[2024-01-25 18:17:05,544] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:17:05,549] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:17:05,549] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa625062-41ac-4b99-8498-440c0561ced8/dqc_reference
[2024-01-25 18:17:06,712] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:17:06,713] [INFO] Task started: Prodigal
[2024-01-25 18:17:06,713] [INFO] Running command: gunzip -c /var/lib/cwl/stgd78c23c5-02c2-456b-a53c-05320e53cf5c/GCF_000974985.2_ASM97498v2_genomic.fna.gz | prodigal -d GCF_000974985.2_ASM97498v2_genomic.fna/cds.fna -a GCF_000974985.2_ASM97498v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:17:28,099] [INFO] Task succeeded: Prodigal
[2024-01-25 18:17:28,099] [INFO] Task started: HMMsearch
[2024-01-25 18:17:28,100] [INFO] Running command: hmmsearch --tblout GCF_000974985.2_ASM97498v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa625062-41ac-4b99-8498-440c0561ced8/dqc_reference/reference_markers.hmm GCF_000974985.2_ASM97498v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:17:28,429] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:17:28,430] [INFO] Found 6/6 markers.
[2024-01-25 18:17:28,493] [INFO] Query marker FASTA was written to GCF_000974985.2_ASM97498v2_genomic.fna/markers.fasta
[2024-01-25 18:17:28,494] [INFO] Task started: Blastn
[2024-01-25 18:17:28,494] [INFO] Running command: blastn -query GCF_000974985.2_ASM97498v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa625062-41ac-4b99-8498-440c0561ced8/dqc_reference/reference_markers.fasta -out GCF_000974985.2_ASM97498v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:29,777] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:29,779] [INFO] Selected 26 target genomes.
[2024-01-25 18:17:29,780] [INFO] Target genome list was writen to GCF_000974985.2_ASM97498v2_genomic.fna/target_genomes.txt
[2024-01-25 18:17:29,790] [INFO] Task started: fastANI
[2024-01-25 18:17:29,790] [INFO] Running command: fastANI --query /var/lib/cwl/stgd78c23c5-02c2-456b-a53c-05320e53cf5c/GCF_000974985.2_ASM97498v2_genomic.fna.gz --refList GCF_000974985.2_ASM97498v2_genomic.fna/target_genomes.txt --output GCF_000974985.2_ASM97498v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:18:33,716] [INFO] Task succeeded: fastANI
[2024-01-25 18:18:33,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa625062-41ac-4b99-8498-440c0561ced8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:18:33,717] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa625062-41ac-4b99-8498-440c0561ced8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:18:33,733] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:18:33,733] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:18:33,733] [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 mangrovisoli	strain=MUSC 149	GCA_000974985.2	1428628	1428628	type	True	100.0	2950	2960	95	conclusive
Streptomyces adustus	strain=NBRC 109810	GCA_009377175.1	1609272	1609272	type	True	85.1367	1835	2960	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	85.009	1837	2960	95	below_threshold
Streptomyces cellostaticus	strain=DSM 40189	GCA_001513965.1	67285	67285	type	True	84.896	1808	2960	95	below_threshold
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	84.8457	1673	2960	95	below_threshold
Streptomyces hyaluromycini	strain=NBRC 110483	GCA_002217755.1	1377993	1377993	type	True	84.8056	1953	2960	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	84.7805	1699	2960	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	84.7304	1787	2960	95	below_threshold
Streptomyces longwoodensis	strain=DSM 41677	GCA_001514125.1	68231	68231	type	True	84.7108	1735	2960	95	below_threshold
Streptomyces humi	strain=MUSC 119	GCA_001005085.2	1428620	1428620	type	True	84.7062	1926	2960	95	below_threshold
Streptomyces brasiliensis	strain=JCM 3086	GCA_014647875.1	1954	1954	type	True	84.6784	1779	2960	95	below_threshold
Streptomyces fuscichromogenes	strain=CGMCC 4.7110	GCA_014645815.1	1324013	1324013	type	True	84.6715	1892	2960	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	84.6688	1533	2960	95	below_threshold
Streptomyces griseoruber	strain=DSM 40281	GCA_001514205.1	1943	1943	type	True	84.5659	1851	2960	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.5647	1875	2960	95	below_threshold
Streptomyces phaeofaciens	strain=JCM 4125	GCA_014648915.1	68254	68254	type	True	84.5087	1944	2960	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	84.491	1352	2960	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	84.4612	1890	2960	95	below_threshold
Streptomyces alanosinicus	strain=JCM 4714	GCA_014650595.1	68171	68171	type	True	84.4134	1772	2960	95	below_threshold
Streptomyces cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	84.4054	1779	2960	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	84.2989	1613	2960	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	84.2285	1647	2960	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	84.2187	1607	2960	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.1489	1594	2960	95	below_threshold
Streptomyces pilosus	strain=JCM 4403	GCA_014649835.1	28893	28893	type	True	83.9341	1553	2960	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	83.2885	1691	2960	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:18:33,735] [INFO] DFAST Taxonomy check result was written to GCF_000974985.2_ASM97498v2_genomic.fna/tc_result.tsv
[2024-01-25 18:18:33,736] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:18:33,736] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:18:33,736] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa625062-41ac-4b99-8498-440c0561ced8/dqc_reference/checkm_data
[2024-01-25 18:18:33,737] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:18:33,842] [INFO] Task started: CheckM
[2024-01-25 18:18:33,842] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000974985.2_ASM97498v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000974985.2_ASM97498v2_genomic.fna/checkm_input GCF_000974985.2_ASM97498v2_genomic.fna/checkm_result
[2024-01-25 18:20:41,067] [INFO] Task succeeded: CheckM
[2024-01-25 18:20:41,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:20:41,094] [INFO] ===== Completeness check finished =====
[2024-01-25 18:20:41,094] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:20:41,095] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000974985.2_ASM97498v2_genomic.fna/markers.fasta)
[2024-01-25 18:20:41,095] [INFO] Task started: Blastn
[2024-01-25 18:20:41,095] [INFO] Running command: blastn -query GCF_000974985.2_ASM97498v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa625062-41ac-4b99-8498-440c0561ced8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000974985.2_ASM97498v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:20:43,225] [INFO] Task succeeded: Blastn
[2024-01-25 18:20:43,228] [INFO] Selected 26 target genomes.
[2024-01-25 18:20:43,228] [INFO] Target genome list was writen to GCF_000974985.2_ASM97498v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:20:43,269] [INFO] Task started: fastANI
[2024-01-25 18:20:43,269] [INFO] Running command: fastANI --query /var/lib/cwl/stgd78c23c5-02c2-456b-a53c-05320e53cf5c/GCF_000974985.2_ASM97498v2_genomic.fna.gz --refList GCF_000974985.2_ASM97498v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000974985.2_ASM97498v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:21:43,886] [INFO] Task succeeded: fastANI
[2024-01-25 18:21:43,901] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:21:43,902] [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_000974985.2	s__Streptomyces mangrovisoli	100.0	2950	2960	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_004346005.1	s__Streptomyces sp004346005	84.9396	1844	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513965.1	s__Streptomyces cellostaticus	84.8875	1810	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280195.1	s__Streptomyces galbus	84.8223	1677	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.53	0.96	0.94	3	-
GCF_001514125.1	s__Streptomyces longwoodensis	84.6929	1738	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.95	95.95	0.86	0.86	2	-
GCF_014596915.1	s__Streptomyces sp014596915	84.6828	1681	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384795.1	s__Streptomyces sp003384795	84.6792	1865	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905845.1	s__Streptomyces sp001905845	84.6779	1681	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647875.1	s__Streptomyces brasiliensis	84.6692	1780	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009604455.1	s__Streptomyces sp009604455	84.6596	1850	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011193355.1	s__Streptomyces sp011193355	84.6489	1604	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645815.1	s__Streptomyces fuscichromogenes	84.6184	1902	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015163075.1	s__Streptomyces sp015163075	84.5671	1873	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514205.1	s__Streptomyces griseoruber	84.5644	1852	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	84.4868	1795	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001654495.1	s__Streptomyces sp001654495	84.4862	1585	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.91	96.91	0.92	0.92	2	-
GCF_000761215.1	s__Streptomyces glaucescens	84.4838	1578	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002128465.1	s__Streptomyces pharetrae	84.4725	1489	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752655.1	s__Streptomyces griseorubiginosus_A	84.4298	1807	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004028635.1	s__Streptomyces cyaneus	84.4016	1779	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650595.1	s__Streptomyces alanosinicus	84.3995	1775	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721605.1	s__Streptomyces sp000721605	84.3336	1584	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363835.1	s__Streptomyces sp004363835	84.3297	1858	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203535.1	s__Streptomyces griseostramineus	84.2532	1643	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.88	99.76	0.99	0.98	3	-
GCF_003261055.1	s__Streptomyces cadmiisoli	84.1332	1675	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.22	99.22	0.88	0.88	2	-
GCF_000725125.1	s__Streptomyces toyocaensis	83.9758	1495	2960	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 18:21:43,903] [INFO] GTDB search result was written to GCF_000974985.2_ASM97498v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:21:43,904] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:21:43,908] [INFO] DFAST_QC result json was written to GCF_000974985.2_ASM97498v2_genomic.fna/dqc_result.json
[2024-01-25 18:21:43,908] [INFO] DFAST_QC completed!
[2024-01-25 18:21:43,908] [INFO] Total running time: 0h4m38s