[2024-01-24 14:14:00,292] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:00,295] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:00,296] [INFO] DQC Reference Directory: /var/lib/cwl/stg45be19fd-8310-466b-991f-5c2589d5302a/dqc_reference
[2024-01-24 14:14:01,612] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:01,613] [INFO] Task started: Prodigal
[2024-01-24 14:14:01,614] [INFO] Running command: gunzip -c /var/lib/cwl/stg056de839-4e2e-4f44-bcd8-cf5f7931918d/GCF_009828745.1_ASM982874v1_genomic.fna.gz | prodigal -d GCF_009828745.1_ASM982874v1_genomic.fna/cds.fna -a GCF_009828745.1_ASM982874v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:06,847] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:06,847] [INFO] Task started: HMMsearch
[2024-01-24 14:14:06,848] [INFO] Running command: hmmsearch --tblout GCF_009828745.1_ASM982874v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45be19fd-8310-466b-991f-5c2589d5302a/dqc_reference/reference_markers.hmm GCF_009828745.1_ASM982874v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:07,246] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:07,247] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg056de839-4e2e-4f44-bcd8-cf5f7931918d/GCF_009828745.1_ASM982874v1_genomic.fna.gz]
[2024-01-24 14:14:07,281] [INFO] Query marker FASTA was written to GCF_009828745.1_ASM982874v1_genomic.fna/markers.fasta
[2024-01-24 14:14:07,282] [INFO] Task started: Blastn
[2024-01-24 14:14:07,282] [INFO] Running command: blastn -query GCF_009828745.1_ASM982874v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45be19fd-8310-466b-991f-5c2589d5302a/dqc_reference/reference_markers.fasta -out GCF_009828745.1_ASM982874v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:08,272] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:08,275] [INFO] Selected 19 target genomes.
[2024-01-24 14:14:08,276] [INFO] Target genome list was writen to GCF_009828745.1_ASM982874v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:08,294] [INFO] Task started: fastANI
[2024-01-24 14:14:08,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg056de839-4e2e-4f44-bcd8-cf5f7931918d/GCF_009828745.1_ASM982874v1_genomic.fna.gz --refList GCF_009828745.1_ASM982874v1_genomic.fna/target_genomes.txt --output GCF_009828745.1_ASM982874v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:19,436] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:19,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45be19fd-8310-466b-991f-5c2589d5302a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:19,437] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45be19fd-8310-466b-991f-5c2589d5302a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:19,444] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:14:19,445] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:19,445] [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
Erysipelothrix anatis	strain=D17_0559-3-2-1	GCA_009828745.1	2683713	2683713	type	True	100.0	714	717	95	conclusive
Erysipelothrix aquatica	strain=VA92-K48	GCA_009828775.2	2683714	2683714	type	True	92.1405	578	717	95	below_threshold
Erysipelothrix piscisicarius	strain=15TAL0474	GCA_003931795.1	2485784	2485784	type	True	78.4937	110	717	95	below_threshold
Erysipelothrix rhusiopathiae	strain=NCTC8163	GCA_900637845.1	1648	1648	type	True	78.4374	105	717	95	below_threshold
Erysipelothrix rhusiopathiae	strain=ATCC 19414	GCA_000160815.2	1648	1648	type	True	78.3762	108	717	95	below_threshold
Erysipelothrix inopinata	strain=DSM 15511	GCA_014396165.1	225084	225084	type	True	78.3639	122	717	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:19,447] [INFO] DFAST Taxonomy check result was written to GCF_009828745.1_ASM982874v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:19,448] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:19,448] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:19,448] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45be19fd-8310-466b-991f-5c2589d5302a/dqc_reference/checkm_data
[2024-01-24 14:14:19,450] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:19,477] [INFO] Task started: CheckM
[2024-01-24 14:14:19,477] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009828745.1_ASM982874v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009828745.1_ASM982874v1_genomic.fna/checkm_input GCF_009828745.1_ASM982874v1_genomic.fna/checkm_result
[2024-01-24 14:14:45,631] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:45,632] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:45,653] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:45,653] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:45,653] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009828745.1_ASM982874v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:45,654] [INFO] Task started: Blastn
[2024-01-24 14:14:45,654] [INFO] Running command: blastn -query GCF_009828745.1_ASM982874v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45be19fd-8310-466b-991f-5c2589d5302a/dqc_reference/reference_markers_gtdb.fasta -out GCF_009828745.1_ASM982874v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:46,469] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:46,473] [INFO] Selected 17 target genomes.
[2024-01-24 14:14:46,473] [INFO] Target genome list was writen to GCF_009828745.1_ASM982874v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:46,491] [INFO] Task started: fastANI
[2024-01-24 14:14:46,491] [INFO] Running command: fastANI --query /var/lib/cwl/stg056de839-4e2e-4f44-bcd8-cf5f7931918d/GCF_009828745.1_ASM982874v1_genomic.fna.gz --refList GCF_009828745.1_ASM982874v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009828745.1_ASM982874v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:52,974] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:52,988] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:52,988] [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_011301115.1	s__Erysipelothrix sp011301115	98.842	658	717	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Erysipelothrix	95.0	98.38	96.88	0.92	0.88	5	conclusive
GCF_009828765.1	s__Erysipelothrix sp009828765	92.1708	603	717	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Erysipelothrix	95.0	97.70	95.43	0.92	0.86	3	-
GCF_011299615.1	s__Erysipelothrix sp011299615	79.1381	130	717	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Erysipelothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003931795.1	s__Erysipelothrix piscisicarius	78.4635	112	717	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Erysipelothrix	95.0	98.72	98.37	0.91	0.89	4	-
GCF_011400295.1	s__Erysipelothrix sp011400295	78.4326	116	717	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Erysipelothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637845.1	s__Erysipelothrix rhusiopathiae	78.4253	106	717	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Erysipelothrix	95.0	98.98	96.63	0.95	0.91	13	-
GCF_014396165.1	s__Erysipelothrix inopinata	78.3543	124	717	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Erysipelothrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:52,991] [INFO] GTDB search result was written to GCF_009828745.1_ASM982874v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:52,991] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:52,995] [INFO] DFAST_QC result json was written to GCF_009828745.1_ASM982874v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:52,996] [INFO] DFAST_QC completed!
[2024-01-24 14:14:52,996] [INFO] Total running time: 0h0m53s