_ASM1515959v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:19,826] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:19,826] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:19,827] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46708488-d911-4eda-8f76-e42ec3afdcd7/dqc_reference/checkm_data
[2024-01-24 12:45:19,828] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:19,865] [INFO] Task started: CheckM
[2024-01-24 12:45:19,865] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015159595.1_ASM1515959v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015159595.1_ASM1515959v1_genomic.fna/checkm_input GCF_015159595.1_ASM1515959v1_genomic.fna/checkm_result
[2024-01-24 12:45:51,560] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:51,562] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:51,587] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:51,588] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:51,588] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015159595.1_ASM1515959v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:51,589] [INFO] Task started: Blastn
[2024-01-24 12:45:51,589] [INFO] Running command: blastn -query GCF_015159595.1_ASM1515959v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46708488-d911-4eda-8f76-e42ec3afdcd7/dqc_reference/reference_markers_gtdb.fasta -out GCF_015159595.1_ASM1515959v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:52,648] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:52,652] [INFO] Selected 27 target genomes.
[2024-01-24 12:45:52,653] [INFO] Target genome list was writen to GCF_015159595.1_ASM1515959v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:52,694] [INFO] Task started: fastANI
[2024-01-24 12:45:52,694] [INFO] Running command: fastANI --query /var/lib/cwl/stg69229edf-b6e1-42ff-aed0-0c0fb929c423/GCF_015159595.1_ASM1515959v1_genomic.fna.gz --refList GCF_015159595.1_ASM1515959v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015159595.1_ASM1515959v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:07,113] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:07,132] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:07,132] [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_015159595.1	s__Pelethocola sp015159595	100.0	1168	1172	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pelethocola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004123145.1	s__Oliverpabstia faecicola	82.1498	64	1172	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	97.72	97.58	0.88	0.80	5	-
GCA_002409525.1	s__Pelethocola sp002409525	81.7672	458	1172	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pelethocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018866245.1	s__Pelethocola sp018866245	80.6418	255	1172	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pelethocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002361775.1	s__Oliverpabstia sp002361775	77.5042	57	1172	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	99.87	99.86	0.91	0.89	3	-
GCA_900539175.1	s__Pelethocola sp900539175	77.117	133	1172	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pelethocola	95.0	99.69	99.49	0.84	0.76	3	-
GCF_015557635.1	s__Fusicatenibacter saccharivorans	77.0915	57	1172	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter	95.0	97.82	97.27	0.86	0.77	91	-
GCA_004562915.1	s__Oliverpabstia sp004562915	77.0288	56	1172	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004556655.1	s__Oliverpabstia sp004556655	76.927	52	1172	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009883055.1	s__Blautia_A sp900548245	76.5171	57	1172	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.63	98.37	0.88	0.85	5	-
GCF_000425525.1	s__Ruminococcus_G gauvreauii	76.4122	52	1172	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_G	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013302405.1	s__Blautia_A caecimuris	76.3644	52	1172	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.97	96.45	0.87	0.70	11	-
GCF_009707925.1	s__Blautia_A luti	76.302	53	1172	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.33	97.04	0.87	0.84	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:07,136] [INFO] GTDB search result was written to GCF_015159595.1_ASM1515959v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:07,136] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:07,140] [INFO] DFAST_QC result json was written to GCF_015159595.1_ASM1515959v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:07,140] [INFO] DFAST_QC completed!
[2024-01-24 12:46:07,141] [INFO] Total running time: 0h1m13s