[2024-01-24 12:06:14,736] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,738] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,739] [INFO] DQC Reference Directory: /var/lib/cwl/stg6380dfa4-92e1-4a62-a9fd-7d2474995f7e/dqc_reference
[2024-01-24 12:06:16,161] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:16,162] [INFO] Task started: Prodigal
[2024-01-24 12:06:16,162] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9c77e2b-46c5-4bcb-a23f-9dc6b93460ce/GCF_005405925.1_ASM540592v1_genomic.fna.gz | prodigal -d GCF_005405925.1_ASM540592v1_genomic.fna/cds.fna -a GCF_005405925.1_ASM540592v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:09,549] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:09,549] [INFO] Task started: HMMsearch
[2024-01-24 12:07:09,549] [INFO] Running command: hmmsearch --tblout GCF_005405925.1_ASM540592v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6380dfa4-92e1-4a62-a9fd-7d2474995f7e/dqc_reference/reference_markers.hmm GCF_005405925.1_ASM540592v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:10,019] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:10,020] [INFO] Found 6/6 markers.
[2024-01-24 12:07:10,110] [INFO] Query marker FASTA was written to GCF_005405925.1_ASM540592v1_genomic.fna/markers.fasta
[2024-01-24 12:07:10,110] [INFO] Task started: Blastn
[2024-01-24 12:07:10,110] [INFO] Running command: blastn -query GCF_005405925.1_ASM540592v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6380dfa4-92e1-4a62-a9fd-7d2474995f7e/dqc_reference/reference_markers.fasta -out GCF_005405925.1_ASM540592v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:11,404] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:11,408] [INFO] Selected 17 target genomes.
[2024-01-24 12:07:11,408] [INFO] Target genome list was writen to GCF_005405925.1_ASM540592v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:11,418] [INFO] Task started: fastANI
[2024-01-24 12:07:11,418] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9c77e2b-46c5-4bcb-a23f-9dc6b93460ce/GCF_005405925.1_ASM540592v1_genomic.fna.gz --refList GCF_005405925.1_ASM540592v1_genomic.fna/target_genomes.txt --output GCF_005405925.1_ASM540592v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:08:04,046] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:04,047] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6380dfa4-92e1-4a62-a9fd-7d2474995f7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:08:04,047] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6380dfa4-92e1-4a62-a9fd-7d2474995f7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:08:04,071] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:08:04,071] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:08:04,071] [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 antimycoticus	strain=NBRC 12839	GCA_005405925.1	68175	68175	type	True	100.0	3723	3724	95	inconclusive
Streptomyces yatensis	strain=DSM 41771	GCA_018069625.1	155177	155177	type	True	95.9875	3025	3724	95	inconclusive
Streptomyces iranensis	strain=DSM 41954	GCA_017874715.1	576784	576784	type	True	92.2768	2865	3724	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	92.2494	2994	3724	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_003675955.1	1226757	1226757	type	True	92.2195	3012	3724	95	below_threshold
Streptomyces sabulosicollis	strain=PRKS01-29	GCA_016103465.1	2715963	2715963	type	True	92.16	2272	3724	95	below_threshold
Streptomyces javensis	strain=DSM 41764	GCA_016103505.1	114698	114698	type	True	91.8026	2189	3724	95	below_threshold
Streptomyces hygroscopicus subsp. hygroscopicus	strain=NBRC 13472	GCA_001553455.1	68042	1912	type	True	90.4915	2123	3724	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	81.0514	1421	3724	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	80.3048	1323	3724	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	80.271	1499	3724	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	80.2392	1173	3724	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	80.1882	1451	3724	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	80.1663	1328	3724	95	below_threshold
Streptomyces griseoruber	strain=DSM 40281	GCA_001514205.1	1943	1943	type	True	80.1463	1526	3724	95	below_threshold
Streptomyces humi	strain=MUSC 119	GCA_001005085.2	1428620	1428620	type	True	79.8738	1550	3724	95	below_threshold
Streptomyces fuscichromogenes	strain=CGMCC 4.7110	GCA_014645815.1	1324013	1324013	type	True	79.8124	1543	3724	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:08:04,073] [INFO] DFAST Taxonomy check result was written to GCF_005405925.1_ASM540592v1_genomic.fna/tc_result.tsv
[2024-01-24 12:08:04,073] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:08:04,074] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:08:04,074] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6380dfa4-92e1-4a62-a9fd-7d2474995f7e/dqc_reference/checkm_data
[2024-01-24 12:08:04,075] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:08:04,171] [INFO] Task started: CheckM
[2024-01-24 12:08:04,171] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005405925.1_ASM540592v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005405925.1_ASM540592v1_genomic.fna/checkm_input GCF_005405925.1_ASM540592v1_genomic.fna/checkm_result
[2024-01-24 12:11:53,646] [INFO] Task succeeded: CheckM
[2024-01-24 12:11:53,647] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:11:53,684] [INFO] ===== Completeness check finished =====
[2024-01-24 12:11:53,684] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:11:53,684] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005405925.1_ASM540592v1_genomic.fna/markers.fasta)
[2024-01-24 12:11:53,685] [INFO] Task started: Blastn
[2024-01-24 12:11:53,685] [INFO] Running command: blastn -query GCF_005405925.1_ASM540592v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6380dfa4-92e1-4a62-a9fd-7d2474995f7e/dqc_reference/reference_markers_gtdb.fasta -out GCF_005405925.1_ASM540592v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:11:55,713] [INFO] Task succeeded: Blastn
[2024-01-24 12:11:55,719] [INFO] Selected 13 target genomes.
[2024-01-24 12:11:55,719] [INFO] Target genome list was writen to GCF_005405925.1_ASM540592v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:11:55,748] [INFO] Task started: fastANI
[2024-01-24 12:11:55,748] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9c77e2b-46c5-4bcb-a23f-9dc6b93460ce/GCF_005405925.1_ASM540592v1_genomic.fna.gz --refList GCF_005405925.1_ASM540592v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005405925.1_ASM540592v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:12:40,572] [INFO] Task succeeded: fastANI
[2024-01-24 12:12:40,605] [INFO] Found 13 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 12:12:40,605] [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_005405925.1	s__Streptomyces antimycoticus	100.0	3723	3724	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.0185	97.28	96.80	0.85	0.81	7	inconclusive
GCF_018069625.1	s__Streptomyces yatensis	95.9946	3024	3724	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.0185	N/A	N/A	N/A	N/A	1	-
GCF_000147815.2	s__Streptomyces violaceusniger_A	95.3318	2961	3724	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3301	95.69	95.54	0.80	0.80	4	inconclusive
GCF_017874715.1	s__Streptomyces iranensis	92.2896	2862	3724	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.67	99.98	99.98	1.00	1.00	2	-
GCF_018138715.1	s__Streptomyces asiaticus	92.1776	2890	3724	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	95.36	0.90	0.81	10	-
GCF_016741935.1	s__Streptomyces sp016741935	92.1691	2912	3724	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0488	N/A	N/A	N/A	N/A	1	-
GCA_005405945.1	s__Streptomyces violaceusniger	92.0243	2779	3724	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.67	97.67	0.85	0.85	2	-
GCF_015689475.1	s__Streptomyces solisilvae	92.0182	2816	3724	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.71	97.94	0.94	0.86	10	-
GCF_001553455.1	s__Streptomyces hygroscopicus	90.4933	2122	3724	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.24	98.00	0.92	0.90	7	-
GCF_008369065.1	s__Streptomyces sp008369065	80.3354	1468	3724	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	80.11	1537	3724	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814875.1	s__Streptomyces sp003814875	79.8622	1578	3724	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000242715.1	s__Streptomyces acidiscabies	79.002	1342	3724	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.11	97.67	0.95	0.89	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:12:40,608] [INFO] GTDB search result was written to GCF_005405925.1_ASM540592v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:12:40,608] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:12:40,613] [INFO] DFAST_QC result json was written to GCF_005405925.1_ASM540592v1_genomic.fna/dqc_result.json
[2024-01-24 12:12:40,613] [INFO] DFAST_QC completed!
[2024-01-24 12:12:40,613] [INFO] Total running time: 0h6m26s