[2024-01-24 13:49:45,516] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:45,518] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:45,519] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c76b74c-2927-4a13-a7b7-cf6dc1534166/dqc_reference
[2024-01-24 13:49:46,969] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:46,970] [INFO] Task started: Prodigal
[2024-01-24 13:49:46,970] [INFO] Running command: gunzip -c /var/lib/cwl/stg647bc3e3-2f92-412e-866a-44e3f8ddc5c5/GCF_001866645.1_ASM186664v1_genomic.fna.gz | prodigal -d GCF_001866645.1_ASM186664v1_genomic.fna/cds.fna -a GCF_001866645.1_ASM186664v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:07,986] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:07,986] [INFO] Task started: HMMsearch
[2024-01-24 13:50:07,986] [INFO] Running command: hmmsearch --tblout GCF_001866645.1_ASM186664v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c76b74c-2927-4a13-a7b7-cf6dc1534166/dqc_reference/reference_markers.hmm GCF_001866645.1_ASM186664v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:08,354] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:08,356] [INFO] Found 6/6 markers.
[2024-01-24 13:50:08,416] [INFO] Query marker FASTA was written to GCF_001866645.1_ASM186664v1_genomic.fna/markers.fasta
[2024-01-24 13:50:08,416] [INFO] Task started: Blastn
[2024-01-24 13:50:08,417] [INFO] Running command: blastn -query GCF_001866645.1_ASM186664v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c76b74c-2927-4a13-a7b7-cf6dc1534166/dqc_reference/reference_markers.fasta -out GCF_001866645.1_ASM186664v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:09,662] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:09,665] [INFO] Selected 20 target genomes.
[2024-01-24 13:50:09,665] [INFO] Target genome list was writen to GCF_001866645.1_ASM186664v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:09,672] [INFO] Task started: fastANI
[2024-01-24 13:50:09,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg647bc3e3-2f92-412e-866a-44e3f8ddc5c5/GCF_001866645.1_ASM186664v1_genomic.fna.gz --refList GCF_001866645.1_ASM186664v1_genomic.fna/target_genomes.txt --output GCF_001866645.1_ASM186664v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:47,408] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:47,408] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c76b74c-2927-4a13-a7b7-cf6dc1534166/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:47,409] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c76b74c-2927-4a13-a7b7-cf6dc1534166/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:47,432] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:47,432] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:47,432] [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 colonosanans	strain=MUSC 93	GCA_001866645.1	1428652	1428652	type	True	100.0	2249	2259	95	conclusive
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	86.8637	1358	2259	95	below_threshold
Streptomyces nodosus	strain=DSM 40109	GCA_014205035.1	40318	40318	type	True	86.1759	1398	2259	95	below_threshold
Streptomyces nodosus	strain=ATCC 14899	GCA_000819545.1	40318	40318	type	True	86.1672	1398	2259	95	below_threshold
Streptomyces nodosus	strain=ATCC 14899	GCA_008704995.1	40318	40318	type	True	86.1192	1404	2259	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	84.5577	1320	2259	95	below_threshold
Streptomyces triticisoli	strain=NEAU-DSCPA1-4-4	GCA_003270085.1	2182797	2182797	type	True	84.5395	1210	2259	95	below_threshold
Streptomyces anandii	strain=JCM 4720	GCA_014650655.1	285454	285454	type	True	84.4334	1339	2259	95	below_threshold
Streptomyces spiralis	strain=JCM 3302	GCA_014654675.1	66376	66376	type	True	84.3614	1379	2259	95	below_threshold
Streptomyces carpinensis	strain=NRRL B-16921	GCA_002154505.1	66369	66369	type	True	84.3284	1313	2259	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	84.2221	1270	2259	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	84.199	1327	2259	95	below_threshold
Streptomyces brasiliensis	strain=JCM 3086	GCA_014647875.1	1954	1954	type	True	84.1932	1437	2259	95	below_threshold
Streptomyces phyllanthi	strain=TISTR 2346	GCA_009377205.1	1803180	1803180	type	True	84.0341	1157	2259	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	83.9921	1370	2259	95	below_threshold
Streptomyces puniciscabiei	strain=DSM 41929	GCA_006715785.1	164348	164348	type	True	83.9788	1367	2259	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	83.8862	1350	2259	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	83.8387	1346	2259	95	below_threshold
Streptomyces thermoviolaceus subsp. thermoviolaceus	strain=NBRC 13905	GCA_012034235.1	66860	1952	type	True	83.4456	1129	2259	95	below_threshold
Streptomyces thermoviolaceus subsp. thermoviolaceus	strain=JCM 4843	GCA_014650975.1	66860	1952	type	True	83.3738	1147	2259	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:47,434] [INFO] DFAST Taxonomy check result was written to GCF_001866645.1_ASM186664v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:47,434] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:47,435] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:47,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c76b74c-2927-4a13-a7b7-cf6dc1534166/dqc_reference/checkm_data
[2024-01-24 13:50:47,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:47,506] [INFO] Task started: CheckM
[2024-01-24 13:50:47,506] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001866645.1_ASM186664v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001866645.1_ASM186664v1_genomic.fna/checkm_input GCF_001866645.1_ASM186664v1_genomic.fna/checkm_result
[2024-01-24 13:51:50,815] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:50,817] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 13:51:50,844] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:50,845] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:50,845] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001866645.1_ASM186664v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:50,845] [INFO] Task started: Blastn
[2024-01-24 13:51:50,846] [INFO] Running command: blastn -query GCF_001866645.1_ASM186664v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c76b74c-2927-4a13-a7b7-cf6dc1534166/dqc_reference/reference_markers_gtdb.fasta -out GCF_001866645.1_ASM186664v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:52,792] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:52,796] [INFO] Selected 14 target genomes.
[2024-01-24 13:51:52,796] [INFO] Target genome list was writen to GCF_001866645.1_ASM186664v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:52,816] [INFO] Task started: fastANI
[2024-01-24 13:51:52,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg647bc3e3-2f92-412e-866a-44e3f8ddc5c5/GCF_001866645.1_ASM186664v1_genomic.fna.gz --refList GCF_001866645.1_ASM186664v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001866645.1_ASM186664v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:19,100] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:19,114] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:19,115] [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_001866645.1	s__Streptomyces colonosanans	100.0	2249	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001417775.1	s__Streptomyces sp001417775	87.5405	1427	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014905555.1	s__Streptomyces sp014905555	86.9247	1398	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920635.1	s__Streptomyces sp002920635	86.7521	1377	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704995.1	s__Streptomyces nodosus	86.1366	1401	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.42	97.72	0.96	0.87	5	-
GCF_001507435.1	s__Streptomyces sp001507435	86.0861	1440	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.91	96.23	0.91	0.88	3	-
GCF_003270085.1	s__Streptomyces triticisoli	84.5434	1208	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654675.1	s__Streptomyces spiralis	84.3547	1380	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.07	98.07	0.87	0.87	2	-
GCF_002154505.1	s__Streptomyces carpinensis	84.3132	1315	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009377205.1	s__Streptomyces phyllanthi	84.0704	1154	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715785.1	s__Streptomyces puniciscabiei	83.9825	1366	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.70	95.42	0.91	0.82	3	-
GCF_004124325.1	s__Streptomyces sp004124325	83.8976	1287	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001866665.1	s__Streptomyces monashensis	83.8295	1347	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.09	95.09	0.78	0.78	2	-
GCF_000317595.1	s__Streptomyces ipomoeae	83.7178	1200	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.29	98.81	0.89	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:19,116] [INFO] GTDB search result was written to GCF_001866645.1_ASM186664v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:19,117] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:19,124] [INFO] DFAST_QC result json was written to GCF_001866645.1_ASM186664v1_genomic.fna/dqc_result.json
[2024-01-24 13:52:19,125] [INFO] DFAST_QC completed!
[2024-01-24 13:52:19,125] [INFO] Total running time: 0h2m34s