[2024-01-24 11:59:13,821] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:13,824] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:13,824] [INFO] DQC Reference Directory: /var/lib/cwl/stg06beb38e-405e-4d4c-9ea5-32c1285ac362/dqc_reference
[2024-01-24 11:59:15,081] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:15,082] [INFO] Task started: Prodigal
[2024-01-24 11:59:15,082] [INFO] Running command: gunzip -c /var/lib/cwl/stg39678299-6b7c-46dc-ac91-2f3a7577c347/GCF_020037025.1_ASM2003702v1_genomic.fna.gz | prodigal -d GCF_020037025.1_ASM2003702v1_genomic.fna/cds.fna -a GCF_020037025.1_ASM2003702v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:33,813] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:33,814] [INFO] Task started: HMMsearch
[2024-01-24 11:59:33,814] [INFO] Running command: hmmsearch --tblout GCF_020037025.1_ASM2003702v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06beb38e-405e-4d4c-9ea5-32c1285ac362/dqc_reference/reference_markers.hmm GCF_020037025.1_ASM2003702v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:34,293] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:34,294] [INFO] Found 6/6 markers.
[2024-01-24 11:59:34,360] [INFO] Query marker FASTA was written to GCF_020037025.1_ASM2003702v1_genomic.fna/markers.fasta
[2024-01-24 11:59:34,361] [INFO] Task started: Blastn
[2024-01-24 11:59:34,361] [INFO] Running command: blastn -query GCF_020037025.1_ASM2003702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06beb38e-405e-4d4c-9ea5-32c1285ac362/dqc_reference/reference_markers.fasta -out GCF_020037025.1_ASM2003702v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:35,808] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:35,812] [INFO] Selected 22 target genomes.
[2024-01-24 11:59:35,812] [INFO] Target genome list was writen to GCF_020037025.1_ASM2003702v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:35,820] [INFO] Task started: fastANI
[2024-01-24 11:59:35,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg39678299-6b7c-46dc-ac91-2f3a7577c347/GCF_020037025.1_ASM2003702v1_genomic.fna.gz --refList GCF_020037025.1_ASM2003702v1_genomic.fna/target_genomes.txt --output GCF_020037025.1_ASM2003702v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:17,697] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:17,697] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06beb38e-405e-4d4c-9ea5-32c1285ac362/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:17,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06beb38e-405e-4d4c-9ea5-32c1285ac362/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:17,718] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:00:17,718] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:17,718] [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 huiliensis	strain=SCA2-4	GCA_020037025.1	2876027	2876027	type	True	100.0	2286	2305	95	conclusive
Streptomyces mobaraensis	strain=DSM 40847	GCA_017916255.1	35621	35621	type	True	92.2329	1873	2305	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_000342125.1	35621	35621	type	True	92.1492	1788	2305	95	below_threshold
Streptomyces caatingaensis	strain=CMAA 1322	GCA_001187435.1	1678637	1678637	type	True	85.6054	1496	2305	95	below_threshold
Streptomyces olivoverticillatus	strain=CECT 3266	GCA_014203555.1	66427	66427	type	True	84.2186	1198	2305	95	below_threshold
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	83.8796	1352	2305	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	83.8533	1358	2305	95	below_threshold
Streptomyces morookaense	strain=JCM 4793	GCA_014656115.1	1970	1970	type	True	83.5119	1313	2305	95	below_threshold
Streptomyces eurocidicus	strain=NRRL ISP-5604	GCA_015475845.1	66423	66423	type	True	83.3863	1364	2305	95	below_threshold
Streptomyces eurocidicus	strain=ATCC 27428	GCA_002891295.1	66423	66423	type	True	83.3392	1379	2305	95	below_threshold
Streptomyces klenkii	strain=KCTC 29202	GCA_003626645.1	1420899	1420899	type	True	83.3384	1371	2305	95	below_threshold
Streptomyces roseifaciens	strain=MBT76	GCA_001445655.1	1488406	1488406	type	True	83.3168	1410	2305	95	below_threshold
Streptomyces hiroshimensis	strain=JCM 4586	GCA_014650335.1	66424	66424	type	True	83.2402	1364	2305	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	83.0219	1401	2305	95	below_threshold
Streptomyces orinoci	strain=NRRL B-3379	GCA_003121295.1	67339	67339	type	True	82.9082	1261	2305	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	80.7808	1115	2305	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	80.6668	998	2305	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	80.6335	1193	2305	95	below_threshold
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	80.5985	1164	2305	95	below_threshold
Streptomyces durbertensis	strain=DSM 104538	GCA_014156695.1	2448886	2448886	type	True	80.5733	777	2305	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	80.4491	1139	2305	95	below_threshold
Actinacidiphila rubida	strain=CGMCC 4.2026	GCA_900110255.1	310780	310780	type	True	79.6637	1071	2305	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:17,720] [INFO] DFAST Taxonomy check result was written to GCF_020037025.1_ASM2003702v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:17,720] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:17,720] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:17,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06beb38e-405e-4d4c-9ea5-32c1285ac362/dqc_reference/checkm_data
[2024-01-24 12:00:17,722] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:17,790] [INFO] Task started: CheckM
[2024-01-24 12:00:17,791] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020037025.1_ASM2003702v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020037025.1_ASM2003702v1_genomic.fna/checkm_input GCF_020037025.1_ASM2003702v1_genomic.fna/checkm_result
[2024-01-24 12:01:44,997] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:44,998] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:45,026] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:45,026] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:45,027] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020037025.1_ASM2003702v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:45,027] [INFO] Task started: Blastn
[2024-01-24 12:01:45,027] [INFO] Running command: blastn -query GCF_020037025.1_ASM2003702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06beb38e-405e-4d4c-9ea5-32c1285ac362/dqc_reference/reference_markers_gtdb.fasta -out GCF_020037025.1_ASM2003702v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:47,299] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:47,303] [INFO] Selected 18 target genomes.
[2024-01-24 12:01:47,303] [INFO] Target genome list was writen to GCF_020037025.1_ASM2003702v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:47,316] [INFO] Task started: fastANI
[2024-01-24 12:01:47,316] [INFO] Running command: fastANI --query /var/lib/cwl/stg39678299-6b7c-46dc-ac91-2f3a7577c347/GCF_020037025.1_ASM2003702v1_genomic.fna.gz --refList GCF_020037025.1_ASM2003702v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020037025.1_ASM2003702v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:02:21,728] [INFO] Task succeeded: fastANI
[2024-01-24 12:02:21,745] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:02:21,745] [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_014253015.1	s__Streptomyces sp014253015	92.3838	1823	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916255.1	s__Streptomyces mobaraensis	92.2426	1872	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.59	99.19	0.96	0.92	3	-
GCF_013055795.1	s__Streptomyces sp013055795	88.8032	1711	2305	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	85.9845	1470	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187435.1	s__Streptomyces caatingaensis	85.6278	1493	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203555.1	s__Streptomyces olivoverticillatus	84.2533	1194	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002939475.1	s__Streptomyces cinnamoneus_A	83.8206	1305	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014650495.1	s__Streptomyces cinnamoneus	83.786	1351	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018614525.1	s__Streptomyces sp018614525	83.5935	1218	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003011965.1	s__Streptomyces nondiastaticus	83.4843	1315	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2548	N/A	N/A	N/A	N/A	1	-
GCF_000719265.1	s__Streptomyces roseoverticillatus	83.3736	1318	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2548	N/A	N/A	N/A	N/A	1	-
GCF_003626645.1	s__Streptomyces klenkii	83.3699	1365	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.37	99.37	0.96	0.96	2	-
GCF_002192455.1	s__Streptomyces albireticuli_B	83.3485	1400	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001445655.1	s__Streptomyces roseifaciens	83.2995	1413	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.88	0.88	2	-
GCF_003270085.1	s__Streptomyces triticisoli	80.7176	952	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001746425.1	s__Streptomyces subrutilus_A	80.6125	1071	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001278075.1	s__Streptomyces pristinaespiralis	80.4722	1078	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.86	99.72	0.99	0.98	3	-
GCF_019049285.1	s__Streptomyces sp019049285	80.1945	1099	2305	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 12:02:21,747] [INFO] GTDB search result was written to GCF_020037025.1_ASM2003702v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:02:21,747] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:02:21,752] [INFO] DFAST_QC result json was written to GCF_020037025.1_ASM2003702v1_genomic.fna/dqc_result.json
[2024-01-24 12:02:21,752] [INFO] DFAST_QC completed!
[2024-01-24 12:02:21,752] [INFO] Total running time: 0h3m8s