[2024-01-24 10:57:11,345] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:11,347] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:11,347] [INFO] DQC Reference Directory: /var/lib/cwl/stg9449d363-e2ed-4d23-a4aa-458014b78a15/dqc_reference
[2024-01-24 10:57:12,644] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:12,645] [INFO] Task started: Prodigal
[2024-01-24 10:57:12,645] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d741088-8ae8-4d79-9b1b-afb4e3891c4e/GCF_014982805.1_ASM1498280v1_genomic.fna.gz | prodigal -d GCF_014982805.1_ASM1498280v1_genomic.fna/cds.fna -a GCF_014982805.1_ASM1498280v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:21,817] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:21,818] [INFO] Task started: HMMsearch
[2024-01-24 10:57:21,818] [INFO] Running command: hmmsearch --tblout GCF_014982805.1_ASM1498280v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9449d363-e2ed-4d23-a4aa-458014b78a15/dqc_reference/reference_markers.hmm GCF_014982805.1_ASM1498280v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:22,068] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:22,069] [INFO] Found 6/6 markers.
[2024-01-24 10:57:22,098] [INFO] Query marker FASTA was written to GCF_014982805.1_ASM1498280v1_genomic.fna/markers.fasta
[2024-01-24 10:57:22,099] [INFO] Task started: Blastn
[2024-01-24 10:57:22,099] [INFO] Running command: blastn -query GCF_014982805.1_ASM1498280v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9449d363-e2ed-4d23-a4aa-458014b78a15/dqc_reference/reference_markers.fasta -out GCF_014982805.1_ASM1498280v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:22,850] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:22,853] [INFO] Selected 11 target genomes.
[2024-01-24 10:57:22,853] [INFO] Target genome list was writen to GCF_014982805.1_ASM1498280v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:22,869] [INFO] Task started: fastANI
[2024-01-24 10:57:22,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d741088-8ae8-4d79-9b1b-afb4e3891c4e/GCF_014982805.1_ASM1498280v1_genomic.fna.gz --refList GCF_014982805.1_ASM1498280v1_genomic.fna/target_genomes.txt --output GCF_014982805.1_ASM1498280v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:30,165] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:30,166] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9449d363-e2ed-4d23-a4aa-458014b78a15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:30,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9449d363-e2ed-4d23-a4aa-458014b78a15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:30,176] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:57:30,176] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:57:30,176] [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
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	81.7946	445	978	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_000157955.1	214851	214851	type	True	81.7523	443	978	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	80.0362	275	978	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	79.2055	245	978	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	79.085	247	978	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	78.9598	257	978	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	78.6946	242	978	95	below_threshold
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	78.5228	233	978	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:30,178] [INFO] DFAST Taxonomy check result was written to GCF_014982805.1_ASM1498280v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:30,178] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:30,178] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:30,178] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9449d363-e2ed-4d23-a4aa-458014b78a15/dqc_reference/checkm_data
[2024-01-24 10:57:30,180] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:30,213] [INFO] Task started: CheckM
[2024-01-24 10:57:30,213] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014982805.1_ASM1498280v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014982805.1_ASM1498280v1_genomic.fna/checkm_input GCF_014982805.1_ASM1498280v1_genomic.fna/checkm_result
[2024-01-24 10:58:02,402] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:02,403] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:02,419] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:02,419] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:02,420] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014982805.1_ASM1498280v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:02,420] [INFO] Task started: Blastn
[2024-01-24 10:58:02,421] [INFO] Running command: blastn -query GCF_014982805.1_ASM1498280v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9449d363-e2ed-4d23-a4aa-458014b78a15/dqc_reference/reference_markers_gtdb.fasta -out GCF_014982805.1_ASM1498280v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:03,734] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:03,737] [INFO] Selected 11 target genomes.
[2024-01-24 10:58:03,738] [INFO] Target genome list was writen to GCF_014982805.1_ASM1498280v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:03,747] [INFO] Task started: fastANI
[2024-01-24 10:58:03,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d741088-8ae8-4d79-9b1b-afb4e3891c4e/GCF_014982805.1_ASM1498280v1_genomic.fna.gz --refList GCF_014982805.1_ASM1498280v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014982805.1_ASM1498280v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:10,601] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:10,611] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:10,611] [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_014982805.1	s__Gemmiger sp014982805	100.0	977	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019114415.1	s__Gemmiger faecavium	87.9294	662	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119495.1	s__Gemmiger stercorigallinarum	82.7175	437	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.30	97.15	0.83	0.66	4	-
GCA_904390925.1	s__Gemmiger sp904390925	82.6691	437	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019120395.1	s__Gemmiger faecigallinarum	82.508	475	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016900095.1	s__Gemmiger formicilis_A	82.0664	479	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214345.1	s__Gemmiger sp905214345	81.1781	448	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119365.1	s__Gemmiger stercoripullorum	79.6598	320	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.12	98.12	0.82	0.82	2	-
GCA_019112725.1	s__Faecalibacterium intestinipullorum	79.063	233	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.50	98.50	0.82	0.82	2	-
GCF_004345265.1	s__Fournierella massiliensis	78.9766	256	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	99.99	99.99	1.00	1.00	3	-
GCA_900548355.1	s__Gemmiger avicola	78.8024	266	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.64	98.58	0.86	0.84	5	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:10,613] [INFO] GTDB search result was written to GCF_014982805.1_ASM1498280v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:10,613] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:10,616] [INFO] DFAST_QC result json was written to GCF_014982805.1_ASM1498280v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:10,616] [INFO] DFAST_QC completed!
[2024-01-24 10:58:10,616] [INFO] Total running time: 0h0m59s