[2024-01-24 14:56:23,821] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:56:23,824] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:56:23,824] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a9bb139-a4b8-4031-80cc-f04645aafc9f/dqc_reference
[2024-01-24 14:56:26,554] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:56:26,557] [INFO] Task started: Prodigal
[2024-01-24 14:56:26,559] [INFO] Running command: gunzip -c /var/lib/cwl/stgccd956c5-7363-431c-88a3-b5d1bf977c1e/GCF_014648655.1_ASM1464865v1_genomic.fna.gz | prodigal -d GCF_014648655.1_ASM1464865v1_genomic.fna/cds.fna -a GCF_014648655.1_ASM1464865v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:59,162] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:59,162] [INFO] Task started: HMMsearch
[2024-01-24 14:56:59,162] [INFO] Running command: hmmsearch --tblout GCF_014648655.1_ASM1464865v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a9bb139-a4b8-4031-80cc-f04645aafc9f/dqc_reference/reference_markers.hmm GCF_014648655.1_ASM1464865v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:59,687] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:59,689] [INFO] Found 6/6 markers.
[2024-01-24 14:56:59,780] [INFO] Query marker FASTA was written to GCF_014648655.1_ASM1464865v1_genomic.fna/markers.fasta
[2024-01-24 14:56:59,780] [INFO] Task started: Blastn
[2024-01-24 14:56:59,780] [INFO] Running command: blastn -query GCF_014648655.1_ASM1464865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a9bb139-a4b8-4031-80cc-f04645aafc9f/dqc_reference/reference_markers.fasta -out GCF_014648655.1_ASM1464865v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:01,226] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:01,229] [INFO] Selected 19 target genomes.
[2024-01-24 14:57:01,229] [INFO] Target genome list was writen to GCF_014648655.1_ASM1464865v1_genomic.fna/target_genomes.txt
[2024-01-24 14:57:01,251] [INFO] Task started: fastANI
[2024-01-24 14:57:01,252] [INFO] Running command: fastANI --query /var/lib/cwl/stgccd956c5-7363-431c-88a3-b5d1bf977c1e/GCF_014648655.1_ASM1464865v1_genomic.fna.gz --refList GCF_014648655.1_ASM1464865v1_genomic.fna/target_genomes.txt --output GCF_014648655.1_ASM1464865v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:57:39,246] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:39,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a9bb139-a4b8-4031-80cc-f04645aafc9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:57:39,247] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a9bb139-a4b8-4031-80cc-f04645aafc9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:57:39,262] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:57:39,262] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:57:39,262] [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 atratus	strain=JCM 3386	GCA_014648655.1	1893	1893	suspected-type	True	100.0	3161	3170	95	conclusive
Streptomyces gelaticus	strain=JCM 4376	GCA_014649535.1	285446	285446	type	True	89.7937	2014	3170	95	below_threshold
Streptomyces brevispora	strain=DSM 42059	GCA_007829885.1	887462	887462	type	True	86.9376	1740	3170	95	below_threshold
Streptomyces poriferorum	strain=P01-B04	GCA_019399235.1	2798799	2798799	type	True	86.3866	1636	3170	95	below_threshold
Streptomyces fulvorobeus	strain=DSM 41455	GCA_013409565.1	284028	284028	type	True	84.9729	1390	3170	95	below_threshold
Streptomyces microflavus	strain=JCM 4496	GCA_014650075.1	1919	1919	type	True	84.6112	1653	3170	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	84.5402	1303	3170	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	84.4675	1736	3170	95	below_threshold
Streptomyces cavourensis	strain=DSM 41795	GCA_006788935.1	67258	67258	type	True	84.4633	1567	3170	95	below_threshold
Streptomyces parvus	strain=NRRL B-1455	GCA_008632535.1	66428	66428	type	True	84.3823	1510	3170	95	below_threshold
Streptomyces cavourensis	strain=JCM 4298	GCA_014649215.1	67258	67258	type	True	84.352	1553	3170	95	below_threshold
Streptomyces griseus	strain=DSM 40236	GCA_900105705.1	1911	1911	type	True	84.3319	1651	3170	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	84.2467	1529	3170	95	below_threshold
Streptomyces nojiriensis	strain=NBRC 13794	GCA_016755855.1	66374	66374	type	True	81.3029	1352	3170	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_017639205.1	66374	66374	type	True	81.2983	1349	3170	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_014648615.1	66374	66374	type	True	81.2277	1351	3170	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	81.0179	1194	3170	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	80.892	1358	3170	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	80.202	1272	3170	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:57:39,264] [INFO] DFAST Taxonomy check result was written to GCF_014648655.1_ASM1464865v1_genomic.fna/tc_result.tsv
[2024-01-24 14:57:39,265] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:57:39,265] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:57:39,265] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a9bb139-a4b8-4031-80cc-f04645aafc9f/dqc_reference/checkm_data
[2024-01-24 14:57:39,266] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:57:39,363] [INFO] Task started: CheckM
[2024-01-24 14:57:39,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648655.1_ASM1464865v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648655.1_ASM1464865v1_genomic.fna/checkm_input GCF_014648655.1_ASM1464865v1_genomic.fna/checkm_result
[2024-01-24 14:59:31,676] [INFO] Task succeeded: CheckM
[2024-01-24 14:59:31,677] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:59:31,712] [INFO] ===== Completeness check finished =====
[2024-01-24 14:59:31,712] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:59:31,713] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648655.1_ASM1464865v1_genomic.fna/markers.fasta)
[2024-01-24 14:59:31,714] [INFO] Task started: Blastn
[2024-01-24 14:59:31,714] [INFO] Running command: blastn -query GCF_014648655.1_ASM1464865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a9bb139-a4b8-4031-80cc-f04645aafc9f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648655.1_ASM1464865v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:59:33,770] [INFO] Task succeeded: Blastn
[2024-01-24 14:59:33,775] [INFO] Selected 12 target genomes.
[2024-01-24 14:59:33,775] [INFO] Target genome list was writen to GCF_014648655.1_ASM1464865v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:59:33,788] [INFO] Task started: fastANI
[2024-01-24 14:59:33,789] [INFO] Running command: fastANI --query /var/lib/cwl/stgccd956c5-7363-431c-88a3-b5d1bf977c1e/GCF_014648655.1_ASM1464865v1_genomic.fna.gz --refList GCF_014648655.1_ASM1464865v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648655.1_ASM1464865v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:00:02,900] [INFO] Task succeeded: fastANI
[2024-01-24 15:00:02,915] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:00:02,916] [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_014648655.1	s__Streptomyces atratus	100.0	3161	3170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.41	98.41	0.88	0.88	2	conclusive
GCF_900091955.1	s__Streptomyces sp900091955	94.5924	2340	3170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119365.1	s__Streptomyces atratus_B	90.0837	2068	3170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649535.1	s__Streptomyces gelaticus	89.8103	2012	3170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091725.1	s__Streptomyces sp900091725	89.4942	2052	3170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003846175.1	s__Streptomyces sp003846175	89.3751	2198	3170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008120935.1	s__Streptomyces sp008120935	88.4158	2030	3170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745675.1	s__Streptomyces atratus_A	87.8923	1692	3170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116325.1	s__Streptomyces sp900116325	87.6582	1785	3170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.66	95.15	0.89	0.84	4	-
GCF_001905125.1	s__Streptomyces sp001905125	85.9132	1904	3170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905505.1	s__Streptomyces sp001905505	84.5867	1640	3170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650675.1	s__Streptomyces anulatus	84.4998	1729	3170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.62	96.42	0.89	0.81	27	-
--------------------------------------------------------------------------------
[2024-01-24 15:00:02,918] [INFO] GTDB search result was written to GCF_014648655.1_ASM1464865v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:00:02,919] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:00:02,924] [INFO] DFAST_QC result json was written to GCF_014648655.1_ASM1464865v1_genomic.fna/dqc_result.json
[2024-01-24 15:00:02,924] [INFO] DFAST_QC completed!
[2024-01-24 15:00:02,924] [INFO] Total running time: 0h3m39s