[2024-01-24 13:32:28,416] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:28,418] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:28,418] [INFO] DQC Reference Directory: /var/lib/cwl/stgab5b8f8f-5122-47f7-98c2-b4638ac688cd/dqc_reference
[2024-01-24 13:32:29,657] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:29,657] [INFO] Task started: Prodigal
[2024-01-24 13:32:29,658] [INFO] Running command: gunzip -c /var/lib/cwl/stgc84f488c-eee4-4f6f-90cd-7ba56495e1b7/GCF_020521255.1_ASM2052125v1_genomic.fna.gz | prodigal -d GCF_020521255.1_ASM2052125v1_genomic.fna/cds.fna -a GCF_020521255.1_ASM2052125v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:55,830] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:55,831] [INFO] Task started: HMMsearch
[2024-01-24 13:32:55,831] [INFO] Running command: hmmsearch --tblout GCF_020521255.1_ASM2052125v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab5b8f8f-5122-47f7-98c2-b4638ac688cd/dqc_reference/reference_markers.hmm GCF_020521255.1_ASM2052125v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:56,495] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:56,496] [INFO] Found 6/6 markers.
[2024-01-24 13:32:56,593] [INFO] Query marker FASTA was written to GCF_020521255.1_ASM2052125v1_genomic.fna/markers.fasta
[2024-01-24 13:32:56,593] [INFO] Task started: Blastn
[2024-01-24 13:32:56,593] [INFO] Running command: blastn -query GCF_020521255.1_ASM2052125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab5b8f8f-5122-47f7-98c2-b4638ac688cd/dqc_reference/reference_markers.fasta -out GCF_020521255.1_ASM2052125v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:58,251] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:58,254] [INFO] Selected 16 target genomes.
[2024-01-24 13:32:58,255] [INFO] Target genome list was writen to GCF_020521255.1_ASM2052125v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:58,272] [INFO] Task started: fastANI
[2024-01-24 13:32:58,272] [INFO] Running command: fastANI --query /var/lib/cwl/stgc84f488c-eee4-4f6f-90cd-7ba56495e1b7/GCF_020521255.1_ASM2052125v1_genomic.fna.gz --refList GCF_020521255.1_ASM2052125v1_genomic.fna/target_genomes.txt --output GCF_020521255.1_ASM2052125v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:43,766] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:43,767] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab5b8f8f-5122-47f7-98c2-b4638ac688cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:43,767] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab5b8f8f-5122-47f7-98c2-b4638ac688cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:43,780] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:33:43,780] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:43,780] [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 hydrogenans	strain=NBRC 13475	GCA_020521255.1	1873719	1873719	type	True	100.0	3181	3337	95	conclusive
Streptomyces hydrogenans	strain=JCM 4771	GCA_014656075.1	1873719	1873719	type	True	99.9037	2631	3337	95	conclusive
Streptomyces filamentosus	strain=JCM 4122	GCA_014654895.1	67294	67294	type	True	91.3336	2118	3337	95	below_threshold
Streptomyces omiyaensis	strain=JCM 4806	GCA_014650895.1	68247	68247	type	True	91.322	2132	3337	95	below_threshold
Streptomyces roseolus	strain=JCM 4411	GCA_014649855.1	67358	67358	type	True	91.281	2022	3337	95	below_threshold
Streptomyces termitum	strain=JCM 4518	GCA_014650175.1	67368	67368	type	True	89.648	1882	3337	95	below_threshold
Streptomyces vietnamensis	strain=GIM4.0001	GCA_000830005.1	362257	362257	type	True	87.0965	1926	3337	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_021432215.1	54571	54571	type	True	87.0179	1468	3337	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	86.8952	1914	3337	95	below_threshold
Streptomyces zaomyceticus	strain=JCM 4864	GCA_014656215.1	68286	68286	type	True	86.6843	1876	3337	95	below_threshold
Streptomyces laurentii	strain=ATCC 31255	GCA_002355495.1	39478	39478	type	True	85.0188	1693	3337	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	83.0319	1126	3337	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	82.8634	1174	3337	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.6611	1418	3337	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	82.641	1519	3337	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	76.2065	626	3337	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:43,782] [INFO] DFAST Taxonomy check result was written to GCF_020521255.1_ASM2052125v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:43,783] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:43,783] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:43,783] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab5b8f8f-5122-47f7-98c2-b4638ac688cd/dqc_reference/checkm_data
[2024-01-24 13:33:43,785] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:43,878] [INFO] Task started: CheckM
[2024-01-24 13:33:43,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020521255.1_ASM2052125v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020521255.1_ASM2052125v1_genomic.fna/checkm_input GCF_020521255.1_ASM2052125v1_genomic.fna/checkm_result
[2024-01-24 13:35:46,000] [INFO] Task succeeded: CheckM
[2024-01-24 13:35:46,002] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 13.54%
Strain heterogeneity: 85.71%
--------------------------------------------------------------------------------
[2024-01-24 13:35:46,031] [INFO] ===== Completeness check finished =====
[2024-01-24 13:35:46,032] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:35:46,032] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020521255.1_ASM2052125v1_genomic.fna/markers.fasta)
[2024-01-24 13:35:46,032] [INFO] Task started: Blastn
[2024-01-24 13:35:46,033] [INFO] Running command: blastn -query GCF_020521255.1_ASM2052125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab5b8f8f-5122-47f7-98c2-b4638ac688cd/dqc_reference/reference_markers_gtdb.fasta -out GCF_020521255.1_ASM2052125v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:48,593] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:48,598] [INFO] Selected 12 target genomes.
[2024-01-24 13:35:48,598] [INFO] Target genome list was writen to GCF_020521255.1_ASM2052125v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:35:48,667] [INFO] Task started: fastANI
[2024-01-24 13:35:48,668] [INFO] Running command: fastANI --query /var/lib/cwl/stgc84f488c-eee4-4f6f-90cd-7ba56495e1b7/GCF_020521255.1_ASM2052125v1_genomic.fna.gz --refList GCF_020521255.1_ASM2052125v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020521255.1_ASM2052125v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:36:20,911] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:20,926] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:36:20,926] [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_014656075.1	s__Streptomyces hydrogenans	99.9037	2631	3337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	97.53	0.88	0.87	3	conclusive
GCF_012927245.1	s__Streptomyces sp012927245	91.8102	1974	3337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000719555.1	s__Streptomyces sp000719555	91.5977	1973	3337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654895.1	s__Streptomyces filamentosus	91.3447	2117	3337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.28	96.27	0.93	0.92	4	-
GCF_014650895.1	s__Streptomyces omiyaensis	91.3217	2130	3337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649855.1	s__Streptomyces roseolus	91.2973	2019	3337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650175.1	s__Streptomyces termitum	89.6495	1882	3337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649755.1	s__Streptomyces litmocidini	86.8801	1855	3337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.07	95.07	0.85	0.85	2	-
GCA_000717735.1	s__Streptomyces griseoluteus_A	86.7349	1796	3337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	-
GCF_000716445.1	s__Streptomyces wedmorensis	86.5691	1961	3337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	97.63	0.94	0.88	3	-
GCA_002355495.1	s__Streptomyces laurentii	85.0405	1693	3337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002911015.1	s__Streptomyces populi	81.4917	1484	3337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:36:20,928] [INFO] GTDB search result was written to GCF_020521255.1_ASM2052125v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:36:20,928] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:36:20,932] [INFO] DFAST_QC result json was written to GCF_020521255.1_ASM2052125v1_genomic.fna/dqc_result.json
[2024-01-24 13:36:20,932] [INFO] DFAST_QC completed!
[2024-01-24 13:36:20,932] [INFO] Total running time: 0h3m53s