[2024-01-25 18:44:05,804] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:44:05,805] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:44:05,805] [INFO] DQC Reference Directory: /var/lib/cwl/stgef55cbfa-c4b6-4ac2-8491-46329db745eb/dqc_reference
[2024-01-25 18:44:06,935] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:44:06,935] [INFO] Task started: Prodigal
[2024-01-25 18:44:06,936] [INFO] Running command: gunzip -c /var/lib/cwl/stg00722089-c092-4d66-8953-636020040028/GCF_014651075.1_ASM1465107v1_genomic.fna.gz | prodigal -d GCF_014651075.1_ASM1465107v1_genomic.fna/cds.fna -a GCF_014651075.1_ASM1465107v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:44:25,961] [INFO] Task succeeded: Prodigal
[2024-01-25 18:44:25,961] [INFO] Task started: HMMsearch
[2024-01-25 18:44:25,961] [INFO] Running command: hmmsearch --tblout GCF_014651075.1_ASM1465107v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef55cbfa-c4b6-4ac2-8491-46329db745eb/dqc_reference/reference_markers.hmm GCF_014651075.1_ASM1465107v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:44:26,271] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:44:26,272] [INFO] Found 6/6 markers.
[2024-01-25 18:44:26,329] [INFO] Query marker FASTA was written to GCF_014651075.1_ASM1465107v1_genomic.fna/markers.fasta
[2024-01-25 18:44:26,330] [INFO] Task started: Blastn
[2024-01-25 18:44:26,330] [INFO] Running command: blastn -query GCF_014651075.1_ASM1465107v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef55cbfa-c4b6-4ac2-8491-46329db745eb/dqc_reference/reference_markers.fasta -out GCF_014651075.1_ASM1465107v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:27,533] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:27,536] [INFO] Selected 21 target genomes.
[2024-01-25 18:44:27,536] [INFO] Target genome list was writen to GCF_014651075.1_ASM1465107v1_genomic.fna/target_genomes.txt
[2024-01-25 18:44:27,544] [INFO] Task started: fastANI
[2024-01-25 18:44:27,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg00722089-c092-4d66-8953-636020040028/GCF_014651075.1_ASM1465107v1_genomic.fna.gz --refList GCF_014651075.1_ASM1465107v1_genomic.fna/target_genomes.txt --output GCF_014651075.1_ASM1465107v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:45:09,127] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:09,127] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef55cbfa-c4b6-4ac2-8491-46329db745eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:45:09,128] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef55cbfa-c4b6-4ac2-8491-46329db745eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:45:09,139] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:45:09,140] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:45:09,140] [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 djakartensis	strain=JCM 4957	GCA_014651075.1	68193	68193	type	True	100.0	2516	2520	95	conclusive
Streptomyces coeruleorubidus	strain=ATCC 13740	GCA_008705135.1	116188	116188	suspected-type	True	90.549	2023	2520	95	below_threshold
Streptomyces lomondensis	strain=JCM 4866	GCA_014651035.1	68229	68229	type	True	90.4668	1948	2520	95	below_threshold
Streptomyces swartbergensis	strain=HMC13	GCA_002148965.1	487165	487165	type	True	90.4123	1766	2520	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	90.4106	1947	2520	95	below_threshold
Streptomyces africanus	strain=NRRL B-24243	GCA_002150735.1	231024	231024	type	True	90.3953	1753	2520	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	90.276	2005	2520	95	below_threshold
Streptomyces purpurascens	strain=JCM 4509	GCA_014650155.1	1924	1924	type	True	90.2759	1991	2520	95	below_threshold
Streptomyces massasporeus	strain=JCM 4139	GCA_014648995.1	67324	67324	type	True	89.8281	1971	2520	95	below_threshold
Streptomyces tuirus	strain=JCM 4255	GCA_014701095.1	68278	68278	type	True	89.7887	1870	2520	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_005869865.1	2382123	2382123	type	True	89.7413	1982	2520	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_007655005.1	2382123	2382123	type	True	89.7234	1983	2520	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	89.5343	1607	2520	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	89.5139	1793	2520	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	86.4176	1659	2520	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	86.2572	1689	2520	95	below_threshold
Streptomyces viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	86.2341	1352	2520	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	86.042	1648	2520	95	below_threshold
Streptomyces calvus	strain=JCM 4326	GCA_014649315.1	67282	67282	type	True	85.9931	1654	2520	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.497	1413	2520	95	below_threshold
Streptomyces prasinus	strain=NRRL B-2712	GCA_001419705.1	67345	67345	type	True	85.0157	1268	2520	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:45:09,144] [INFO] DFAST Taxonomy check result was written to GCF_014651075.1_ASM1465107v1_genomic.fna/tc_result.tsv
[2024-01-25 18:45:09,146] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:45:09,146] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:45:09,146] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef55cbfa-c4b6-4ac2-8491-46329db745eb/dqc_reference/checkm_data
[2024-01-25 18:45:09,147] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:45:09,218] [INFO] Task started: CheckM
[2024-01-25 18:45:09,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651075.1_ASM1465107v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651075.1_ASM1465107v1_genomic.fna/checkm_input GCF_014651075.1_ASM1465107v1_genomic.fna/checkm_result
[2024-01-25 18:46:53,445] [INFO] Task succeeded: CheckM
[2024-01-25 18:46:53,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:46:53,498] [INFO] ===== Completeness check finished =====
[2024-01-25 18:46:53,498] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:46:53,499] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651075.1_ASM1465107v1_genomic.fna/markers.fasta)
[2024-01-25 18:46:53,499] [INFO] Task started: Blastn
[2024-01-25 18:46:53,499] [INFO] Running command: blastn -query GCF_014651075.1_ASM1465107v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef55cbfa-c4b6-4ac2-8491-46329db745eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651075.1_ASM1465107v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:55,572] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:55,575] [INFO] Selected 16 target genomes.
[2024-01-25 18:46:55,575] [INFO] Target genome list was writen to GCF_014651075.1_ASM1465107v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:46:55,589] [INFO] Task started: fastANI
[2024-01-25 18:46:55,590] [INFO] Running command: fastANI --query /var/lib/cwl/stg00722089-c092-4d66-8953-636020040028/GCF_014651075.1_ASM1465107v1_genomic.fna.gz --refList GCF_014651075.1_ASM1465107v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651075.1_ASM1465107v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:47:30,377] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:30,387] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:47:30,387] [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_014651075.1	s__Streptomyces djakartensis	100.0	2516	2520	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_000717875.1	s__Streptomyces sp000717875	93.6115	2077	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.70	99.70	0.96	0.96	2	-
GCA_018195615.1	s__Streptomyces tuirus_A	91.9409	1926	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000158955.1	s__Streptomyces viridochromogenes_B	91.1642	2032	2520	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	90.7218	2015	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	4	-
GCF_014651035.1	s__Streptomyces lomondensis	90.4669	1948	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150735.1	s__Streptomyces africanus	90.3951	1753	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000696115.1	s__Streptomyces olindensis	90.3604	1965	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202475.1	s__Streptomyces paradoxus	90.0551	1960	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237655.1	s__Streptomyces sp002237655	89.5482	1936	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280065.1	s__Streptomyces sp001280065	89.4332	1953	2520	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	86.5413	1731	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704515.1	s__Streptomyces viridosporus	86.3685	1573	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.42	99.12	0.96	0.94	4	-
GCF_014203535.1	s__Streptomyces griseostramineus	86.2845	1686	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.88	99.76	0.99	0.98	3	-
GCF_006782915.1	s__Streptomyces calvus	85.9841	1659	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.66	99.31	0.97	0.96	5	-
GCF_012034205.1	s__Streptomyces sp012034205	85.1952	1524	2520	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 18:47:30,390] [INFO] GTDB search result was written to GCF_014651075.1_ASM1465107v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:47:30,391] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:47:30,396] [INFO] DFAST_QC result json was written to GCF_014651075.1_ASM1465107v1_genomic.fna/dqc_result.json
[2024-01-25 18:47:30,396] [INFO] DFAST_QC completed!
[2024-01-25 18:47:30,396] [INFO] Total running time: 0h3m25s