[2024-01-24 12:47:14,014] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:14,016] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:14,016] [INFO] DQC Reference Directory: /var/lib/cwl/stg58de7d50-a8c6-45fe-a209-b18d90abf019/dqc_reference
[2024-01-24 12:47:15,479] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:15,480] [INFO] Task started: Prodigal
[2024-01-24 12:47:15,480] [INFO] Running command: gunzip -c /var/lib/cwl/stg47b43a8e-3f24-46b5-b80a-4e11ebd3d961/GCF_004345265.1_ASM434526v1_genomic.fna.gz | prodigal -d GCF_004345265.1_ASM434526v1_genomic.fna/cds.fna -a GCF_004345265.1_ASM434526v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:26,600] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:26,601] [INFO] Task started: HMMsearch
[2024-01-24 12:47:26,601] [INFO] Running command: hmmsearch --tblout GCF_004345265.1_ASM434526v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58de7d50-a8c6-45fe-a209-b18d90abf019/dqc_reference/reference_markers.hmm GCF_004345265.1_ASM434526v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:26,917] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:26,918] [INFO] Found 6/6 markers.
[2024-01-24 12:47:26,955] [INFO] Query marker FASTA was written to GCF_004345265.1_ASM434526v1_genomic.fna/markers.fasta
[2024-01-24 12:47:26,956] [INFO] Task started: Blastn
[2024-01-24 12:47:26,956] [INFO] Running command: blastn -query GCF_004345265.1_ASM434526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58de7d50-a8c6-45fe-a209-b18d90abf019/dqc_reference/reference_markers.fasta -out GCF_004345265.1_ASM434526v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:27,773] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:27,776] [INFO] Selected 10 target genomes.
[2024-01-24 12:47:27,776] [INFO] Target genome list was writen to GCF_004345265.1_ASM434526v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:27,780] [INFO] Task started: fastANI
[2024-01-24 12:47:27,781] [INFO] Running command: fastANI --query /var/lib/cwl/stg47b43a8e-3f24-46b5-b80a-4e11ebd3d961/GCF_004345265.1_ASM434526v1_genomic.fna.gz --refList GCF_004345265.1_ASM434526v1_genomic.fna/target_genomes.txt --output GCF_004345265.1_ASM434526v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:33,759] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:33,759] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58de7d50-a8c6-45fe-a209-b18d90abf019/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:33,759] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58de7d50-a8c6-45fe-a209-b18d90abf019/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:33,768] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:33,769] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:33,769] [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
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	100.0	1197	1205	95	conclusive
Ruthenibacterium lactatiformans	strain=585-1	GCA_000949455.1	1550024	1550024	suspected-type	True	81.6389	230	1205	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	80.5682	248	1205	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	80.4177	254	1205	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_000157955.1	214851	214851	type	True	79.7695	246	1205	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	79.7633	241	1205	95	below_threshold
Neglectibacter timonensis	strain=SN17	GCA_900048895.1	1776382	1776382	type	True	79.5317	58	1205	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	79.2518	227	1205	95	below_threshold
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	78.8349	239	1205	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	78.5653	213	1205	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:33,775] [INFO] DFAST Taxonomy check result was written to GCF_004345265.1_ASM434526v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:33,775] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:33,775] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:33,775] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58de7d50-a8c6-45fe-a209-b18d90abf019/dqc_reference/checkm_data
[2024-01-24 12:47:33,777] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:33,824] [INFO] Task started: CheckM
[2024-01-24 12:47:33,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004345265.1_ASM434526v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004345265.1_ASM434526v1_genomic.fna/checkm_input GCF_004345265.1_ASM434526v1_genomic.fna/checkm_result
[2024-01-24 12:48:09,959] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:09,961] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:09,984] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:09,985] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:09,985] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004345265.1_ASM434526v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:09,986] [INFO] Task started: Blastn
[2024-01-24 12:48:09,986] [INFO] Running command: blastn -query GCF_004345265.1_ASM434526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58de7d50-a8c6-45fe-a209-b18d90abf019/dqc_reference/reference_markers_gtdb.fasta -out GCF_004345265.1_ASM434526v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:11,256] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:11,260] [INFO] Selected 10 target genomes.
[2024-01-24 12:48:11,260] [INFO] Target genome list was writen to GCF_004345265.1_ASM434526v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:11,283] [INFO] Task started: fastANI
[2024-01-24 12:48:11,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg47b43a8e-3f24-46b5-b80a-4e11ebd3d961/GCF_004345265.1_ASM434526v1_genomic.fna.gz --refList GCF_004345265.1_ASM434526v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004345265.1_ASM434526v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:18,629] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:18,643] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:18,643] [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_004345265.1	s__Fournierella massiliensis	100.0	1197	1205	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	99.99	99.99	1.00	1.00	3	conclusive
GCF_002159185.1	s__Fournierella sp002159185	91.3618	841	1205	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161595.1	s__Fournierella sp002161595	90.8307	847	1205	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	98.81	98.81	0.92	0.92	2	-
GCF_002160145.1	s__Fournierella sp002160145	90.8034	802	1205	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	98.11	98.11	0.91	0.91	2	-
GCA_004558145.1	s__Fournierella excrementavium	81.4457	431	1205	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	97.60	97.45	0.91	0.87	5	-
GCA_019116345.1	s__Fournierella merdipullorum	81.4324	360	1205	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119025.1	s__Fournierella excrementigallinarum	81.1156	373	1205	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118765.1	s__Fournierella merdavium	81.0734	400	1205	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160955.1	s__Gemmiger_A avium	81.0261	405	1205	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger_A	95.0	98.36	98.15	0.86	0.80	3	-
GCA_019115305.1	s__Anaerofilum excrementigallinarum	79.421	259	1205	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerofilum	95.0	98.54	98.54	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:18,645] [INFO] GTDB search result was written to GCF_004345265.1_ASM434526v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:18,645] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:18,650] [INFO] DFAST_QC result json was written to GCF_004345265.1_ASM434526v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:18,650] [INFO] DFAST_QC completed!
[2024-01-24 12:48:18,651] [INFO] Total running time: 0h1m5s