[2024-01-25 19:49:50,516] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:49:50,521] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:49:50,521] [INFO] DQC Reference Directory: /var/lib/cwl/stg4cf3400e-bb40-4eac-83d8-3f31812eb571/dqc_reference
[2024-01-25 19:49:51,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:49:51,643] [INFO] Task started: Prodigal
[2024-01-25 19:49:51,643] [INFO] Running command: gunzip -c /var/lib/cwl/stg2969fe0e-6cc8-4505-9d45-838dd7c5c8c9/GCF_000469305.1_ASM46930v1_genomic.fna.gz | prodigal -d GCF_000469305.1_ASM46930v1_genomic.fna/cds.fna -a GCF_000469305.1_ASM46930v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:49:55,002] [INFO] Task succeeded: Prodigal
[2024-01-25 19:49:55,002] [INFO] Task started: HMMsearch
[2024-01-25 19:49:55,002] [INFO] Running command: hmmsearch --tblout GCF_000469305.1_ASM46930v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4cf3400e-bb40-4eac-83d8-3f31812eb571/dqc_reference/reference_markers.hmm GCF_000469305.1_ASM46930v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:49:55,184] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:49:55,185] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2969fe0e-6cc8-4505-9d45-838dd7c5c8c9/GCF_000469305.1_ASM46930v1_genomic.fna.gz]
[2024-01-25 19:49:55,205] [INFO] Query marker FASTA was written to GCF_000469305.1_ASM46930v1_genomic.fna/markers.fasta
[2024-01-25 19:49:55,205] [INFO] Task started: Blastn
[2024-01-25 19:49:55,205] [INFO] Running command: blastn -query GCF_000469305.1_ASM46930v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4cf3400e-bb40-4eac-83d8-3f31812eb571/dqc_reference/reference_markers.fasta -out GCF_000469305.1_ASM46930v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:55,750] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:55,753] [INFO] Selected 20 target genomes.
[2024-01-25 19:49:55,753] [INFO] Target genome list was writen to GCF_000469305.1_ASM46930v1_genomic.fna/target_genomes.txt
[2024-01-25 19:49:55,762] [INFO] Task started: fastANI
[2024-01-25 19:49:55,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg2969fe0e-6cc8-4505-9d45-838dd7c5c8c9/GCF_000469305.1_ASM46930v1_genomic.fna.gz --refList GCF_000469305.1_ASM46930v1_genomic.fna/target_genomes.txt --output GCF_000469305.1_ASM46930v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:50:04,616] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:04,616] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4cf3400e-bb40-4eac-83d8-3f31812eb571/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:50:04,616] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4cf3400e-bb40-4eac-83d8-3f31812eb571/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:50:04,622] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:50:04,623] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:50:04,623] [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
Faecalitalea cylindroides	strain=ATCC 27803	GCA_000469305.1	39483	39483	type	True	100.0	592	592	95	conclusive
Faecalicoccus pleomorphus	strain=DSM 20574	GCA_000420345.1	1323	1323	type	True	78.6165	112	592	95	below_threshold
Faecalicoccus pleomorphus	strain=NCTC11087	GCA_900459315.1	1323	1323	type	True	78.5981	116	592	95	below_threshold
Holdemanella porci	strain=LKV-472-APC-3	GCA_009696075.1	2652276	2652276	suspected-type	True	78.1608	116	592	95	below_threshold
Faecalicoccus acidiformans	strain=DSM 26963	GCA_014202635.1	915173	915173	type	True	77.8851	93	592	95	below_threshold
Holdemanella biformis	strain=DSM 3989	GCA_000156655.1	1735	1735	suspected-type	True	77.8362	135	592	95	below_threshold
Floccifex porci	strain=LKV-178-WT-2G	GCA_009696175.1	2606629	2606629	type	True	77.7221	83	592	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:50:04,624] [INFO] DFAST Taxonomy check result was written to GCF_000469305.1_ASM46930v1_genomic.fna/tc_result.tsv
[2024-01-25 19:50:04,624] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:50:04,625] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:50:04,625] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4cf3400e-bb40-4eac-83d8-3f31812eb571/dqc_reference/checkm_data
[2024-01-25 19:50:04,626] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:50:04,650] [INFO] Task started: CheckM
[2024-01-25 19:50:04,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000469305.1_ASM46930v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000469305.1_ASM46930v1_genomic.fna/checkm_input GCF_000469305.1_ASM46930v1_genomic.fna/checkm_result
[2024-01-25 19:50:22,550] [INFO] Task succeeded: CheckM
[2024-01-25 19:50:22,552] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:50:22,593] [INFO] ===== Completeness check finished =====
[2024-01-25 19:50:22,593] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:50:22,593] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000469305.1_ASM46930v1_genomic.fna/markers.fasta)
[2024-01-25 19:50:22,593] [INFO] Task started: Blastn
[2024-01-25 19:50:22,593] [INFO] Running command: blastn -query GCF_000469305.1_ASM46930v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4cf3400e-bb40-4eac-83d8-3f31812eb571/dqc_reference/reference_markers_gtdb.fasta -out GCF_000469305.1_ASM46930v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:23,441] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:23,444] [INFO] Selected 18 target genomes.
[2024-01-25 19:50:23,444] [INFO] Target genome list was writen to GCF_000469305.1_ASM46930v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:50:23,468] [INFO] Task started: fastANI
[2024-01-25 19:50:23,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg2969fe0e-6cc8-4505-9d45-838dd7c5c8c9/GCF_000469305.1_ASM46930v1_genomic.fna.gz --refList GCF_000469305.1_ASM46930v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000469305.1_ASM46930v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:50:30,654] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:30,663] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:50:30,663] [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_000469305.1	s__Faecalitalea cylindroides	100.0	592	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalitalea	95.0	98.51	97.31	0.84	0.75	12	conclusive
GCF_009696075.1	s__Holdemanella porci	78.1786	115	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	96.44	95.01	0.80	0.66	21	-
GCF_003458715.1	s__Holdemanella sp003458715	77.9569	113	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	97.81	97.17	0.85	0.77	7	-
GCF_003436425.1	s__Holdemanella sp003436425	77.935	125	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	98.46	97.77	0.88	0.82	5	-
GCF_014202635.1	s__Faecalicoccus acidiformans	77.8851	93	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalicoccus	95.0	98.13	97.66	0.90	0.87	3	-
GCF_000156655.1	s__Holdemanella biformis	77.8583	134	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	96.82	95.86	0.79	0.56	17	-
GCA_902399855.1	s__Faecalicoccus sp900546545	77.7494	118	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalicoccus	95.0413	99.03	98.24	0.89	0.80	8	-
GCA_900547815.1	s__Holdemanella sp900547815	77.7327	112	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	97.44	96.94	0.79	0.75	3	-
GCF_009696175.1	s__Floccifex porci	77.7221	83	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Floccifex	95.0	99.09	99.09	0.94	0.94	2	-
GCA_900754615.1	s__Holdemanella sp900754615	77.6113	118	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003480165.1	s__Absicoccus sp000434355	77.3837	71	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Absicoccus	95.0	99.44	99.16	0.95	0.93	5	-
GCA_900556915.1	s__Holdemanella sp900556915	77.2337	78	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	96.25	96.18	0.85	0.83	3	-
GCA_000403415.2	s__Dubosiella sp000403415	76.7623	52	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Dubosiella	95.0	99.26	99.26	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:50:30,665] [INFO] GTDB search result was written to GCF_000469305.1_ASM46930v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:50:30,665] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:50:30,669] [INFO] DFAST_QC result json was written to GCF_000469305.1_ASM46930v1_genomic.fna/dqc_result.json
[2024-01-25 19:50:30,669] [INFO] DFAST_QC completed!
[2024-01-25 19:50:30,669] [INFO] Total running time: 0h0m40s