[2024-01-25 19:40:50,559] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:40:50,561] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:40:50,561] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d1f4936-8ded-4212-bdc7-f04a8958f6ab/dqc_reference
[2024-01-25 19:40:51,761] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:40:51,761] [INFO] Task started: Prodigal
[2024-01-25 19:40:51,761] [INFO] Running command: gunzip -c /var/lib/cwl/stg4262ff1d-396a-41ed-881c-5ffa3dd5c55c/GCF_025642135.1_ASM2564213v1_genomic.fna.gz | prodigal -d GCF_025642135.1_ASM2564213v1_genomic.fna/cds.fna -a GCF_025642135.1_ASM2564213v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:41:19,164] [INFO] Task succeeded: Prodigal
[2024-01-25 19:41:19,164] [INFO] Task started: HMMsearch
[2024-01-25 19:41:19,164] [INFO] Running command: hmmsearch --tblout GCF_025642135.1_ASM2564213v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d1f4936-8ded-4212-bdc7-f04a8958f6ab/dqc_reference/reference_markers.hmm GCF_025642135.1_ASM2564213v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:41:19,487] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:41:19,488] [INFO] Found 6/6 markers.
[2024-01-25 19:41:19,554] [INFO] Query marker FASTA was written to GCF_025642135.1_ASM2564213v1_genomic.fna/markers.fasta
[2024-01-25 19:41:19,554] [INFO] Task started: Blastn
[2024-01-25 19:41:19,554] [INFO] Running command: blastn -query GCF_025642135.1_ASM2564213v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d1f4936-8ded-4212-bdc7-f04a8958f6ab/dqc_reference/reference_markers.fasta -out GCF_025642135.1_ASM2564213v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:41:20,779] [INFO] Task succeeded: Blastn
[2024-01-25 19:41:20,782] [INFO] Selected 22 target genomes.
[2024-01-25 19:41:20,783] [INFO] Target genome list was writen to GCF_025642135.1_ASM2564213v1_genomic.fna/target_genomes.txt
[2024-01-25 19:41:20,828] [INFO] Task started: fastANI
[2024-01-25 19:41:20,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg4262ff1d-396a-41ed-881c-5ffa3dd5c55c/GCF_025642135.1_ASM2564213v1_genomic.fna.gz --refList GCF_025642135.1_ASM2564213v1_genomic.fna/target_genomes.txt --output GCF_025642135.1_ASM2564213v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:42:04,790] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:04,790] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d1f4936-8ded-4212-bdc7-f04a8958f6ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:42:04,791] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d1f4936-8ded-4212-bdc7-f04a8958f6ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:42:04,804] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:42:04,804] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:42:04,805] [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 glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	87.1286	1823	3120	95	below_threshold
Streptomyces colonosanans	strain=MUSC 93	GCA_001866645.1	1428652	1428652	type	True	86.6882	1449	3120	95	below_threshold
Streptomyces nodosus	strain=ATCC 14899	GCA_000819545.1	40318	40318	type	True	85.8561	1628	3120	95	below_threshold
Streptomyces nodosus	strain=ATCC 14899	GCA_008704995.1	40318	40318	type	True	85.8349	1647	3120	95	below_threshold
Streptomyces nodosus	strain=DSM 40109	GCA_014205035.1	40318	40318	type	True	85.7791	1645	3120	95	below_threshold
Streptomyces anandii	strain=JCM 4720	GCA_014650655.1	285454	285454	type	True	84.8998	1721	3120	95	below_threshold
Streptomyces spiralis	strain=JCM 3302	GCA_014654675.1	66376	66376	type	True	84.7703	1868	3120	95	below_threshold
Streptomyces carpinensis	strain=NRRL B-16921	GCA_002154505.1	66369	66369	type	True	84.707	1682	3120	95	below_threshold
Streptomyces bungoensis	strain=DSM 41781	GCA_001514215.1	285568	285568	type	True	84.6512	1725	3120	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	84.5837	1732	3120	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	84.578	1680	3120	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	84.5755	1525	3120	95	below_threshold
Streptomyces olivaceoviridis	strain=JCM 4499	GCA_014650115.1	1921	1921	type	True	84.4265	1872	3120	95	below_threshold
Streptomyces fodineus	strain=TW1S1	GCA_001735805.1	1904616	1904616	type	True	84.4205	1843	3120	95	below_threshold
Streptomyces canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	84.4022	1869	3120	95	below_threshold
Streptomyces viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	84.3352	1326	3120	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	84.3021	1645	3120	95	below_threshold
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	84.2956	1650	3120	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	84.287	1643	3120	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.2854	1381	3120	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	84.2525	1666	3120	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.226	1879	3120	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:42:04,806] [INFO] DFAST Taxonomy check result was written to GCF_025642135.1_ASM2564213v1_genomic.fna/tc_result.tsv
[2024-01-25 19:42:04,807] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:42:04,807] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:42:04,807] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d1f4936-8ded-4212-bdc7-f04a8958f6ab/dqc_reference/checkm_data
[2024-01-25 19:42:04,808] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:42:04,895] [INFO] Task started: CheckM
[2024-01-25 19:42:04,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025642135.1_ASM2564213v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025642135.1_ASM2564213v1_genomic.fna/checkm_input GCF_025642135.1_ASM2564213v1_genomic.fna/checkm_result
[2024-01-25 19:45:28,500] [INFO] Task succeeded: CheckM
[2024-01-25 19:45:28,501] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:45:28,531] [INFO] ===== Completeness check finished =====
[2024-01-25 19:45:28,531] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:45:28,532] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025642135.1_ASM2564213v1_genomic.fna/markers.fasta)
[2024-01-25 19:45:28,533] [INFO] Task started: Blastn
[2024-01-25 19:45:28,533] [INFO] Running command: blastn -query GCF_025642135.1_ASM2564213v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d1f4936-8ded-4212-bdc7-f04a8958f6ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_025642135.1_ASM2564213v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:30,613] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:30,616] [INFO] Selected 16 target genomes.
[2024-01-25 19:45:30,616] [INFO] Target genome list was writen to GCF_025642135.1_ASM2564213v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:45:30,632] [INFO] Task started: fastANI
[2024-01-25 19:45:30,632] [INFO] Running command: fastANI --query /var/lib/cwl/stg4262ff1d-396a-41ed-881c-5ffa3dd5c55c/GCF_025642135.1_ASM2564213v1_genomic.fna.gz --refList GCF_025642135.1_ASM2564213v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025642135.1_ASM2564213v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:46:05,116] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:05,126] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:46:05,127] [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_014905555.1	s__Streptomyces sp014905555	96.3347	2411	3120	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_002920635.1	s__Streptomyces sp002920635	94.3538	2298	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001417775.1	s__Streptomyces sp001417775	87.6267	1871	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001866645.1	s__Streptomyces colonosanans	86.6802	1449	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507435.1	s__Streptomyces sp001507435	86.0596	1894	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.91	96.23	0.91	0.88	3	-
GCF_008704995.1	s__Streptomyces nodosus	85.797	1651	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.42	97.72	0.96	0.87	5	-
GCF_014650655.1	s__Streptomyces anandii	84.8846	1723	3120	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	84.7634	1868	3120	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	84.7031	1682	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704515.1	s__Streptomyces viridosporus	84.6035	1520	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.42	99.12	0.96	0.94	4	-
GCF_014656055.1	s__Streptomyces griseosporeus	84.5821	1731	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.70	98.69	0.95	0.95	3	-
GCF_014534645.1	s__Streptomyces sp014534645	84.5493	1686	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905845.1	s__Streptomyces sp001905845	84.4991	1702	3120	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	84.3233	1638	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.88	99.76	0.99	0.98	3	-
GCF_005280195.1	s__Streptomyces galbus	84.2851	1652	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.53	0.96	0.94	3	-
GCF_000317595.1	s__Streptomyces ipomoeae	83.9595	1623	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.29	98.81	0.89	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-25 19:46:05,128] [INFO] GTDB search result was written to GCF_025642135.1_ASM2564213v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:46:05,128] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:46:05,132] [INFO] DFAST_QC result json was written to GCF_025642135.1_ASM2564213v1_genomic.fna/dqc_result.json
[2024-01-25 19:46:05,132] [INFO] DFAST_QC completed!
[2024-01-25 19:46:05,132] [INFO] Total running time: 0h5m15s