[2024-01-24 12:37:37,931] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:37,933] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:37,933] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d6ec4cf-920f-4484-b24d-67f5061065d4/dqc_reference
[2024-01-24 12:37:41,016] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:41,017] [INFO] Task started: Prodigal
[2024-01-24 12:37:41,018] [INFO] Running command: gunzip -c /var/lib/cwl/stg4e9a87ee-f8d7-4238-9989-60038f462479/GCF_025150745.1_ASM2515074v1_genomic.fna.gz | prodigal -d GCF_025150745.1_ASM2515074v1_genomic.fna/cds.fna -a GCF_025150745.1_ASM2515074v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:46,954] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:46,955] [INFO] Task started: HMMsearch
[2024-01-24 12:37:46,955] [INFO] Running command: hmmsearch --tblout GCF_025150745.1_ASM2515074v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d6ec4cf-920f-4484-b24d-67f5061065d4/dqc_reference/reference_markers.hmm GCF_025150745.1_ASM2515074v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:47,204] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:47,206] [INFO] Found 6/6 markers.
[2024-01-24 12:37:47,232] [INFO] Query marker FASTA was written to GCF_025150745.1_ASM2515074v1_genomic.fna/markers.fasta
[2024-01-24 12:37:47,232] [INFO] Task started: Blastn
[2024-01-24 12:37:47,232] [INFO] Running command: blastn -query GCF_025150745.1_ASM2515074v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d6ec4cf-920f-4484-b24d-67f5061065d4/dqc_reference/reference_markers.fasta -out GCF_025150745.1_ASM2515074v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:48,544] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:48,550] [INFO] Selected 19 target genomes.
[2024-01-24 12:37:48,551] [INFO] Target genome list was writen to GCF_025150745.1_ASM2515074v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:48,645] [INFO] Task started: fastANI
[2024-01-24 12:37:48,645] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e9a87ee-f8d7-4238-9989-60038f462479/GCF_025150745.1_ASM2515074v1_genomic.fna.gz --refList GCF_025150745.1_ASM2515074v1_genomic.fna/target_genomes.txt --output GCF_025150745.1_ASM2515074v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:59,243] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:59,244] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d6ec4cf-920f-4484-b24d-67f5061065d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:59,245] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d6ec4cf-920f-4484-b24d-67f5061065d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:59,261] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:37:59,261] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:59,261] [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
Eubacterium ventriosum	strain=ATCC 27560	GCA_025150745.1	39496	39496	suspected-type	True	100.0	952	952	95	conclusive
Eubacterium ventriosum	strain=ATCC 27560	GCA_000153885.1	39496	39496	suspected-type	True	99.9825	938	952	95	conclusive
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	83.7129	89	952	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	81.5434	50	952	95	below_threshold
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	79.2446	94	952	95	below_threshold
Jutongia hominis	strain=BX3	GCA_014384965.1	2763664	2763664	type	True	78.1892	67	952	95	below_threshold
Eubacterium uniforme	strain=ATCC 35992	GCA_900167115.1	39495	39495	type	True	78.0939	108	952	95	below_threshold
Pseudobutyrivibrio xylanivorans	strain=DSM 14809	GCA_900141825.1	185007	185007	type	True	77.0341	50	952	95	below_threshold
Mobilisporobacter senegalensis	strain=DSM 26537	GCA_003752155.1	1329262	1329262	type	True	75.9459	57	952	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:59,263] [INFO] DFAST Taxonomy check result was written to GCF_025150745.1_ASM2515074v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:59,264] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:59,264] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:59,265] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d6ec4cf-920f-4484-b24d-67f5061065d4/dqc_reference/checkm_data
[2024-01-24 12:37:59,266] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:59,299] [INFO] Task started: CheckM
[2024-01-24 12:37:59,300] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025150745.1_ASM2515074v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025150745.1_ASM2515074v1_genomic.fna/checkm_input GCF_025150745.1_ASM2515074v1_genomic.fna/checkm_result
[2024-01-24 12:38:23,612] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:23,613] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:23,644] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:23,644] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:23,645] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025150745.1_ASM2515074v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:23,646] [INFO] Task started: Blastn
[2024-01-24 12:38:23,646] [INFO] Running command: blastn -query GCF_025150745.1_ASM2515074v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d6ec4cf-920f-4484-b24d-67f5061065d4/dqc_reference/reference_markers_gtdb.fasta -out GCF_025150745.1_ASM2515074v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:24,675] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:24,680] [INFO] Selected 13 target genomes.
[2024-01-24 12:38:24,680] [INFO] Target genome list was writen to GCF_025150745.1_ASM2515074v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:24,710] [INFO] Task started: fastANI
[2024-01-24 12:38:24,711] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e9a87ee-f8d7-4238-9989-60038f462479/GCF_025150745.1_ASM2515074v1_genomic.fna.gz --refList GCF_025150745.1_ASM2515074v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025150745.1_ASM2515074v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:31,738] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:31,748] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:31,748] [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_000153885.1	s__Eubacterium_G ventriosum	99.9825	938	952	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.27	97.67	0.81	0.64	20	conclusive
GCA_900764695.1	s__Eubacterium_G sp900764695	92.5201	385	952	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003460505.1	s__Eubacterium_G sp000435815	82.195	362	952	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.79	97.65	0.84	0.54	8	-
GCA_900548465.1	s__Eubacterium_G sp900548465	82.0582	313	952	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	97.75	97.64	0.80	0.72	3	-
GCF_003479405.1	s__Eubacterium_G sp000432355	81.3617	322	952	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	99.22	97.56	0.94	0.86	9	-
GCA_900550135.1	s__Eubacterium_G sp900550135	79.895	259	952	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.87	97.32	0.76	0.74	4	-
GCA_910574895.1	s__Eubacterium_G sp910574895	78.9745	215	952	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016292095.1	s__Eubacterium_G sp016292095	78.6175	159	952	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584795.1	s__Eubacterium_G sp910584795	78.6029	204	952	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141825.1	s__Pseudobutyrivibrio xylanivorans	77.0341	50	952	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pseudobutyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:31,752] [INFO] GTDB search result was written to GCF_025150745.1_ASM2515074v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:31,752] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:31,760] [INFO] DFAST_QC result json was written to GCF_025150745.1_ASM2515074v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:31,760] [INFO] DFAST_QC completed!
[2024-01-24 12:38:31,760] [INFO] Total running time: 0h0m54s