[2024-01-25 20:03:50,687] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:50,689] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:50,689] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7a755ad-9e87-46cb-a761-2d64f7fbc63a/dqc_reference
[2024-01-25 20:03:51,807] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:51,808] [INFO] Task started: Prodigal
[2024-01-25 20:03:51,808] [INFO] Running command: gunzip -c /var/lib/cwl/stg33564914-d2af-49e0-b942-e389b974bfe1/GCF_001419705.1_ASM141970v1_genomic.fna.gz | prodigal -d GCF_001419705.1_ASM141970v1_genomic.fna/cds.fna -a GCF_001419705.1_ASM141970v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:04:08,597] [INFO] Task succeeded: Prodigal
[2024-01-25 20:04:08,598] [INFO] Task started: HMMsearch
[2024-01-25 20:04:08,598] [INFO] Running command: hmmsearch --tblout GCF_001419705.1_ASM141970v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7a755ad-9e87-46cb-a761-2d64f7fbc63a/dqc_reference/reference_markers.hmm GCF_001419705.1_ASM141970v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:04:08,890] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:04:08,891] [INFO] Found 6/6 markers.
[2024-01-25 20:04:08,943] [INFO] Query marker FASTA was written to GCF_001419705.1_ASM141970v1_genomic.fna/markers.fasta
[2024-01-25 20:04:08,944] [INFO] Task started: Blastn
[2024-01-25 20:04:08,944] [INFO] Running command: blastn -query GCF_001419705.1_ASM141970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7a755ad-9e87-46cb-a761-2d64f7fbc63a/dqc_reference/reference_markers.fasta -out GCF_001419705.1_ASM141970v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:10,186] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:10,189] [INFO] Selected 15 target genomes.
[2024-01-25 20:04:10,189] [INFO] Target genome list was writen to GCF_001419705.1_ASM141970v1_genomic.fna/target_genomes.txt
[2024-01-25 20:04:10,195] [INFO] Task started: fastANI
[2024-01-25 20:04:10,195] [INFO] Running command: fastANI --query /var/lib/cwl/stg33564914-d2af-49e0-b942-e389b974bfe1/GCF_001419705.1_ASM141970v1_genomic.fna.gz --refList GCF_001419705.1_ASM141970v1_genomic.fna/target_genomes.txt --output GCF_001419705.1_ASM141970v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:04:36,965] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:36,965] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7a755ad-9e87-46cb-a761-2d64f7fbc63a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:04:36,966] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7a755ad-9e87-46cb-a761-2d64f7fbc63a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:04:36,975] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:04:36,975] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:04:36,975] [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 prasinus	strain=NRRL B-2712	GCA_001419705.1	67345	67345	type	True	100.0	2008	2033	95	conclusive
Streptomyces prasinopilosus	strain=NRRL B-2711	GCA_001419695.1	67344	67344	type	True	94.2075	1212	2033	95	below_threshold
Streptomyces hirsutus	strain=NRRL B-2713	GCA_001418415.1	35620	35620	type	True	93.26	1451	2033	95	below_threshold
Streptomyces viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	87.6491	1306	2033	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	87.6168	1433	2033	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	87.6079	1436	2033	95	below_threshold
Streptomyces griseoflavus	strain=JCM 4479	GCA_014649995.1	35619	35619	type	True	86.8584	1422	2033	95	below_threshold
Streptomyces malachitofuscus	strain=JCM 4493	GCA_014650055.1	67322	67322	type	True	86.6184	1381	2033	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.3195	1345	2033	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	85.1706	1310	2033	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	85.0705	1203	2033	95	below_threshold
Streptomyces anthocyanicus	strain=JCM 5058	GCA_014651155.1	68174	68174	type	True	84.9266	1302	2033	95	below_threshold
Streptomyces rubrogriseus	strain=NBRC 15455	GCA_003112595.1	194673	194673	type	True	84.7583	1339	2033	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	84.138	1175	2033	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	82.3463	1203	2033	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:04:36,982] [INFO] DFAST Taxonomy check result was written to GCF_001419705.1_ASM141970v1_genomic.fna/tc_result.tsv
[2024-01-25 20:04:36,982] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:04:36,982] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:04:36,982] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7a755ad-9e87-46cb-a761-2d64f7fbc63a/dqc_reference/checkm_data
[2024-01-25 20:04:36,983] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:04:37,054] [INFO] Task started: CheckM
[2024-01-25 20:04:37,054] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001419705.1_ASM141970v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001419705.1_ASM141970v1_genomic.fna/checkm_input GCF_001419705.1_ASM141970v1_genomic.fna/checkm_result
[2024-01-25 20:05:38,412] [INFO] Task succeeded: CheckM
[2024-01-25 20:05:38,413] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:05:38,432] [INFO] ===== Completeness check finished =====
[2024-01-25 20:05:38,432] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:05:38,433] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001419705.1_ASM141970v1_genomic.fna/markers.fasta)
[2024-01-25 20:05:38,433] [INFO] Task started: Blastn
[2024-01-25 20:05:38,433] [INFO] Running command: blastn -query GCF_001419705.1_ASM141970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7a755ad-9e87-46cb-a761-2d64f7fbc63a/dqc_reference/reference_markers_gtdb.fasta -out GCF_001419705.1_ASM141970v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:40,533] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:40,536] [INFO] Selected 9 target genomes.
[2024-01-25 20:05:40,536] [INFO] Target genome list was writen to GCF_001419705.1_ASM141970v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:05:40,542] [INFO] Task started: fastANI
[2024-01-25 20:05:40,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg33564914-d2af-49e0-b942-e389b974bfe1/GCF_001419705.1_ASM141970v1_genomic.fna.gz --refList GCF_001419705.1_ASM141970v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001419705.1_ASM141970v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:05:57,965] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:57,972] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:05:57,972] [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_001419705.1	s__Streptomyces prasinus	100.0	2008	2033	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.87	97.75	0.84	0.80	4	conclusive
GCF_900101585.1	s__Streptomyces prasinopilosus	94.4648	1636	2033	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418415.1	s__Streptomyces hirsutus	93.2764	1450	2033	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.60	97.60	0.78	0.78	2	-
GCF_000829695.1	s__Streptomyces sp000829695	91.2134	1471	2033	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.65	99.65	0.91	0.91	2	-
GCF_003143855.1	s__Streptomyces sp003143855	89.7316	1465	2033	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.79	0.79	2	-
GCF_019049255.1	s__Streptomyces sp019049255	87.1057	1479	2033	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001279005.1	s__Streptomyces caelestis_A	87.044	1437	2033	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.79	99.58	0.97	0.96	3	-
GCA_014656175.1	s__Streptomyces werraensis	85.7276	1358	2033	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651155.1	s__Streptomyces anthocyanicus	84.9002	1308	2033	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	99.40	98.26	0.96	0.83	31	-
--------------------------------------------------------------------------------
[2024-01-25 20:05:57,973] [INFO] GTDB search result was written to GCF_001419705.1_ASM141970v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:05:57,974] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:05:57,977] [INFO] DFAST_QC result json was written to GCF_001419705.1_ASM141970v1_genomic.fna/dqc_result.json
[2024-01-25 20:05:57,977] [INFO] DFAST_QC completed!
[2024-01-25 20:05:57,977] [INFO] Total running time: 0h2m7s