[2024-01-24 11:35:23,528] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:23,538] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:23,539] [INFO] DQC Reference Directory: /var/lib/cwl/stgaaa95b9e-d41b-4105-a918-02b1e17fe109/dqc_reference
[2024-01-24 11:35:26,239] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,240] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,241] [INFO] Running command: gunzip -c /var/lib/cwl/stg45e91e72-dad8-40dd-84f3-9b57bd7e562c/GCF_014297355.1_ASM1429735v1_genomic.fna.gz | prodigal -d GCF_014297355.1_ASM1429735v1_genomic.fna/cds.fna -a GCF_014297355.1_ASM1429735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:34,879] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:34,879] [INFO] Task started: HMMsearch
[2024-01-24 11:35:34,880] [INFO] Running command: hmmsearch --tblout GCF_014297355.1_ASM1429735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaaa95b9e-d41b-4105-a918-02b1e17fe109/dqc_reference/reference_markers.hmm GCF_014297355.1_ASM1429735v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:35,244] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:35,245] [INFO] Found 6/6 markers.
[2024-01-24 11:35:35,282] [INFO] Query marker FASTA was written to GCF_014297355.1_ASM1429735v1_genomic.fna/markers.fasta
[2024-01-24 11:35:35,283] [INFO] Task started: Blastn
[2024-01-24 11:35:35,283] [INFO] Running command: blastn -query GCF_014297355.1_ASM1429735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaaa95b9e-d41b-4105-a918-02b1e17fe109/dqc_reference/reference_markers.fasta -out GCF_014297355.1_ASM1429735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:35,958] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:35,962] [INFO] Selected 15 target genomes.
[2024-01-24 11:35:35,962] [INFO] Target genome list was writen to GCF_014297355.1_ASM1429735v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:35,968] [INFO] Task started: fastANI
[2024-01-24 11:35:35,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg45e91e72-dad8-40dd-84f3-9b57bd7e562c/GCF_014297355.1_ASM1429735v1_genomic.fna.gz --refList GCF_014297355.1_ASM1429735v1_genomic.fna/target_genomes.txt --output GCF_014297355.1_ASM1429735v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:46,010] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:46,011] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaaa95b9e-d41b-4105-a918-02b1e17fe109/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:46,011] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaaa95b9e-d41b-4105-a918-02b1e17fe109/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:46,024] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:46,024] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:46,024] [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 intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	100.0	1139	1140	95	conclusive
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	84.7869	700	1140	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	84.6106	720	1140	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	82.2141	358	1140	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	81.8112	344	1140	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	80.5315	189	1140	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	80.4717	353	1140	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	80.4299	339	1140	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	79.9417	323	1140	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	79.7973	123	1140	95	below_threshold
Jutongia hominis	strain=BX3	GCA_014384965.1	2763664	2763664	type	True	79.3513	60	1140	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	78.5235	114	1140	95	below_threshold
Blautia hydrogenotrophica	strain=DSM 10507	GCA_000157975.1	53443	53443	type	True	77.4098	77	1140	95	below_threshold
Anaerostipes butyraticus	strain=JCM 17466	GCA_016586355.1	645466	645466	type	True	77.2394	58	1140	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:46,026] [INFO] DFAST Taxonomy check result was written to GCF_014297355.1_ASM1429735v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:46,026] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:46,026] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:46,027] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaaa95b9e-d41b-4105-a918-02b1e17fe109/dqc_reference/checkm_data
[2024-01-24 11:35:46,028] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:46,061] [INFO] Task started: CheckM
[2024-01-24 11:35:46,062] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014297355.1_ASM1429735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014297355.1_ASM1429735v1_genomic.fna/checkm_input GCF_014297355.1_ASM1429735v1_genomic.fna/checkm_result
[2024-01-24 11:36:17,814] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:17,816] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:17,837] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:17,837] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:17,838] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014297355.1_ASM1429735v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:17,838] [INFO] Task started: Blastn
[2024-01-24 11:36:17,838] [INFO] Running command: blastn -query GCF_014297355.1_ASM1429735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaaa95b9e-d41b-4105-a918-02b1e17fe109/dqc_reference/reference_markers_gtdb.fasta -out GCF_014297355.1_ASM1429735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:18,926] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:18,929] [INFO] Selected 8 target genomes.
[2024-01-24 11:36:18,929] [INFO] Target genome list was writen to GCF_014297355.1_ASM1429735v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:18,936] [INFO] Task started: fastANI
[2024-01-24 11:36:18,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg45e91e72-dad8-40dd-84f3-9b57bd7e562c/GCF_014297355.1_ASM1429735v1_genomic.fna.gz --refList GCF_014297355.1_ASM1429735v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014297355.1_ASM1429735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:25,444] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:25,455] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:25,455] [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_000210015.1	s__Blautia_A obeum_B	98.4419	970	1140	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	conclusive
GCA_900066355.1	s__Blautia_A sp900066355	94.9022	890	1140	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_900120195.1	s__Blautia_A sp900120195	94.4179	877	1140	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.52	98.42	0.85	0.83	5	-
GCF_000153905.1	s__Blautia_A obeum	84.7687	702	1140	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_009883055.1	s__Blautia_A sp900548245	83.4401	582	1140	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_003461245.1	s__Blautia_A sp000436615	83.3799	613	1140	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.75	98.36	0.88	0.81	8	-
GCF_018918125.1	s__Blautia_A sp018918125	83.3114	608	1140	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_900551715.1	s__Blautia_A sp900551715	80.5281	399	1140	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 11:36:25,457] [INFO] GTDB search result was written to GCF_014297355.1_ASM1429735v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:25,458] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:25,462] [INFO] DFAST_QC result json was written to GCF_014297355.1_ASM1429735v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:25,462] [INFO] DFAST_QC completed!
[2024-01-24 11:36:25,463] [INFO] Total running time: 0h1m2s