[2024-01-25 17:54:35,838] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:54:35,839] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:54:35,839] [INFO] DQC Reference Directory: /var/lib/cwl/stg30e0c4f2-3554-4a73-b69b-7ebc2ab49bfa/dqc_reference
[2024-01-25 17:54:37,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:54:37,023] [INFO] Task started: Prodigal
[2024-01-25 17:54:37,023] [INFO] Running command: gunzip -c /var/lib/cwl/stg6bc4fa1d-5382-416f-8b0c-47b94340dac6/GCF_000718155.1_ASM71815v1_genomic.fna.gz | prodigal -d GCF_000718155.1_ASM71815v1_genomic.fna/cds.fna -a GCF_000718155.1_ASM71815v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:54:56,803] [INFO] Task succeeded: Prodigal
[2024-01-25 17:54:56,803] [INFO] Task started: HMMsearch
[2024-01-25 17:54:56,803] [INFO] Running command: hmmsearch --tblout GCF_000718155.1_ASM71815v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30e0c4f2-3554-4a73-b69b-7ebc2ab49bfa/dqc_reference/reference_markers.hmm GCF_000718155.1_ASM71815v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:54:57,134] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:54:57,135] [INFO] Found 6/6 markers.
[2024-01-25 17:54:57,202] [INFO] Query marker FASTA was written to GCF_000718155.1_ASM71815v1_genomic.fna/markers.fasta
[2024-01-25 17:54:57,202] [INFO] Task started: Blastn
[2024-01-25 17:54:57,202] [INFO] Running command: blastn -query GCF_000718155.1_ASM71815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30e0c4f2-3554-4a73-b69b-7ebc2ab49bfa/dqc_reference/reference_markers.fasta -out GCF_000718155.1_ASM71815v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:58,459] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:58,462] [INFO] Selected 21 target genomes.
[2024-01-25 17:54:58,462] [INFO] Target genome list was writen to GCF_000718155.1_ASM71815v1_genomic.fna/target_genomes.txt
[2024-01-25 17:54:58,496] [INFO] Task started: fastANI
[2024-01-25 17:54:58,496] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bc4fa1d-5382-416f-8b0c-47b94340dac6/GCF_000718155.1_ASM71815v1_genomic.fna.gz --refList GCF_000718155.1_ASM71815v1_genomic.fna/target_genomes.txt --output GCF_000718155.1_ASM71815v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:55:42,161] [INFO] Task succeeded: fastANI
[2024-01-25 17:55:42,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30e0c4f2-3554-4a73-b69b-7ebc2ab49bfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:55:42,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30e0c4f2-3554-4a73-b69b-7ebc2ab49bfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:55:42,182] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:55:42,182] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:55:42,182] [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 katrae	strain=NRRL ISP-5550	GCA_000966975.1	68223	68223	type	True	88.2211	1446	2717	95	below_threshold
Streptomyces vinaceus	strain=ATCC 27476	GCA_008704935.1	1960	1960	type	True	87.1743	1819	2717	95	below_threshold
Streptomyces goshikiensis	strain=JCM 4640	GCA_014650555.1	1942	1942	type	True	87.1472	1845	2717	95	below_threshold
Streptomyces vinaceus	strain=JCM 4849	GCA_014656155.1	1960	1960	type	True	87.0861	1848	2717	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_014648615.1	66374	66374	type	True	86.9955	1904	2717	95	below_threshold
Streptomyces spororaveus	strain=NBRC 15456	GCA_016755875.1	284039	284039	type	True	86.9898	1835	2717	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_017639205.1	66374	66374	type	True	86.9254	1918	2717	95	below_threshold
Streptomyces xanthophaeus	strain=NRRL B-5414	GCA_000725805.1	67385	67385	type	True	86.8957	1839	2717	95	below_threshold
Streptomyces virginiae	strain=NRRL ISP-5094	GCA_000720455.1	1961	1961	suspected-type	True	86.8852	1808	2717	95	below_threshold
Streptomyces cirratus	strain=JCM 4738	GCA_014650775.1	68187	68187	type	True	86.8621	1745	2717	95	below_threshold
Streptomyces xanthophaeus	strain=NBRC 12829	GCA_016755895.1	67385	67385	type	True	86.7959	1866	2717	95	below_threshold
Streptomyces subrutilus	strain=JCM 4834	GCA_014650935.1	36818	36818	type	True	86.7844	1687	2717	95	below_threshold
Streptomyces subrutilus	strain=ATCC 27467	GCA_008704535.1	36818	36818	type	True	86.7386	1724	2717	95	below_threshold
Streptomyces amritsarensis	strain=MTCC 11845	GCA_001953875.1	681158	681158	type	True	86.7289	1703	2717	95	below_threshold
Streptomyces avidinii	strain=DSM 40526	GCA_017874515.1	1895	1895	type	True	86.7199	1817	2717	95	below_threshold
Streptomyces yangpuensis	strain=fd2-tb	GCA_001005295.1	1648182	1648182	type	True	86.6845	1745	2717	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	81.5471	1296	2717	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	81.3944	1391	2717	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.1869	1156	2717	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	80.7781	1329	2717	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	80.7175	1342	2717	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:55:42,187] [INFO] DFAST Taxonomy check result was written to GCF_000718155.1_ASM71815v1_genomic.fna/tc_result.tsv
[2024-01-25 17:55:42,187] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:55:42,187] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:55:42,187] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30e0c4f2-3554-4a73-b69b-7ebc2ab49bfa/dqc_reference/checkm_data
[2024-01-25 17:55:42,188] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:55:42,270] [INFO] Task started: CheckM
[2024-01-25 17:55:42,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000718155.1_ASM71815v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000718155.1_ASM71815v1_genomic.fna/checkm_input GCF_000718155.1_ASM71815v1_genomic.fna/checkm_result
[2024-01-25 17:57:24,398] [INFO] Task succeeded: CheckM
[2024-01-25 17:57:24,399] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:57:24,422] [INFO] ===== Completeness check finished =====
[2024-01-25 17:57:24,422] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:57:24,423] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000718155.1_ASM71815v1_genomic.fna/markers.fasta)
[2024-01-25 17:57:24,423] [INFO] Task started: Blastn
[2024-01-25 17:57:24,423] [INFO] Running command: blastn -query GCF_000718155.1_ASM71815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30e0c4f2-3554-4a73-b69b-7ebc2ab49bfa/dqc_reference/reference_markers_gtdb.fasta -out GCF_000718155.1_ASM71815v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:57:26,562] [INFO] Task succeeded: Blastn
[2024-01-25 17:57:26,565] [INFO] Selected 17 target genomes.
[2024-01-25 17:57:26,565] [INFO] Target genome list was writen to GCF_000718155.1_ASM71815v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:57:26,581] [INFO] Task started: fastANI
[2024-01-25 17:57:26,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bc4fa1d-5382-416f-8b0c-47b94340dac6/GCF_000718155.1_ASM71815v1_genomic.fna.gz --refList GCF_000718155.1_ASM71815v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000718155.1_ASM71815v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:58:05,230] [INFO] Task succeeded: fastANI
[2024-01-25 17:58:05,242] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:58:05,242] [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_002803845.1	s__Streptomyces lavendulae_C	99.9605	2688	2717	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.97	0.99	0.99	3	conclusive
GCF_003950035.1	s__Streptomyces sp000158895	88.3319	1968	2717	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.52	95.50	0.87	0.87	3	-
GCF_002028425.1	s__Streptomyces katrae_A	88.2741	1852	2717	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.60	99.44	0.97	0.94	4	-
GCF_000717915.1	s__Streptomyces sp000717915	87.4659	1729	2717	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.92	95.47	0.90	0.89	4	-
GCF_014650555.1	s__Streptomyces goshikiensis	87.1295	1847	2717	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.27	96.91	0.89	0.81	10	-
GCF_008642275.1	s__Streptomyces venezuelae_E	87.1251	1762	2717	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720145.1	s__Streptomyces sp000720145	87.1158	1856	2717	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002080455.1	s__Streptomyces sp002080455	87.0291	1792	2717	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.34	98.21	0.92	0.90	7	-
GCF_001279725.1	s__Streptomyces sp001279725	86.9829	1661	2717	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016755875.1	s__Streptomyces spororaveus	86.9734	1837	2717	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017639205.1	s__Streptomyces nojiriensis	86.9711	1911	2717	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000725805.1	s__Streptomyces xanthophaeus	86.8978	1838	2717	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.79	99.60	0.97	0.96	3	-
GCF_003148825.1	s__Streptomyces sp003148825	86.8606	1797	2717	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.84	95.84	0.87	0.86	3	-
GCA_001298555.1	s__Streptomyces sp001298555	86.8136	1791	2717	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716685.1	s__Streptomyces virginiae_A	86.7251	1837	2717	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.46	95.91	0.89	0.84	3	-
GCF_003287935.1	s__Streptomyces sp003287935	86.4786	1776	2717	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.55	99.55	0.95	0.95	2	-
GCF_004795055.1	s__Streptomyces sp004795055	86.4177	1706	2717	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 17:58:05,247] [INFO] GTDB search result was written to GCF_000718155.1_ASM71815v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:58:05,247] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:58:05,251] [INFO] DFAST_QC result json was written to GCF_000718155.1_ASM71815v1_genomic.fna/dqc_result.json
[2024-01-25 17:58:05,251] [INFO] DFAST_QC completed!
[2024-01-25 17:58:05,251] [INFO] Total running time: 0h3m29s