[2024-01-25 20:06:35,587] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:06:35,599] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:06:35,599] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7561ddc-5f10-4647-abf3-8577f483d1cf/dqc_reference
[2024-01-25 20:06:36,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:06:36,788] [INFO] Task started: Prodigal
[2024-01-25 20:06:36,788] [INFO] Running command: gunzip -c /var/lib/cwl/stg31cf94e2-b490-46cc-bc10-fb83b321fb23/GCF_016481305.1_ASM1648130v1_genomic.fna.gz | prodigal -d GCF_016481305.1_ASM1648130v1_genomic.fna/cds.fna -a GCF_016481305.1_ASM1648130v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:06:39,747] [INFO] Task succeeded: Prodigal
[2024-01-25 20:06:39,747] [INFO] Task started: HMMsearch
[2024-01-25 20:06:39,748] [INFO] Running command: hmmsearch --tblout GCF_016481305.1_ASM1648130v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7561ddc-5f10-4647-abf3-8577f483d1cf/dqc_reference/reference_markers.hmm GCF_016481305.1_ASM1648130v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:06:39,974] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:06:39,975] [INFO] Found 6/6 markers.
[2024-01-25 20:06:39,991] [INFO] Query marker FASTA was written to GCF_016481305.1_ASM1648130v1_genomic.fna/markers.fasta
[2024-01-25 20:06:39,991] [INFO] Task started: Blastn
[2024-01-25 20:06:39,991] [INFO] Running command: blastn -query GCF_016481305.1_ASM1648130v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7561ddc-5f10-4647-abf3-8577f483d1cf/dqc_reference/reference_markers.fasta -out GCF_016481305.1_ASM1648130v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:40,544] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:40,547] [INFO] Selected 20 target genomes.
[2024-01-25 20:06:40,548] [INFO] Target genome list was writen to GCF_016481305.1_ASM1648130v1_genomic.fna/target_genomes.txt
[2024-01-25 20:06:40,570] [INFO] Task started: fastANI
[2024-01-25 20:06:40,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg31cf94e2-b490-46cc-bc10-fb83b321fb23/GCF_016481305.1_ASM1648130v1_genomic.fna.gz --refList GCF_016481305.1_ASM1648130v1_genomic.fna/target_genomes.txt --output GCF_016481305.1_ASM1648130v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:06:47,583] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:47,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7561ddc-5f10-4647-abf3-8577f483d1cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:06:47,583] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7561ddc-5f10-4647-abf3-8577f483d1cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:06:47,591] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:06:47,591] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:06:47,592] [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
Streptococcus pacificus	strain=CSL7591	GCA_016481305.1	2740577	2740577	type	True	100.0	544	546	95	conclusive
Streptococcus zalophi	strain=CSL7508	GCA_016481285.1	640031	640031	type	True	87.8449	453	546	95	below_threshold
Streptococcus marimammalium	strain=DSM 18627	GCA_000380045.1	269666	269666	type	True	84.6152	403	546	95	below_threshold
Streptococcus lutetiensis	strain=NCTC13774	GCA_900475675.1	150055	150055	type	True	78.4419	91	546	95	below_threshold
Streptococcus vicugnae	strain=SL1232	GCA_016461705.1	2740579	2740579	type	True	78.3092	98	546	95	below_threshold
Streptococcus agalactiae	strain=NCTC8181	GCA_900458965.1	1311	1311	suspected-type	True	78.2714	92	546	95	below_threshold
Streptococcus agalactiae	strain=ATCC 13813	GCA_000186445.1	1311	1311	type	True	78.1966	88	546	95	below_threshold
Streptococcus catagoni	strain=99-1/2017	GCA_011421425.1	2654874	2654874	type	True	78.0861	89	546	95	below_threshold
Streptococcus penaeicida	strain=CAIM 1838	GCA_002887775.1	1765960	1765960	type	True	78.053	98	546	95	below_threshold
Streptococcus pyogenes	strain=PartK-Spyogenes-RM8376	GCA_022869605.1	1314	1314	type	True	78.0511	93	546	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	78.029	68	546	95	below_threshold
Streptococcus didelphis	strain=DSM 15616	GCA_000380005.1	102886	102886	type	True	77.9405	108	546	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:06:47,593] [INFO] DFAST Taxonomy check result was written to GCF_016481305.1_ASM1648130v1_genomic.fna/tc_result.tsv
[2024-01-25 20:06:47,593] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:06:47,593] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:06:47,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7561ddc-5f10-4647-abf3-8577f483d1cf/dqc_reference/checkm_data
[2024-01-25 20:06:47,594] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:06:47,614] [INFO] Task started: CheckM
[2024-01-25 20:06:47,614] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016481305.1_ASM1648130v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016481305.1_ASM1648130v1_genomic.fna/checkm_input GCF_016481305.1_ASM1648130v1_genomic.fna/checkm_result
[2024-01-25 20:07:02,818] [INFO] Task succeeded: CheckM
[2024-01-25 20:07:02,819] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:07:02,834] [INFO] ===== Completeness check finished =====
[2024-01-25 20:07:02,834] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:07:02,834] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016481305.1_ASM1648130v1_genomic.fna/markers.fasta)
[2024-01-25 20:07:02,834] [INFO] Task started: Blastn
[2024-01-25 20:07:02,834] [INFO] Running command: blastn -query GCF_016481305.1_ASM1648130v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7561ddc-5f10-4647-abf3-8577f483d1cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_016481305.1_ASM1648130v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:03,634] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:03,636] [INFO] Selected 17 target genomes.
[2024-01-25 20:07:03,636] [INFO] Target genome list was writen to GCF_016481305.1_ASM1648130v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:07:03,655] [INFO] Task started: fastANI
[2024-01-25 20:07:03,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg31cf94e2-b490-46cc-bc10-fb83b321fb23/GCF_016481305.1_ASM1648130v1_genomic.fna.gz --refList GCF_016481305.1_ASM1648130v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016481305.1_ASM1648130v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:07:10,397] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:10,406] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:07:10,406] [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_016481305.1	s__Streptococcus pacificus	100.0	544	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016481285.1	s__Streptococcus zalophi	87.8449	453	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380045.1	s__Streptococcus marimammalium	84.6152	403	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003674745.1	s__Streptococcus iniae	78.3546	90	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.92	98.80	0.96	0.87	94	-
GCF_900101445.1	s__Streptococcus equinus_B	78.3532	90	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.22	0.90	0.87	9	-
GCF_016461705.1	s__Streptococcus vicugnae	78.3092	98	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.43	98.30	0.94	0.90	4	-
GCF_000186445.1	s__Streptococcus agalactiae	78.2042	89	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.63	98.18	0.88	0.63	1516	-
GCA_905221325.1	s__Streptococcus sp905221325	78.1897	68	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015594605.1	s__Streptococcus sp015594605	78.1615	81	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002055535.1	s__Streptococcus pyogenes	78.144	93	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.85	98.36	0.95	0.87	2144	-
GCF_002887775.1	s__Streptococcus penaeicida	78.053	98	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104225.1	s__Streptococcus equinus_D	78.0035	96	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001074155.1	s__Streptococcus pseudopneumoniae_A	77.9417	59	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:07:10,407] [INFO] GTDB search result was written to GCF_016481305.1_ASM1648130v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:07:10,408] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:07:10,412] [INFO] DFAST_QC result json was written to GCF_016481305.1_ASM1648130v1_genomic.fna/dqc_result.json
[2024-01-25 20:07:10,412] [INFO] DFAST_QC completed!
[2024-01-25 20:07:10,412] [INFO] Total running time: 0h0m35s