[2024-01-24 10:47:06,552] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,555] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,555] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9e93c0d-38e6-4274-8747-146121b27bed/dqc_reference
[2024-01-24 10:47:12,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,102] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,103] [INFO] Running command: gunzip -c /var/lib/cwl/stg25d24f09-bb41-4f6f-8430-c38dda9b394f/GCF_014650995.1_ASM1465099v1_genomic.fna.gz | prodigal -d GCF_014650995.1_ASM1465099v1_genomic.fna/cds.fna -a GCF_014650995.1_ASM1465099v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:42,214] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:42,214] [INFO] Task started: HMMsearch
[2024-01-24 10:47:42,215] [INFO] Running command: hmmsearch --tblout GCF_014650995.1_ASM1465099v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9e93c0d-38e6-4274-8747-146121b27bed/dqc_reference/reference_markers.hmm GCF_014650995.1_ASM1465099v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:42,609] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:42,610] [INFO] Found 6/6 markers.
[2024-01-24 10:47:42,687] [INFO] Query marker FASTA was written to GCF_014650995.1_ASM1465099v1_genomic.fna/markers.fasta
[2024-01-24 10:47:42,687] [INFO] Task started: Blastn
[2024-01-24 10:47:42,688] [INFO] Running command: blastn -query GCF_014650995.1_ASM1465099v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9e93c0d-38e6-4274-8747-146121b27bed/dqc_reference/reference_markers.fasta -out GCF_014650995.1_ASM1465099v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:44,114] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:44,121] [INFO] Selected 25 target genomes.
[2024-01-24 10:47:44,121] [INFO] Target genome list was writen to GCF_014650995.1_ASM1465099v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:44,147] [INFO] Task started: fastANI
[2024-01-24 10:47:44,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg25d24f09-bb41-4f6f-8430-c38dda9b394f/GCF_014650995.1_ASM1465099v1_genomic.fna.gz --refList GCF_014650995.1_ASM1465099v1_genomic.fna/target_genomes.txt --output GCF_014650995.1_ASM1465099v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:37,792] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:37,793] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9e93c0d-38e6-4274-8747-146121b27bed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:37,793] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9e93c0d-38e6-4274-8747-146121b27bed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:37,811] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:37,811] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:37,811] [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 viridiviolaceus	strain=JCM 4855	GCA_014650995.1	68282	68282	type	True	100.0	2987	2989	95	conclusive
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	92.0761	2176	2989	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	88.9626	1962	2989	95	below_threshold
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	88.9049	1931	2989	95	below_threshold
Streptomyces ambofaciens	strain=ATCC 23877	GCA_001267885.1	1889	1889	type	True	88.3116	1920	2989	95	below_threshold
Streptomyces hyderabadensis	strain=JCM 17657	GCA_020404845.1	598549	598549	type	True	88.0138	1879	2989	95	below_threshold
Streptomyces tendae	strain=JCM 4610	GCA_014650435.1	1932	1932	type	True	87.9612	1917	2989	95	below_threshold
Streptomyces olivaceus	strain=NRRL B-3009	GCA_000721235.1	47716	47716	type	True	87.1147	1795	2989	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	87.0471	1545	2989	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	86.6739	1865	2989	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	86.6156	1867	2989	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	86.3937	1835	2989	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	86.1682	1792	2989	95	below_threshold
Streptomyces swartbergensis	strain=HMC13	GCA_002148965.1	487165	487165	type	True	86.1199	1611	2989	95	below_threshold
Streptomyces purpurascens	strain=JCM 4509	GCA_014650155.1	1924	1924	type	True	86.0199	1859	2989	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	85.9605	1862	2989	95	below_threshold
Streptomyces malachitofuscus	strain=JCM 4493	GCA_014650055.1	67322	67322	type	True	85.8988	1744	2989	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	85.7187	1513	2989	95	below_threshold
Streptomyces naganishii	strain=JCM 4654	GCA_014650575.1	285447	285447	type	True	85.308	1654	2989	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.0404	1614	2989	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	85.0151	1826	2989	95	below_threshold
Streptomyces filipinensis	strain=JCM 4369	GCA_014649495.1	66887	66887	type	True	84.652	1747	2989	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	84.5961	1730	2989	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	81.5572	1341	2989	95	below_threshold
Streptomyces omiyaensis	strain=JCM 4806	GCA_014650895.1	68247	68247	type	True	81.4386	1454	2989	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:37,814] [INFO] DFAST Taxonomy check result was written to GCF_014650995.1_ASM1465099v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:37,815] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:37,815] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:37,815] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9e93c0d-38e6-4274-8747-146121b27bed/dqc_reference/checkm_data
[2024-01-24 10:48:37,816] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:37,896] [INFO] Task started: CheckM
[2024-01-24 10:48:37,896] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650995.1_ASM1465099v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650995.1_ASM1465099v1_genomic.fna/checkm_input GCF_014650995.1_ASM1465099v1_genomic.fna/checkm_result
[2024-01-24 10:50:48,468] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:48,469] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:48,489] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:48,490] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:48,490] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650995.1_ASM1465099v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:48,490] [INFO] Task started: Blastn
[2024-01-24 10:50:48,490] [INFO] Running command: blastn -query GCF_014650995.1_ASM1465099v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9e93c0d-38e6-4274-8747-146121b27bed/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650995.1_ASM1465099v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:50,589] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:50,593] [INFO] Selected 22 target genomes.
[2024-01-24 10:50:50,593] [INFO] Target genome list was writen to GCF_014650995.1_ASM1465099v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:50,635] [INFO] Task started: fastANI
[2024-01-24 10:50:50,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg25d24f09-bb41-4f6f-8430-c38dda9b394f/GCF_014650995.1_ASM1465099v1_genomic.fna.gz --refList GCF_014650995.1_ASM1465099v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650995.1_ASM1465099v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:51:35,078] [INFO] Task succeeded: fastANI
[2024-01-24 10:51:35,095] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:51:35,095] [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_014650995.1	s__Streptomyces viridiviolaceus	100.0	2987	2989	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_014534645.1	s__Streptomyces sp014534645	92.0733	2175	2989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648815.1	s__Streptomyces flaveolus	88.9775	1960	2989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005225.1	s__Streptomyces pactum_A	88.7779	1910	2989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.98	0.98	2	-
GCF_002005565.1	s__Streptomyces sp002005565	88.7242	1727	2989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001267885.1	s__Streptomyces ambofaciens	88.3447	1915	2989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.23	99.23	0.92	0.92	2	-
GCF_014650435.1	s__Streptomyces tendae	87.9358	1921	2989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.72	95.62	0.85	0.82	7	-
GCF_003112595.1	s__Streptomyces rubrogriseus	87.8193	1909	2989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	N/A	N/A	N/A	N/A	1	-
GCA_003248315.1	s__Streptomyces sp003248315	87.6256	1845	2989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721235.1	s__Streptomyces olivaceus	87.1431	1791	2989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.53	98.10	0.91	0.89	6	-
GCF_009852415.1	s__Streptomyces sp009852415	86.7517	1848	2989	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	86.6124	1867	2989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.88	99.76	0.99	0.98	3	-
GCF_001905725.1	s__Streptomyces sp001905725	86.2426	1814	2989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900236475.1	s__Streptomyces chartreusis_D	86.2058	1827	2989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	4	-
GCF_006782915.1	s__Streptomyces calvus	86.1833	1773	2989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.66	99.31	0.97	0.96	5	-
GCF_002148965.1	s__Streptomyces swartbergensis	86.1354	1609	2989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721605.1	s__Streptomyces sp000721605	86.1282	1748	2989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002128465.1	s__Streptomyces pharetrae	85.6924	1617	2989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014655195.1	s__Streptomyces cellulosae	85.4043	1692	2989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.05	95.87	0.87	0.85	11	-
GCF_016921115.1	s__Streptomyces actuosus_A	84.4833	1608	2989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002982015.1	s__Streptomyces sp002982015	82.0123	1079	2989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756395.1	s__Streptomyces sp016756395	79.3826	1187	2989	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 10:51:35,097] [INFO] GTDB search result was written to GCF_014650995.1_ASM1465099v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:51:35,097] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:51:35,102] [INFO] DFAST_QC result json was written to GCF_014650995.1_ASM1465099v1_genomic.fna/dqc_result.json
[2024-01-24 10:51:35,102] [INFO] DFAST_QC completed!
[2024-01-24 10:51:35,102] [INFO] Total running time: 0h4m29s