[2024-01-24 13:37:04,995] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:04,998] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:04,998] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b2a4f3f-6a7d-41ee-ac8c-92f066b6201d/dqc_reference
[2024-01-24 13:37:06,267] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:06,268] [INFO] Task started: Prodigal
[2024-01-24 13:37:06,268] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d8e929e-efda-4683-bbdc-2909727e0a1c/GCF_014650535.1_ASM1465053v1_genomic.fna.gz | prodigal -d GCF_014650535.1_ASM1465053v1_genomic.fna/cds.fna -a GCF_014650535.1_ASM1465053v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:29,098] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:29,098] [INFO] Task started: HMMsearch
[2024-01-24 13:37:29,098] [INFO] Running command: hmmsearch --tblout GCF_014650535.1_ASM1465053v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b2a4f3f-6a7d-41ee-ac8c-92f066b6201d/dqc_reference/reference_markers.hmm GCF_014650535.1_ASM1465053v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:29,611] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:29,612] [INFO] Found 6/6 markers.
[2024-01-24 13:37:29,674] [INFO] Query marker FASTA was written to GCF_014650535.1_ASM1465053v1_genomic.fna/markers.fasta
[2024-01-24 13:37:29,674] [INFO] Task started: Blastn
[2024-01-24 13:37:29,674] [INFO] Running command: blastn -query GCF_014650535.1_ASM1465053v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b2a4f3f-6a7d-41ee-ac8c-92f066b6201d/dqc_reference/reference_markers.fasta -out GCF_014650535.1_ASM1465053v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:31,053] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:31,056] [INFO] Selected 17 target genomes.
[2024-01-24 13:37:31,056] [INFO] Target genome list was writen to GCF_014650535.1_ASM1465053v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:31,064] [INFO] Task started: fastANI
[2024-01-24 13:37:31,064] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d8e929e-efda-4683-bbdc-2909727e0a1c/GCF_014650535.1_ASM1465053v1_genomic.fna.gz --refList GCF_014650535.1_ASM1465053v1_genomic.fna/target_genomes.txt --output GCF_014650535.1_ASM1465053v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:10,325] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:10,326] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b2a4f3f-6a7d-41ee-ac8c-92f066b6201d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:10,326] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b2a4f3f-6a7d-41ee-ac8c-92f066b6201d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:10,340] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:38:10,340] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:38:10,341] [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 galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	100.0	2558	2558	95	conclusive
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	99.9864	2537	2558	95	conclusive
Streptomyces longwoodensis	strain=DSM 41677	GCA_001514125.1	68231	68231	type	True	94.8833	2232	2558	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	86.0585	1818	2558	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	85.3172	1722	2558	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	85.3032	1682	2558	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	85.2813	1458	2558	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.2677	1704	2558	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.1287	1431	2558	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	85.0862	1672	2558	95	below_threshold
Streptomyces nigra	strain=452	GCA_003074055.1	1827580	1827580	type	True	85.0498	1653	2558	95	below_threshold
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	85.0431	1663	2558	95	below_threshold
Streptomyces gossypiisoli	strain=TRM 44567	GCA_013433285.1	2748864	2748864	type	True	85.0292	1678	2558	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	85.0191	1677	2558	95	below_threshold
Streptomyces fodineus	strain=TW1S1	GCA_001735805.1	1904616	1904616	type	True	84.712	1695	2558	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	84.6336	1302	2558	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	84.3821	1706	2558	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:10,342] [INFO] DFAST Taxonomy check result was written to GCF_014650535.1_ASM1465053v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:10,343] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:10,343] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:10,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b2a4f3f-6a7d-41ee-ac8c-92f066b6201d/dqc_reference/checkm_data
[2024-01-24 13:38:10,344] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:10,421] [INFO] Task started: CheckM
[2024-01-24 13:38:10,421] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650535.1_ASM1465053v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650535.1_ASM1465053v1_genomic.fna/checkm_input GCF_014650535.1_ASM1465053v1_genomic.fna/checkm_result
[2024-01-24 13:39:58,638] [INFO] Task succeeded: CheckM
[2024-01-24 13:39:58,640] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:39:58,664] [INFO] ===== Completeness check finished =====
[2024-01-24 13:39:58,664] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:39:58,665] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650535.1_ASM1465053v1_genomic.fna/markers.fasta)
[2024-01-24 13:39:58,665] [INFO] Task started: Blastn
[2024-01-24 13:39:58,665] [INFO] Running command: blastn -query GCF_014650535.1_ASM1465053v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b2a4f3f-6a7d-41ee-ac8c-92f066b6201d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650535.1_ASM1465053v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:00,782] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:00,786] [INFO] Selected 19 target genomes.
[2024-01-24 13:40:00,786] [INFO] Target genome list was writen to GCF_014650535.1_ASM1465053v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:40:00,838] [INFO] Task started: fastANI
[2024-01-24 13:40:00,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d8e929e-efda-4683-bbdc-2909727e0a1c/GCF_014650535.1_ASM1465053v1_genomic.fna.gz --refList GCF_014650535.1_ASM1465053v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650535.1_ASM1465053v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:40:42,178] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:42,194] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:40:42,195] [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_005280195.1	s__Streptomyces galbus	99.9864	2537	2558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.53	0.96	0.94	3	conclusive
GCF_001514125.1	s__Streptomyces longwoodensis	94.887	2231	2558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.95	95.95	0.86	0.86	2	-
GCF_014656055.1	s__Streptomyces griseosporeus	86.0509	1819	2558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.70	98.69	0.95	0.95	3	-
GCF_002019855.1	s__Streptomyces antibioticus_B	85.9127	1750	2558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.20	96.76	0.94	0.90	5	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	85.869	1794	2558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363835.1	s__Streptomyces sp004363835	85.6672	1802	2558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514205.1	s__Streptomyces griseoruber	85.6642	1783	2558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011193355.1	s__Streptomyces sp011193355	85.6169	1693	2558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000761215.1	s__Streptomyces glaucescens	85.4573	1700	2558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203535.1	s__Streptomyces griseostramineus	85.2849	1684	2558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.88	99.76	0.99	0.98	3	-
GCF_019219825.1	s__Streptomyces sp019219825	85.2088	1615	2558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143935.1	s__Streptomyces sp003143935	85.1815	1778	2558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715395.1	s__Streptomyces sp006715395	85.1023	1785	2558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.35	95.35	0.79	0.79	2	-
GCF_008973465.1	s__Streptomyces sp008973465	85.0479	1683	2558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003074055.1	s__Streptomyces nigra	85.0022	1661	2558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.21	97.15	0.92	0.91	4	-
GCF_001735805.1	s__Streptomyces fodineus	84.7293	1690	2558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049285.1	s__Streptomyces sp019049285	84.6338	1667	2558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857135.1	s__Streptomyces sp009857135	83.9793	1556	2558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009862265.1	s__Streptomyces sp009862265	83.7263	1407	2558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:40:42,196] [INFO] GTDB search result was written to GCF_014650535.1_ASM1465053v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:40:42,197] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:40:42,206] [INFO] DFAST_QC result json was written to GCF_014650535.1_ASM1465053v1_genomic.fna/dqc_result.json
[2024-01-24 13:40:42,206] [INFO] DFAST_QC completed!
[2024-01-24 13:40:42,207] [INFO] Total running time: 0h3m37s