[2024-01-24 13:49:55,256] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:55,258] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:55,258] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb4f3467-1edd-4918-8817-65f8a230604f/dqc_reference
[2024-01-24 13:49:56,480] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:56,481] [INFO] Task started: Prodigal
[2024-01-24 13:49:56,481] [INFO] Running command: gunzip -c /var/lib/cwl/stg26b32660-0bd0-4f97-a653-6ee0984a17b0/GCF_024622975.1_ASM2462297v1_genomic.fna.gz | prodigal -d GCF_024622975.1_ASM2462297v1_genomic.fna/cds.fna -a GCF_024622975.1_ASM2462297v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:05,746] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:05,747] [INFO] Task started: HMMsearch
[2024-01-24 13:50:05,747] [INFO] Running command: hmmsearch --tblout GCF_024622975.1_ASM2462297v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb4f3467-1edd-4918-8817-65f8a230604f/dqc_reference/reference_markers.hmm GCF_024622975.1_ASM2462297v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:06,027] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:06,028] [INFO] Found 6/6 markers.
[2024-01-24 13:50:06,060] [INFO] Query marker FASTA was written to GCF_024622975.1_ASM2462297v1_genomic.fna/markers.fasta
[2024-01-24 13:50:06,061] [INFO] Task started: Blastn
[2024-01-24 13:50:06,061] [INFO] Running command: blastn -query GCF_024622975.1_ASM2462297v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb4f3467-1edd-4918-8817-65f8a230604f/dqc_reference/reference_markers.fasta -out GCF_024622975.1_ASM2462297v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:06,713] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:06,719] [INFO] Selected 13 target genomes.
[2024-01-24 13:50:06,719] [INFO] Target genome list was writen to GCF_024622975.1_ASM2462297v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:06,806] [INFO] Task started: fastANI
[2024-01-24 13:50:06,807] [INFO] Running command: fastANI --query /var/lib/cwl/stg26b32660-0bd0-4f97-a653-6ee0984a17b0/GCF_024622975.1_ASM2462297v1_genomic.fna.gz --refList GCF_024622975.1_ASM2462297v1_genomic.fna/target_genomes.txt --output GCF_024622975.1_ASM2462297v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:15,714] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:15,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb4f3467-1edd-4918-8817-65f8a230604f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:15,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb4f3467-1edd-4918-8817-65f8a230604f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:15,726] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:15,727] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:15,727] [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 caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	100.0	1312	1316	95	conclusive
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	82.2658	361	1316	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	82.1358	348	1316	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	80.9956	308	1316	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	80.1482	317	1316	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	79.8352	342	1316	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	79.8294	343	1316	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	79.6444	153	1316	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	79.308	293	1316	95	below_threshold
Blautia argi	strain=KCTC 15426	GCA_003287895.1	1912897	1912897	type	True	78.6872	165	1316	95	below_threshold
Diplocloster modestus	strain=ASD4241	GCA_019042245.1	2850322	2850322	type	True	78.3185	72	1316	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	77.6815	156	1316	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:15,728] [INFO] DFAST Taxonomy check result was written to GCF_024622975.1_ASM2462297v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:15,729] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:15,729] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:15,729] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb4f3467-1edd-4918-8817-65f8a230604f/dqc_reference/checkm_data
[2024-01-24 13:50:15,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:15,770] [INFO] Task started: CheckM
[2024-01-24 13:50:15,770] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024622975.1_ASM2462297v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024622975.1_ASM2462297v1_genomic.fna/checkm_input GCF_024622975.1_ASM2462297v1_genomic.fna/checkm_result
[2024-01-24 13:50:48,424] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:48,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:48,448] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:48,448] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:48,449] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024622975.1_ASM2462297v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:48,449] [INFO] Task started: Blastn
[2024-01-24 13:50:48,449] [INFO] Running command: blastn -query GCF_024622975.1_ASM2462297v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb4f3467-1edd-4918-8817-65f8a230604f/dqc_reference/reference_markers_gtdb.fasta -out GCF_024622975.1_ASM2462297v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:49,477] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:49,482] [INFO] Selected 12 target genomes.
[2024-01-24 13:50:49,482] [INFO] Target genome list was writen to GCF_024622975.1_ASM2462297v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:49,516] [INFO] Task started: fastANI
[2024-01-24 13:50:49,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg26b32660-0bd0-4f97-a653-6ee0984a17b0/GCF_024622975.1_ASM2462297v1_genomic.fna.gz --refList GCF_024622975.1_ASM2462297v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024622975.1_ASM2462297v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:57,025] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:57,037] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:57,038] [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_013302405.1	s__Blautia_A caecimuris	98.4003	942	1316	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	conclusive
GCA_900541985.1	s__Blautia_A sp900541985	82.4285	540	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.92	99.92	0.93	0.93	2	-
GCA_900551465.1	s__Blautia_A sp900551465	81.529	360	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553515.1	s__Blautia_A sp900553515	81.4821	508	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900066355.1	s__Blautia_A sp900066355	80.4791	329	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.38	98.38	0.93	0.93	2	-
GCF_000210015.1	s__Blautia_A obeum_B	80.2611	339	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.64	98.44	0.85	0.84	7	-
GCF_009883055.1	s__Blautia_A sp900548245	79.9437	325	1316	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_000153905.1	s__Blautia_A obeum	79.8294	343	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.25	97.20	0.82	0.75	45	-
GCF_018918125.1	s__Blautia_A sp018918125	79.0658	301	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115125.1	s__Blautia_A faecipullorum	79.011	367	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.90	97.90	0.82	0.82	2	-
GCA_019118645.1	s__Blautia_A excrementipullorum	78.7396	335	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.86	99.86	0.91	0.91	2	-
GCA_900551715.1	s__Blautia_A sp900551715	78.5055	263	1316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:57,039] [INFO] GTDB search result was written to GCF_024622975.1_ASM2462297v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:57,040] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:57,045] [INFO] DFAST_QC result json was written to GCF_024622975.1_ASM2462297v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:57,045] [INFO] DFAST_QC completed!
[2024-01-24 13:50:57,046] [INFO] Total running time: 0h1m2s