[2024-01-25 20:00:20,617] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:00:20,618] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:00:20,618] [INFO] DQC Reference Directory: /var/lib/cwl/stgef411d80-cf99-4e61-8b07-8c09fa1dc2a3/dqc_reference
[2024-01-25 20:00:21,762] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:00:21,763] [INFO] Task started: Prodigal
[2024-01-25 20:00:21,763] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ecbc443-e5f3-4957-9942-19efacf5a698/GCF_003261055.1_ASM326105v1_genomic.fna.gz | prodigal -d GCF_003261055.1_ASM326105v1_genomic.fna/cds.fna -a GCF_003261055.1_ASM326105v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:00:54,868] [INFO] Task succeeded: Prodigal
[2024-01-25 20:00:54,869] [INFO] Task started: HMMsearch
[2024-01-25 20:00:54,869] [INFO] Running command: hmmsearch --tblout GCF_003261055.1_ASM326105v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef411d80-cf99-4e61-8b07-8c09fa1dc2a3/dqc_reference/reference_markers.hmm GCF_003261055.1_ASM326105v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:00:55,300] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:00:55,301] [INFO] Found 6/6 markers.
[2024-01-25 20:00:55,374] [INFO] Query marker FASTA was written to GCF_003261055.1_ASM326105v1_genomic.fna/markers.fasta
[2024-01-25 20:00:55,374] [INFO] Task started: Blastn
[2024-01-25 20:00:55,374] [INFO] Running command: blastn -query GCF_003261055.1_ASM326105v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef411d80-cf99-4e61-8b07-8c09fa1dc2a3/dqc_reference/reference_markers.fasta -out GCF_003261055.1_ASM326105v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:56,601] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:56,604] [INFO] Selected 28 target genomes.
[2024-01-25 20:00:56,604] [INFO] Target genome list was writen to GCF_003261055.1_ASM326105v1_genomic.fna/target_genomes.txt
[2024-01-25 20:00:56,642] [INFO] Task started: fastANI
[2024-01-25 20:00:56,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ecbc443-e5f3-4957-9942-19efacf5a698/GCF_003261055.1_ASM326105v1_genomic.fna.gz --refList GCF_003261055.1_ASM326105v1_genomic.fna/target_genomes.txt --output GCF_003261055.1_ASM326105v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:01:54,436] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:54,436] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef411d80-cf99-4e61-8b07-8c09fa1dc2a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:01:54,437] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef411d80-cf99-4e61-8b07-8c09fa1dc2a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:01:54,461] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:01:54,461] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:01:54,461] [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 gossypiisoli	strain=TRM 44567	GCA_013433285.1	2748864	2748864	type	True	87.0106	1860	3412	95	below_threshold
Streptomyces spinoverrucosus	strain=JCM 5077	GCA_014651195.1	284043	284043	type	True	86.9388	1897	3412	95	below_threshold
Streptomyces spinoverrucosus	strain=NBRC 14228	GCA_006539505.1	284043	284043	type	True	86.9365	1849	3412	95	below_threshold
Streptomyces chromofuscus	strain=DSM 40273	GCA_015160875.1	42881	42881	type	True	86.7651	1865	3412	95	below_threshold
Streptomyces chromofuscus	strain=JCM 4354	GCA_014649435.1	42881	42881	type	True	86.5476	1930	3412	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	85.6377	1447	3412	95	below_threshold
Streptomyces curacoi	strain=DSM 40107	GCA_001513975.1	146536	146536	type	True	85.3153	1785	3412	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.2667	1788	3412	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.0802	1759	3412	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.9491	1637	3412	95	below_threshold
Streptomyces cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	84.9165	1834	3412	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	84.8132	1930	3412	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.8014	1419	3412	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	84.7795	1869	3412	95	below_threshold
Streptomyces nigra	strain=452	GCA_003074055.1	1827580	1827580	type	True	84.7481	1790	3412	95	below_threshold
Streptomyces zinciresistens	strain=K42	GCA_000225525.2	1073330	1073330	type	True	84.6064	1605	3412	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	84.5649	1706	3412	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	84.5228	1668	3412	95	below_threshold
Streptomyces anandii	strain=JCM 4720	GCA_014650655.1	285454	285454	type	True	84.5112	1660	3412	95	below_threshold
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	84.5054	1695	3412	95	below_threshold
Streptomyces longwoodensis	strain=DSM 41677	GCA_001514125.1	68231	68231	type	True	84.5027	1724	3412	95	below_threshold
Streptomyces kebangsaanensis	strain=SUK12	GCA_001906585.1	864058	864058	type	True	84.4875	1592	3412	95	below_threshold
Streptomyces cellostaticus	strain=DSM 40189	GCA_001513965.1	67285	67285	type	True	84.3693	1752	3412	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	84.3213	1476	3412	95	below_threshold
Streptomyces griseoruber	strain=DSM 40281	GCA_001514205.1	1943	1943	type	True	84.321	1803	3412	95	below_threshold
Streptomyces carpinensis	strain=NRRL B-16921	GCA_002154505.1	66369	66369	type	True	84.1813	1563	3412	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	84.0884	1704	3412	95	below_threshold
Streptomyces mangrovisoli	strain=MUSC 149	GCA_000974985.2	1428628	1428628	type	True	84.0486	1693	3412	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:01:54,462] [INFO] DFAST Taxonomy check result was written to GCF_003261055.1_ASM326105v1_genomic.fna/tc_result.tsv
[2024-01-25 20:01:54,463] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:01:54,463] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:01:54,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef411d80-cf99-4e61-8b07-8c09fa1dc2a3/dqc_reference/checkm_data
[2024-01-25 20:01:54,464] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:01:54,556] [INFO] Task started: CheckM
[2024-01-25 20:01:54,556] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003261055.1_ASM326105v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003261055.1_ASM326105v1_genomic.fna/checkm_input GCF_003261055.1_ASM326105v1_genomic.fna/checkm_result
[2024-01-25 20:05:50,715] [INFO] Task succeeded: CheckM
[2024-01-25 20:05:50,716] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:05:50,740] [INFO] ===== Completeness check finished =====
[2024-01-25 20:05:50,741] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:05:50,742] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003261055.1_ASM326105v1_genomic.fna/markers.fasta)
[2024-01-25 20:05:50,742] [INFO] Task started: Blastn
[2024-01-25 20:05:50,742] [INFO] Running command: blastn -query GCF_003261055.1_ASM326105v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef411d80-cf99-4e61-8b07-8c09fa1dc2a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_003261055.1_ASM326105v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:52,813] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:52,816] [INFO] Selected 22 target genomes.
[2024-01-25 20:05:52,816] [INFO] Target genome list was writen to GCF_003261055.1_ASM326105v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:05:52,840] [INFO] Task started: fastANI
[2024-01-25 20:05:52,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ecbc443-e5f3-4957-9942-19efacf5a698/GCF_003261055.1_ASM326105v1_genomic.fna.gz --refList GCF_003261055.1_ASM326105v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003261055.1_ASM326105v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:06:41,238] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:41,251] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:06:41,252] [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_003261055.1	s__Streptomyces cadmiisoli	100.0	3380	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.22	99.22	0.88	0.88	2	conclusive
GCF_004187715.1	s__Streptomyces sp004187715	88.0072	2021	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015712165.1	s__Streptomyces spinoverrucosus_A	87.0842	1920	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539505.1	s__Streptomyces spinoverrucosus	86.9374	1850	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.41	95.17	0.85	0.79	5	-
GCF_019219825.1	s__Streptomyces sp019219825	86.8531	1788	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015160875.1	s__Streptomyces chromofuscus	86.7296	1870	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.98	0.98	2	-
GCA_002128465.1	s__Streptomyces pharetrae	85.6638	1586	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011193355.1	s__Streptomyces sp011193355	85.5427	1722	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000761215.1	s__Streptomyces glaucescens	85.4351	1722	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070565.1	s__Streptomyces sp018070565	85.3744	1749	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513975.1	s__Streptomyces curacoi	85.2992	1788	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.35	97.22	0.89	0.84	4	-
GCA_000696115.1	s__Streptomyces olindensis	85.1226	1782	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009852415.1	s__Streptomyces sp009852415	85.066	1780	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719285.1	s__Streptomyces bicolor	84.8999	1812	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003074055.1	s__Streptomyces nigra	84.7384	1786	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.21	97.15	0.92	0.91	4	-
GCF_001282115.1	s__Streptomyces sp001282115	84.646	1605	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.95	0.95	0.95	2	-
GCF_001509795.1	s__Streptomyces sp001509795	84.5901	1760	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.33	98.67	0.96	0.93	3	-
GCF_005280195.1	s__Streptomyces galbus	84.5601	1687	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.53	0.96	0.94	3	-
GCF_001514125.1	s__Streptomyces longwoodensis	84.4851	1728	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.95	95.95	0.86	0.86	2	-
GCF_001514205.1	s__Streptomyces griseoruber	84.3345	1799	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720135.1	s__Streptomyces sp000720135	84.2215	1703	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.69	98.69	0.94	0.94	2	-
GCF_000974985.2	s__Streptomyces mangrovisoli	84.0602	1691	3412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:06:41,253] [INFO] GTDB search result was written to GCF_003261055.1_ASM326105v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:06:41,254] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:06:41,258] [INFO] DFAST_QC result json was written to GCF_003261055.1_ASM326105v1_genomic.fna/dqc_result.json
[2024-01-25 20:06:41,258] [INFO] DFAST_QC completed!
[2024-01-25 20:06:41,258] [INFO] Total running time: 0h6m21s