[2024-01-24 13:57:44,909] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:44,912] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:44,913] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c8f65c4-9d0d-4da4-8c96-f0f17e7b9e3f/dqc_reference
[2024-01-24 13:57:46,264] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:46,264] [INFO] Task started: Prodigal
[2024-01-24 13:57:46,265] [INFO] Running command: gunzip -c /var/lib/cwl/stgd82bf4df-e8ff-4605-ae30-2bc5310c21c9/GCF_014621695.1_ASM1462169v1_genomic.fna.gz | prodigal -d GCF_014621695.1_ASM1462169v1_genomic.fna/cds.fna -a GCF_014621695.1_ASM1462169v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:12,508] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:12,509] [INFO] Task started: HMMsearch
[2024-01-24 13:58:12,509] [INFO] Running command: hmmsearch --tblout GCF_014621695.1_ASM1462169v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c8f65c4-9d0d-4da4-8c96-f0f17e7b9e3f/dqc_reference/reference_markers.hmm GCF_014621695.1_ASM1462169v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:12,921] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:12,923] [INFO] Found 6/6 markers.
[2024-01-24 13:58:12,988] [INFO] Query marker FASTA was written to GCF_014621695.1_ASM1462169v1_genomic.fna/markers.fasta
[2024-01-24 13:58:12,989] [INFO] Task started: Blastn
[2024-01-24 13:58:12,989] [INFO] Running command: blastn -query GCF_014621695.1_ASM1462169v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c8f65c4-9d0d-4da4-8c96-f0f17e7b9e3f/dqc_reference/reference_markers.fasta -out GCF_014621695.1_ASM1462169v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:14,417] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:14,421] [INFO] Selected 26 target genomes.
[2024-01-24 13:58:14,421] [INFO] Target genome list was writen to GCF_014621695.1_ASM1462169v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:14,432] [INFO] Task started: fastANI
[2024-01-24 13:58:14,433] [INFO] Running command: fastANI --query /var/lib/cwl/stgd82bf4df-e8ff-4605-ae30-2bc5310c21c9/GCF_014621695.1_ASM1462169v1_genomic.fna.gz --refList GCF_014621695.1_ASM1462169v1_genomic.fna/target_genomes.txt --output GCF_014621695.1_ASM1462169v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:09,727] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:09,728] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c8f65c4-9d0d-4da4-8c96-f0f17e7b9e3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:09,728] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c8f65c4-9d0d-4da4-8c96-f0f17e7b9e3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:09,751] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:09,751] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:09,751] [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 xanthii	strain=CRXT-Y-14	GCA_014621695.1	2768069	2768069	type	True	100.0	2782	2783	95	conclusive
Streptomyces silaceus	strain=NRRL B-24166	GCA_001419745.1	545123	545123	type	True	83.5332	1479	2783	95	below_threshold
Streptomyces atriruber	strain=NRRL B-24165	GCA_001418325.1	545121	545121	type	True	83.3409	1447	2783	95	below_threshold
Streptomyces alfalfae	strain=XY25	GCA_004212445.1	1642299	1642299	type	True	83.0722	1509	2783	95	below_threshold
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	82.8836	1552	2783	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	82.8626	1621	2783	95	below_threshold
Streptomyces dengpaensis	strain=XZHG99	GCA_002946835.1	2049881	2049881	type	True	82.8515	1482	2783	95	below_threshold
Streptomyces spectabilis	strain=JCM 4308	GCA_014649235.1	68270	68270	type	True	82.7681	1615	2783	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	82.7394	1534	2783	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	82.7316	1600	2783	95	below_threshold
Streptomyces longispororuber	strain=JCM 4784	GCA_014656095.1	68230	68230	type	True	82.6501	1558	2783	95	below_threshold
Streptomyces davaonensis	strain=JCM 4913	GCA_000349325.1	348043	348043	type	True	82.6116	1576	2783	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	82.6108	1655	2783	95	below_threshold
Streptomyces recifensis	strain=NRRL B-3811	GCA_002154615.1	67355	67355	type	True	82.6068	1042	2783	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	82.481	1518	2783	95	below_threshold
Streptomyces griseoluteus	strain=JCM 4765	GCA_004784465.1	29306	29306	type	True	82.4486	1333	2783	95	below_threshold
Streptomyces murinus	strain=NRRL B-2286	GCA_002154555.1	33900	33900	type	True	82.4408	1191	2783	95	below_threshold
Streptomyces griseoluteus	strain=JCM 4765	GCA_014656035.1	29306	29306	type	True	82.3996	1352	2783	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	82.3369	1324	2783	95	below_threshold
Streptomyces griseofuscus	strain=DSM 40191	GCA_014673495.1	146922	146922	type	True	82.3296	1448	2783	95	below_threshold
Streptomyces griseoruber	strain=DSM 40281	GCA_001514205.1	1943	1943	type	True	82.2854	1570	2783	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	82.2782	1563	2783	95	below_threshold
Streptomyces malaysiense	strain=MUSC 136	GCA_000980885.2	1428626	1428626	type	True	82.2206	1417	2783	95	below_threshold
Streptomyces griseofuscus	strain=NRRL B-5429	GCA_000718315.1	146922	146922	type	True	82.1599	1432	2783	95	below_threshold
Streptomyces chilikensis	strain=RC 1830	GCA_001642695.2	1194079	1194079	type	True	81.644	1195	2783	95	below_threshold
Streptomyces nitrosporeus	strain=ATCC 12769	GCA_008704555.1	28894	28894	type	True	81.3019	1304	2783	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:09,753] [INFO] DFAST Taxonomy check result was written to GCF_014621695.1_ASM1462169v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:09,753] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:09,753] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:09,753] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c8f65c4-9d0d-4da4-8c96-f0f17e7b9e3f/dqc_reference/checkm_data
[2024-01-24 13:59:09,754] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:09,827] [INFO] Task started: CheckM
[2024-01-24 13:59:09,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014621695.1_ASM1462169v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014621695.1_ASM1462169v1_genomic.fna/checkm_input GCF_014621695.1_ASM1462169v1_genomic.fna/checkm_result
[2024-01-24 14:01:25,623] [INFO] Task succeeded: CheckM
[2024-01-24 14:01:25,625] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:01:25,653] [INFO] ===== Completeness check finished =====
[2024-01-24 14:01:25,654] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:01:25,654] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014621695.1_ASM1462169v1_genomic.fna/markers.fasta)
[2024-01-24 14:01:25,655] [INFO] Task started: Blastn
[2024-01-24 14:01:25,655] [INFO] Running command: blastn -query GCF_014621695.1_ASM1462169v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c8f65c4-9d0d-4da4-8c96-f0f17e7b9e3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014621695.1_ASM1462169v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:01:27,834] [INFO] Task succeeded: Blastn
[2024-01-24 14:01:27,837] [INFO] Selected 13 target genomes.
[2024-01-24 14:01:27,837] [INFO] Target genome list was writen to GCF_014621695.1_ASM1462169v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:01:27,873] [INFO] Task started: fastANI
[2024-01-24 14:01:27,874] [INFO] Running command: fastANI --query /var/lib/cwl/stgd82bf4df-e8ff-4605-ae30-2bc5310c21c9/GCF_014621695.1_ASM1462169v1_genomic.fna.gz --refList GCF_014621695.1_ASM1462169v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014621695.1_ASM1462169v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:02:00,438] [INFO] Task succeeded: fastANI
[2024-01-24 14:02:00,450] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:02:00,450] [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_014621695.1	s__Streptomyces sp014621695	100.0	2782	2783	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_003259365.1	s__Streptomyces sp003259365	86.0451	1838	2783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000373565.1	s__Streptomyces sp000373565	86.0413	1878	2783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_017377775.1	s__Streptomyces sp017377775	86.0034	1944	2783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005495.1	s__Streptomyces sp004005495	84.5026	1775	2783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002803065.1	s__Streptomyces sp002803065	84.3734	1866	2783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001419745.1	s__Streptomyces silaceus	83.4333	1496	2783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.58	99.58	0.96	0.96	2	-
GCF_002300165.1	s__Streptomyces sp002300165	83.0295	1577	2783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.35	96.35	0.87	0.87	2	-
GCF_002813405.1	s__Streptomyces sp002813405	82.7678	1574	2783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827595.1	s__Streptomyces sp007827595	82.3547	1602	2783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720255.1	s__Streptomyces griseus_I	82.34	1536	2783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000980885.2	s__Streptomyces malaysiense	82.2155	1418	2783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317595.1	s__Streptomyces ipomoeae	81.9809	1406	2783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.29	98.81	0.89	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:02:00,453] [INFO] GTDB search result was written to GCF_014621695.1_ASM1462169v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:02:00,453] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:02:00,458] [INFO] DFAST_QC result json was written to GCF_014621695.1_ASM1462169v1_genomic.fna/dqc_result.json
[2024-01-24 14:02:00,459] [INFO] DFAST_QC completed!
[2024-01-24 14:02:00,459] [INFO] Total running time: 0h4m16s