[2024-01-24 14:55:25,988] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:25,992] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:25,992] [INFO] DQC Reference Directory: /var/lib/cwl/stgf17ac211-e8b0-46eb-ad2e-1a52d6683feb/dqc_reference
[2024-01-24 14:55:27,344] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:27,345] [INFO] Task started: Prodigal
[2024-01-24 14:55:27,345] [INFO] Running command: gunzip -c /var/lib/cwl/stg97c40bc5-32fd-47de-8bdc-f309ff0c48d2/GCF_000718255.1_ASM71825v1_genomic.fna.gz | prodigal -d GCF_000718255.1_ASM71825v1_genomic.fna/cds.fna -a GCF_000718255.1_ASM71825v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:42,989] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:42,989] [INFO] Task started: HMMsearch
[2024-01-24 14:55:42,990] [INFO] Running command: hmmsearch --tblout GCF_000718255.1_ASM71825v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf17ac211-e8b0-46eb-ad2e-1a52d6683feb/dqc_reference/reference_markers.hmm GCF_000718255.1_ASM71825v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:43,337] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:43,339] [INFO] Found 6/6 markers.
[2024-01-24 14:55:43,394] [INFO] Query marker FASTA was written to GCF_000718255.1_ASM71825v1_genomic.fna/markers.fasta
[2024-01-24 14:55:43,394] [INFO] Task started: Blastn
[2024-01-24 14:55:43,394] [INFO] Running command: blastn -query GCF_000718255.1_ASM71825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf17ac211-e8b0-46eb-ad2e-1a52d6683feb/dqc_reference/reference_markers.fasta -out GCF_000718255.1_ASM71825v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:44,796] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:44,799] [INFO] Selected 24 target genomes.
[2024-01-24 14:55:44,800] [INFO] Target genome list was writen to GCF_000718255.1_ASM71825v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:44,809] [INFO] Task started: fastANI
[2024-01-24 14:55:44,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg97c40bc5-32fd-47de-8bdc-f309ff0c48d2/GCF_000718255.1_ASM71825v1_genomic.fna.gz --refList GCF_000718255.1_ASM71825v1_genomic.fna/target_genomes.txt --output GCF_000718255.1_ASM71825v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:30,289] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:30,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf17ac211-e8b0-46eb-ad2e-1a52d6683feb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:30,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf17ac211-e8b0-46eb-ad2e-1a52d6683feb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:30,308] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:56:30,308] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:56:30,308] [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
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	84.1224	1290	1977	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	84.0153	1246	1977	95	below_threshold
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	83.8802	1386	1977	95	below_threshold
Actinomadura darangshiensis	strain=DSM 45941	GCA_004349235.1	705336	705336	type	True	83.8618	1294	1977	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	83.7675	1432	1977	95	below_threshold
Actinomadura coerulea	strain=JCM 3320	GCA_014648535.1	46159	46159	type	True	83.7596	1366	1977	95	below_threshold
Actinomadura rubrisoli	strain=H3C3	GCA_004349215.1	2530368	2530368	type	True	83.7453	1242	1977	95	below_threshold
Actinomadura formosensis	strain=NBRC 14204	GCA_001552155.1	60706	60706	type	True	83.741	1239	1977	95	below_threshold
Actinomadura citrea	strain=DSM 43461	GCA_013409045.1	46158	46158	type	True	83.7387	1405	1977	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	83.7043	1417	1977	95	below_threshold
Actinomadura citrea	strain=JCM 3295	GCA_014648455.1	46158	46158	type	True	83.6701	1404	1977	95	below_threshold
Actinomadura coerulea	strain=DSM 43675	GCA_014208105.1	46159	46159	type	True	83.6637	1383	1977	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	83.6558	1388	1977	95	below_threshold
Actinomadura mexicana	strain=DSM 44485	GCA_900188105.1	134959	134959	type	True	83.568	1384	1977	95	below_threshold
Actinomadura decatromicini	strain=CYP1-5	GCA_008121305.1	2604572	2604572	type	True	83.3482	1337	1977	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	83.1491	1294	1977	95	below_threshold
Actinomadura cremea	strain=JCM 3308	GCA_014648495.1	1991	1991	type	True	83.1181	1351	1977	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	82.646	1191	1977	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	81.985	1266	1977	95	below_threshold
Actinomadura viridis	strain=DSM 43175	GCA_015751755.1	58110	58110	type	True	81.5679	1236	1977	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	81.4839	1220	1977	95	below_threshold
Thermomonospora catenispora	strain=3-22-3	GCA_006363815.1	2493090	2493090	type	True	80.0694	903	1977	95	below_threshold
Actinoallomurus spadix	strain=KCTC 9252	GCA_024055725.1	79912	79912	type	True	78.9898	861	1977	95	below_threshold
Actinoallomurus bryophytorum	strain=DSM 102200	GCA_006716425.1	1490222	1490222	type	True	78.4206	788	1977	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:30,310] [INFO] DFAST Taxonomy check result was written to GCF_000718255.1_ASM71825v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:30,311] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:30,311] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:30,311] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf17ac211-e8b0-46eb-ad2e-1a52d6683feb/dqc_reference/checkm_data
[2024-01-24 14:56:30,312] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:30,370] [INFO] Task started: CheckM
[2024-01-24 14:56:30,370] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000718255.1_ASM71825v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000718255.1_ASM71825v1_genomic.fna/checkm_input GCF_000718255.1_ASM71825v1_genomic.fna/checkm_result
[2024-01-24 14:57:39,047] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:39,048] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:39,072] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:39,072] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:39,072] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000718255.1_ASM71825v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:39,073] [INFO] Task started: Blastn
[2024-01-24 14:57:39,073] [INFO] Running command: blastn -query GCF_000718255.1_ASM71825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf17ac211-e8b0-46eb-ad2e-1a52d6683feb/dqc_reference/reference_markers_gtdb.fasta -out GCF_000718255.1_ASM71825v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:41,192] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:41,199] [INFO] Selected 20 target genomes.
[2024-01-24 14:57:41,199] [INFO] Target genome list was writen to GCF_000718255.1_ASM71825v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:41,218] [INFO] Task started: fastANI
[2024-01-24 14:57:41,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg97c40bc5-32fd-47de-8bdc-f309ff0c48d2/GCF_000718255.1_ASM71825v1_genomic.fna.gz --refList GCF_000718255.1_ASM71825v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000718255.1_ASM71825v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:58:20,407] [INFO] Task succeeded: fastANI
[2024-01-24 14:58:20,424] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:58:20,424] [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_000718255.1	s__Spirillospora albida	100.0	1976	1977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004348335.1	s__Spirillospora bangladeshensis	84.0805	1295	1977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005889745.1	s__Spirillospora geliboluensis	84.0762	1241	1977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013211575.1	s__Spirillospora verrucosospora	83.876	1426	1977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.82	95.82	0.89	0.89	2	-
GCF_004349235.1	s__Spirillospora darangshiensis	83.8482	1296	1977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008923205.2	s__Spirillospora physcomitrii	83.788	1397	1977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008327685.1	s__Spirillospora sp008327685	83.7701	1440	1977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409045.1	s__Spirillospora citrea	83.7415	1405	1977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004349215.1	s__Spirillospora rubrisoli	83.7145	1245	1977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014208105.1	s__Spirillospora coerulea	83.6882	1379	1977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900659615.1	s__Spirillospora fibrosa	83.6872	1358	1977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008923365.1	s__Spirillospora montaniterrae	83.6525	1389	1977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188105.1	s__Spirillospora mexicana	83.6043	1378	1977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409365.1	s__Spirillospora luteofluorescens	83.5874	1420	1977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006547145.1	s__Spirillospora sp006547145	83.5841	1415	1977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348535.1	s__Spirillospora sp004348535	83.3873	1189	1977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015751755.1	s__Spirillospora viridis	81.5703	1236	1977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003589885.1	s__Thermomonospora amylolytica	80.5751	1061	1977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	98.39	98.39	0.92	0.92	2	-
GCF_003289645.1	s__Actinomadura_D craniellae	80.0477	1008	1977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006363815.1	s__Thermomonospora catenispora	80.0142	914	1977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:58:20,426] [INFO] GTDB search result was written to GCF_000718255.1_ASM71825v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:58:20,426] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:58:20,432] [INFO] DFAST_QC result json was written to GCF_000718255.1_ASM71825v1_genomic.fna/dqc_result.json
[2024-01-24 14:58:20,433] [INFO] DFAST_QC completed!
[2024-01-24 14:58:20,433] [INFO] Total running time: 0h2m54s