[2024-01-24 12:30:19,336] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:19,338] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:19,339] [INFO] DQC Reference Directory: /var/lib/cwl/stg176ab255-d55d-445f-b475-76c1f5539831/dqc_reference
[2024-01-24 12:30:20,638] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:20,639] [INFO] Task started: Prodigal
[2024-01-24 12:30:20,639] [INFO] Running command: gunzip -c /var/lib/cwl/stg89ad32a0-c989-46a1-b790-cf3d1742d8c4/GCF_016741875.1_ASM1674187v1_genomic.fna.gz | prodigal -d GCF_016741875.1_ASM1674187v1_genomic.fna/cds.fna -a GCF_016741875.1_ASM1674187v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:03,119] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:03,119] [INFO] Task started: HMMsearch
[2024-01-24 12:31:03,119] [INFO] Running command: hmmsearch --tblout GCF_016741875.1_ASM1674187v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg176ab255-d55d-445f-b475-76c1f5539831/dqc_reference/reference_markers.hmm GCF_016741875.1_ASM1674187v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:03,575] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:03,576] [INFO] Found 6/6 markers.
[2024-01-24 12:31:03,654] [INFO] Query marker FASTA was written to GCF_016741875.1_ASM1674187v1_genomic.fna/markers.fasta
[2024-01-24 12:31:03,654] [INFO] Task started: Blastn
[2024-01-24 12:31:03,654] [INFO] Running command: blastn -query GCF_016741875.1_ASM1674187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg176ab255-d55d-445f-b475-76c1f5539831/dqc_reference/reference_markers.fasta -out GCF_016741875.1_ASM1674187v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:05,034] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:05,038] [INFO] Selected 19 target genomes.
[2024-01-24 12:31:05,039] [INFO] Target genome list was writen to GCF_016741875.1_ASM1674187v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:05,083] [INFO] Task started: fastANI
[2024-01-24 12:31:05,083] [INFO] Running command: fastANI --query /var/lib/cwl/stg89ad32a0-c989-46a1-b790-cf3d1742d8c4/GCF_016741875.1_ASM1674187v1_genomic.fna.gz --refList GCF_016741875.1_ASM1674187v1_genomic.fna/target_genomes.txt --output GCF_016741875.1_ASM1674187v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:55,040] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:55,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg176ab255-d55d-445f-b475-76c1f5539831/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:55,041] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg176ab255-d55d-445f-b475-76c1f5539831/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:55,058] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:31:55,058] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:31:55,058] [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 sabulosicollis	strain=PRKS01-29	GCA_016103465.1	2715963	2715963	type	True	85.8878	1681	3206	95	below_threshold
Streptomyces yatensis	strain=DSM 41771	GCA_018069625.1	155177	155177	type	True	85.8364	2003	3206	95	below_threshold
Streptomyces iranensis	strain=DSM 41954	GCA_017874715.1	576784	576784	type	True	85.8209	2024	3206	95	below_threshold
Streptomyces antimycoticus	strain=NBRC 12839	GCA_005405925.1	68175	68175	type	True	85.7715	2018	3206	95	below_threshold
Streptomyces hygroscopicus subsp. hygroscopicus	strain=NBRC 13472	GCA_001553455.1	68042	1912	type	True	85.7382	1710	3206	95	below_threshold
Streptomyces javensis	strain=DSM 41764	GCA_016103505.1	114698	114698	type	True	85.6345	1556	3206	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_000418455.1	1226757	1226757	type	True	85.6312	2044	3206	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_003675955.1	1226757	1226757	type	True	85.6311	2045	3206	95	below_threshold
Streptomyces rapamycinicus	strain=DSM 41530	GCA_014205315.1	1226757	1226757	type	True	85.6309	2028	3206	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	85.6196	2045	3206	95	below_threshold
Streptomyces sparsogenes	strain=DSM 40356	GCA_001969965.1	67365	67365	type	True	84.4411	1572	3206	95	below_threshold
Streptomyces sparsogenes	strain=ATCC 25498	GCA_001704635.1	67365	67365	type	True	84.3324	1680	3206	95	below_threshold
Streptomyces milbemycinicus	strain=NRRL 5739	GCA_002154605.1	476552	476552	type	True	83.9899	1561	3206	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	82.6553	1221	3206	95	below_threshold
Streptomyces pactum	strain=ATCC 27456	GCA_016031615.1	68249	68249	type	True	81.8504	1451	3206	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	80.6089	1143	3206	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	80.3252	1289	3206	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	80.2478	1247	3206	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	80.0466	1321	3206	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:55,060] [INFO] DFAST Taxonomy check result was written to GCF_016741875.1_ASM1674187v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:55,060] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:55,060] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:55,061] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg176ab255-d55d-445f-b475-76c1f5539831/dqc_reference/checkm_data
[2024-01-24 12:31:55,062] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:55,156] [INFO] Task started: CheckM
[2024-01-24 12:31:55,156] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016741875.1_ASM1674187v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016741875.1_ASM1674187v1_genomic.fna/checkm_input GCF_016741875.1_ASM1674187v1_genomic.fna/checkm_result
[2024-01-24 12:34:27,143] [INFO] Task succeeded: CheckM
[2024-01-24 12:34:27,145] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2024-01-24 12:34:27,169] [INFO] ===== Completeness check finished =====
[2024-01-24 12:34:27,169] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:34:27,169] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016741875.1_ASM1674187v1_genomic.fna/markers.fasta)
[2024-01-24 12:34:27,170] [INFO] Task started: Blastn
[2024-01-24 12:34:27,170] [INFO] Running command: blastn -query GCF_016741875.1_ASM1674187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg176ab255-d55d-445f-b475-76c1f5539831/dqc_reference/reference_markers_gtdb.fasta -out GCF_016741875.1_ASM1674187v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:34:29,169] [INFO] Task succeeded: Blastn
[2024-01-24 12:34:29,173] [INFO] Selected 15 target genomes.
[2024-01-24 12:34:29,173] [INFO] Target genome list was writen to GCF_016741875.1_ASM1674187v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:34:29,194] [INFO] Task started: fastANI
[2024-01-24 12:34:29,194] [INFO] Running command: fastANI --query /var/lib/cwl/stg89ad32a0-c989-46a1-b790-cf3d1742d8c4/GCF_016741875.1_ASM1674187v1_genomic.fna.gz --refList GCF_016741875.1_ASM1674187v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016741875.1_ASM1674187v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:35:10,535] [INFO] Task succeeded: fastANI
[2024-01-24 12:35:10,553] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:35:10,553] [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_016741875.1	s__Streptomyces coffeae	100.0	3205	3206	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_013364155.1	s__Streptomyces sp013364155	92.2746	2237	3206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016741935.1	s__Streptomyces sp016741935	85.8999	2054	3206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0488	N/A	N/A	N/A	N/A	1	-
GCF_018069625.1	s__Streptomyces yatensis	85.8597	1998	3206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.0185	N/A	N/A	N/A	N/A	1	-
GCF_001553455.1	s__Streptomyces hygroscopicus	85.7936	1703	3206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.24	98.00	0.92	0.90	7	-
GCA_005405945.1	s__Streptomyces violaceusniger	85.7901	2012	3206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.67	97.67	0.85	0.85	2	-
GCF_000147815.2	s__Streptomyces violaceusniger_A	85.7178	2011	3206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3301	95.69	95.54	0.80	0.80	4	-
GCF_015689475.1	s__Streptomyces solisilvae	85.6742	1993	3206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.71	97.94	0.94	0.86	10	-
GCF_018138715.1	s__Streptomyces asiaticus	85.6734	2094	3206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	95.36	0.90	0.81	10	-
GCF_001417735.1	s__Streptomyces sp001417735	85.6448	1801	3206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000158915.1	s__Streptomyces himastatinicus	85.219	1964	3206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.59	95.41	0.86	0.82	5	-
GCF_001704635.1	s__Streptomyces sparsogenes	84.3809	1670	3206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.81	0.87	0.87	2	-
GCF_002224125.1	s__Streptomyces sp002224125	84.0789	1860	3206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002154605.1	s__Streptomyces milbemycinicus	84.0228	1553	3206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.93	99.93	0.99	0.99	2	-
GCF_007595705.1	s__Streptomyces sp007595705	82.7661	1552	3206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:35:10,557] [INFO] GTDB search result was written to GCF_016741875.1_ASM1674187v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:35:10,557] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:35:10,562] [INFO] DFAST_QC result json was written to GCF_016741875.1_ASM1674187v1_genomic.fna/dqc_result.json
[2024-01-24 12:35:10,562] [INFO] DFAST_QC completed!
[2024-01-24 12:35:10,562] [INFO] Total running time: 0h4m51s