[2024-01-24 13:55:15,060] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:15,062] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:15,062] [INFO] DQC Reference Directory: /var/lib/cwl/stg79324902-a09e-4ea9-bbc6-a2221399ea54/dqc_reference
[2024-01-24 13:55:16,429] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:16,430] [INFO] Task started: Prodigal
[2024-01-24 13:55:16,431] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9066e5d-b5ce-406c-b5cb-95041719a39d/GCF_014930365.1_ASM1493036v1_genomic.fna.gz | prodigal -d GCF_014930365.1_ASM1493036v1_genomic.fna/cds.fna -a GCF_014930365.1_ASM1493036v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:49,724] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:49,725] [INFO] Task started: HMMsearch
[2024-01-24 13:55:49,725] [INFO] Running command: hmmsearch --tblout GCF_014930365.1_ASM1493036v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79324902-a09e-4ea9-bbc6-a2221399ea54/dqc_reference/reference_markers.hmm GCF_014930365.1_ASM1493036v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:50,202] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:50,203] [INFO] Found 6/6 markers.
[2024-01-24 13:55:50,288] [INFO] Query marker FASTA was written to GCF_014930365.1_ASM1493036v1_genomic.fna/markers.fasta
[2024-01-24 13:55:50,289] [INFO] Task started: Blastn
[2024-01-24 13:55:50,289] [INFO] Running command: blastn -query GCF_014930365.1_ASM1493036v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79324902-a09e-4ea9-bbc6-a2221399ea54/dqc_reference/reference_markers.fasta -out GCF_014930365.1_ASM1493036v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:51,693] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:51,697] [INFO] Selected 16 target genomes.
[2024-01-24 13:55:51,697] [INFO] Target genome list was writen to GCF_014930365.1_ASM1493036v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:51,716] [INFO] Task started: fastANI
[2024-01-24 13:55:51,717] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9066e5d-b5ce-406c-b5cb-95041719a39d/GCF_014930365.1_ASM1493036v1_genomic.fna.gz --refList GCF_014930365.1_ASM1493036v1_genomic.fna/target_genomes.txt --output GCF_014930365.1_ASM1493036v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:33,637] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:33,638] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79324902-a09e-4ea9-bbc6-a2221399ea54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:33,638] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79324902-a09e-4ea9-bbc6-a2221399ea54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:33,662] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:33,663] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:33,663] [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
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	100.0	3609	3612	95	conclusive
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	93.728	2761	3612	95	below_threshold
Streptomyces brasiliscabiei	strain=IBSBF 2867	GCA_018927715.1	2736302	2736302	type	True	90.4523	2437	3612	95	below_threshold
Streptomyces phaeolivaceus	strain=GY16	GCA_009184865.1	2653200	2653200	type	True	90.2717	2447	3612	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000340335.2	42235	42235	type	True	90.0722	2357	3612	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000383595.1	42235	42235	type	True	90.0566	2354	3612	95	below_threshold
Streptomyces stelliscabiei	strain=DSM 41803	GCA_014873495.1	146820	146820	type	True	90.0481	2533	3612	95	below_threshold
Streptomyces adelaidensis	strain=CAP261	GCA_016598475.1	2796465	2796465	type	True	89.0488	2248	3612	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	87.6617	1912	3612	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	87.4684	2297	3612	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.1583	2049	3612	95	below_threshold
Streptomyces hokutonensis	strain=R1-NS-10	GCA_000376565.1	1306990	1306990	type	True	83.5008	1963	3612	95	below_threshold
Streptomyces bungoensis	strain=DSM 41781	GCA_001514215.1	285568	285568	type	True	83.2109	1723	3612	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	82.9719	1768	3612	95	below_threshold
Actinacidiphila glaucinigra	strain=CGMCC 4.1858	GCA_900188405.1	235986	235986	type	True	79.9031	1421	3612	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	79.8147	1136	3612	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:33,678] [INFO] DFAST Taxonomy check result was written to GCF_014930365.1_ASM1493036v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:33,679] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:33,679] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:33,680] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79324902-a09e-4ea9-bbc6-a2221399ea54/dqc_reference/checkm_data
[2024-01-24 13:56:33,681] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:33,781] [INFO] Task started: CheckM
[2024-01-24 13:56:33,781] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014930365.1_ASM1493036v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014930365.1_ASM1493036v1_genomic.fna/checkm_input GCF_014930365.1_ASM1493036v1_genomic.fna/checkm_result
[2024-01-24 13:58:38,824] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:38,825] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:38,848] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:38,848] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:38,849] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014930365.1_ASM1493036v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:38,849] [INFO] Task started: Blastn
[2024-01-24 13:58:38,849] [INFO] Running command: blastn -query GCF_014930365.1_ASM1493036v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79324902-a09e-4ea9-bbc6-a2221399ea54/dqc_reference/reference_markers_gtdb.fasta -out GCF_014930365.1_ASM1493036v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:41,126] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:41,129] [INFO] Selected 15 target genomes.
[2024-01-24 13:58:41,129] [INFO] Target genome list was writen to GCF_014930365.1_ASM1493036v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:41,146] [INFO] Task started: fastANI
[2024-01-24 13:58:41,147] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9066e5d-b5ce-406c-b5cb-95041719a39d/GCF_014930365.1_ASM1493036v1_genomic.fna.gz --refList GCF_014930365.1_ASM1493036v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014930365.1_ASM1493036v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:21,005] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:21,020] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:21,021] [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_900114955.1	s__Streptomyces sp900114955	99.4514	3036	3612	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.68	97.04	0.90	0.85	10	conclusive
GCF_000772895.1	s__Streptomyces galbus_A	92.9624	2677	3612	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203845.1	s__Streptomyces scabiei_E	92.5039	2463	3612	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.38	0.80	0.80	2	-
GCF_018927715.1	s__Streptomyces brasiliscabiei	90.487	2431	3612	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184865.1	s__Streptomyces phaeolivaceus	90.272	2447	3612	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001550375.1	s__Streptomyces europaeiscabiei	90.0717	2242	3612	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.72	96.30	0.83	0.82	3	-
GCF_014873495.1	s__Streptomyces stelliscabiei	90.0608	2532	3612	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.87	99.68	0.98	0.96	4	-
GCF_000383595.1	s__Streptomyces bottropensis	90.0479	2356	3612	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.99	99.99	1.00	1.00	3	-
GCF_016598475.1	s__Streptomyces adelaidensis	89.0528	2247	3612	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103585.1	s__Streptomyces sp900103585	84.0672	2090	3612	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014673495.1	s__Streptomyces griseofuscus	82.5983	1647	3612	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	97.0065	98.75	98.11	0.94	0.90	10	-
GCF_007595705.1	s__Streptomyces sp007595705	80.3266	1343	3612	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999245.1	s__Streptomyces sp015999245	80.1991	1194	3612	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188405.1	s__Streptomyces glauciniger	79.8758	1425	3612	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.09	95.09	0.86	0.86	3	-
GCF_015776785.2	s__Kitasatospora sp015776785	78.6814	1007	3612	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:21,022] [INFO] GTDB search result was written to GCF_014930365.1_ASM1493036v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:21,023] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:21,027] [INFO] DFAST_QC result json was written to GCF_014930365.1_ASM1493036v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:21,027] [INFO] DFAST_QC completed!
[2024-01-24 13:59:21,027] [INFO] Total running time: 0h4m6s