[2023-06-19 11:22:59,565] [INFO] DFAST_QC pipeline started.
[2023-06-19 11:22:59,567] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 11:22:59,567] [INFO] DQC Reference Directory: /var/lib/cwl/stg7962b31d-3f9f-4603-ae3e-3cef4f3847d2/dqc_reference
[2023-06-19 11:23:00,700] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 11:23:00,701] [INFO] Task started: Prodigal
[2023-06-19 11:23:00,701] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b594ea7-de9e-4685-853a-960384ad87fc/GCA_014868665.1_ASM1486866v1_genomic.fna.gz | prodigal -d GCA_014868665.1_ASM1486866v1_genomic.fna/cds.fna -a GCA_014868665.1_ASM1486866v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 11:23:06,782] [INFO] Task succeeded: Prodigal
[2023-06-19 11:23:06,783] [INFO] Task started: HMMsearch
[2023-06-19 11:23:06,783] [INFO] Running command: hmmsearch --tblout GCA_014868665.1_ASM1486866v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7962b31d-3f9f-4603-ae3e-3cef4f3847d2/dqc_reference/reference_markers.hmm GCA_014868665.1_ASM1486866v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 11:23:06,948] [INFO] Task succeeded: HMMsearch
[2023-06-19 11:23:06,950] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0b594ea7-de9e-4685-853a-960384ad87fc/GCA_014868665.1_ASM1486866v1_genomic.fna.gz]
[2023-06-19 11:23:06,980] [INFO] Query marker FASTA was written to GCA_014868665.1_ASM1486866v1_genomic.fna/markers.fasta
[2023-06-19 11:23:06,981] [INFO] Task started: Blastn
[2023-06-19 11:23:06,981] [INFO] Running command: blastn -query GCA_014868665.1_ASM1486866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7962b31d-3f9f-4603-ae3e-3cef4f3847d2/dqc_reference/reference_markers.fasta -out GCA_014868665.1_ASM1486866v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 11:23:07,608] [INFO] Task succeeded: Blastn
[2023-06-19 11:23:07,611] [INFO] Selected 7 target genomes.
[2023-06-19 11:23:07,611] [INFO] Target genome list was writen to GCA_014868665.1_ASM1486866v1_genomic.fna/target_genomes.txt
[2023-06-19 11:23:07,612] [INFO] Task started: fastANI
[2023-06-19 11:23:07,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b594ea7-de9e-4685-853a-960384ad87fc/GCA_014868665.1_ASM1486866v1_genomic.fna.gz --refList GCA_014868665.1_ASM1486866v1_genomic.fna/target_genomes.txt --output GCA_014868665.1_ASM1486866v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 11:23:11,495] [INFO] Task succeeded: fastANI
[2023-06-19 11:23:11,496] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7962b31d-3f9f-4603-ae3e-3cef4f3847d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 11:23:11,496] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7962b31d-3f9f-4603-ae3e-3cef4f3847d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 11:23:11,504] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 11:23:11,504] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 11:23:11,504] [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
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	94.4403	519	630	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	84.5382	417	630	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	84.486	423	630	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	83.4485	415	630	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	80.3422	292	630	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	78.5551	120	630	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	77.7729	158	630	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 11:23:11,506] [INFO] DFAST Taxonomy check result was written to GCA_014868665.1_ASM1486866v1_genomic.fna/tc_result.tsv
[2023-06-19 11:23:11,515] [INFO] ===== Taxonomy check completed =====
[2023-06-19 11:23:11,515] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 11:23:11,516] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7962b31d-3f9f-4603-ae3e-3cef4f3847d2/dqc_reference/checkm_data
[2023-06-19 11:23:11,517] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 11:23:11,542] [INFO] Task started: CheckM
[2023-06-19 11:23:11,542] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014868665.1_ASM1486866v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014868665.1_ASM1486866v1_genomic.fna/checkm_input GCA_014868665.1_ASM1486866v1_genomic.fna/checkm_result
[2023-06-19 11:23:34,152] [INFO] Task succeeded: CheckM
[2023-06-19 11:23:34,153] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.24%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 11:23:34,179] [INFO] ===== Completeness check finished =====
[2023-06-19 11:23:34,179] [INFO] ===== Start GTDB Search =====
[2023-06-19 11:23:34,180] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014868665.1_ASM1486866v1_genomic.fna/markers.fasta)
[2023-06-19 11:23:34,180] [INFO] Task started: Blastn
[2023-06-19 11:23:34,180] [INFO] Running command: blastn -query GCA_014868665.1_ASM1486866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7962b31d-3f9f-4603-ae3e-3cef4f3847d2/dqc_reference/reference_markers_gtdb.fasta -out GCA_014868665.1_ASM1486866v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 11:23:35,161] [INFO] Task succeeded: Blastn
[2023-06-19 11:23:35,165] [INFO] Selected 8 target genomes.
[2023-06-19 11:23:35,165] [INFO] Target genome list was writen to GCA_014868665.1_ASM1486866v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 11:23:35,166] [INFO] Task started: fastANI
[2023-06-19 11:23:35,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b594ea7-de9e-4685-853a-960384ad87fc/GCA_014868665.1_ASM1486866v1_genomic.fna.gz --refList GCA_014868665.1_ASM1486866v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014868665.1_ASM1486866v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 11:23:39,670] [INFO] Task succeeded: fastANI
[2023-06-19 11:23:39,677] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 11:23:39,677] [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_003287405.1	s__Faecalibacterium prausnitzii_J	97.2693	552	630	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.32	96.98	0.87	0.83	5	conclusive
GCF_003324185.1	s__Faecalibacterium prausnitzii	94.4403	519	630	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0612	96.64	96.12	0.86	0.79	47	-
GCA_900772565.1	s__Faecalibacterium sp900772565	94.2759	477	630	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002550015.1	s__Faecalibacterium prausnitzii_A	94.1289	501	630	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0612	96.42	95.34	0.88	0.83	7	-
GCA_003449675.1	s__Faecalibacterium sp003449675	93.4172	374	630	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	96.56	96.55	0.80	0.74	3	-
GCA_905215595.1	s__Faecalibacterium sp905215595	93.0989	413	630	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900765105.1	s__Faecalibacterium sp900765105	85.0454	366	630	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.27	98.27	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-19 11:23:39,680] [INFO] GTDB search result was written to GCA_014868665.1_ASM1486866v1_genomic.fna/result_gtdb.tsv
[2023-06-19 11:23:39,681] [INFO] ===== GTDB Search completed =====
[2023-06-19 11:23:39,684] [INFO] DFAST_QC result json was written to GCA_014868665.1_ASM1486866v1_genomic.fna/dqc_result.json
[2023-06-19 11:23:39,684] [INFO] DFAST_QC completed!
[2023-06-19 11:23:39,684] [INFO] Total running time: 0h0m40s