[2024-01-24 12:22:14,161] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:14,163] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:14,163] [INFO] DQC Reference Directory: /var/lib/cwl/stgb13d826e-35b6-4e6a-8a26-cb8b72b9693a/dqc_reference
[2024-01-24 12:22:15,730] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:15,731] [INFO] Task started: Prodigal
[2024-01-24 12:22:15,732] [INFO] Running command: gunzip -c /var/lib/cwl/stg67d69919-1724-442f-9d02-ac4b1bf5f20a/GCF_009739465.1_ASM973946v1_genomic.fna.gz | prodigal -d GCF_009739465.1_ASM973946v1_genomic.fna/cds.fna -a GCF_009739465.1_ASM973946v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:36,085] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:36,085] [INFO] Task started: HMMsearch
[2024-01-24 12:22:36,085] [INFO] Running command: hmmsearch --tblout GCF_009739465.1_ASM973946v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb13d826e-35b6-4e6a-8a26-cb8b72b9693a/dqc_reference/reference_markers.hmm GCF_009739465.1_ASM973946v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:36,518] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:36,520] [INFO] Found 6/6 markers.
[2024-01-24 12:22:36,575] [INFO] Query marker FASTA was written to GCF_009739465.1_ASM973946v1_genomic.fna/markers.fasta
[2024-01-24 12:22:36,575] [INFO] Task started: Blastn
[2024-01-24 12:22:36,575] [INFO] Running command: blastn -query GCF_009739465.1_ASM973946v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb13d826e-35b6-4e6a-8a26-cb8b72b9693a/dqc_reference/reference_markers.fasta -out GCF_009739465.1_ASM973946v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:37,954] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:37,960] [INFO] Selected 29 target genomes.
[2024-01-24 12:22:37,960] [INFO] Target genome list was writen to GCF_009739465.1_ASM973946v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:37,972] [INFO] Task started: fastANI
[2024-01-24 12:22:37,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg67d69919-1724-442f-9d02-ac4b1bf5f20a/GCF_009739465.1_ASM973946v1_genomic.fna.gz --refList GCF_009739465.1_ASM973946v1_genomic.fna/target_genomes.txt --output GCF_009739465.1_ASM973946v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:28,549] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:28,550] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb13d826e-35b6-4e6a-8a26-cb8b72b9693a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:28,550] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb13d826e-35b6-4e6a-8a26-cb8b72b9693a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:28,571] [INFO] Found 29 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:28,571] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:28,571] [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 apocyni	strain=TRM 66233	GCA_009739465.1	2654677	2654677	type	True	100.0	2248	2313	95	conclusive
Streptomyces boluensis	strain=YC537	GCA_009908195.1	1775135	1775135	type	True	83.1753	1181	2313	95	below_threshold
Streptomyces silaceus	strain=NRRL B-24166	GCA_001419745.1	545123	545123	type	True	82.6893	1198	2313	95	below_threshold
Streptomyces alboniger	strain=NRRL B-1832	GCA_001418385.1	132473	132473	type	True	82.546	1153	2313	95	below_threshold
Streptomyces triticagri	strain=NEAU-YY421	GCA_003429565.1	2293568	2293568	type	True	82.4134	1232	2313	95	below_threshold
Streptomyces kanamyceticus	strain=ATCC 12853	GCA_008704495.1	1967	1967	type	True	82.3748	1365	2313	95	below_threshold
Streptomyces kanamyceticus	strain=NRRL B-2535	GCA_001418465.1	1967	1967	type	True	82.3672	1229	2313	95	below_threshold
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	82.0399	1238	2313	95	below_threshold
Streptomyces dengpaensis	strain=XZHG99	GCA_002946835.1	2049881	2049881	type	True	82.0298	1260	2313	95	below_threshold
Streptomyces xanthii	strain=CRXT-Y-14	GCA_014621695.1	2768069	2768069	type	True	81.9156	1259	2313	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	81.8467	1262	2313	95	below_threshold
Streptomyces parvus	strain=NRRL B-1455	GCA_008632535.1	66428	66428	type	True	81.8215	1151	2313	95	below_threshold
Streptomyces davaonensis	strain=JCM 4913	GCA_000349325.1	348043	348043	type	True	81.7933	1292	2313	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	81.7649	1200	2313	95	below_threshold
Streptomyces parvus	strain=JCM 4069	GCA_014648875.1	66428	66428	type	True	81.7466	1243	2313	95	below_threshold
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	81.7434	1214	2313	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	81.7263	1188	2313	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	81.7004	1233	2313	95	below_threshold
Streptomyces microflavus	strain=JCM 4496	GCA_014650075.1	1919	1919	type	True	81.6953	1258	2313	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	81.6364	1216	2313	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	81.6316	1226	2313	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	81.6241	1288	2313	95	below_threshold
Streptomyces poonensis	strain=JCM 4815	GCA_014650915.1	68255	68255	type	True	81.6045	1241	2313	95	below_threshold
Streptomyces gougerotii	strain=JCM 4136	GCA_014648955.1	53448	53448	suspected-type	True	81.3835	1086	2313	95	below_threshold
Streptomyces diastaticus subsp. diastaticus	strain=JCM 4128	GCA_014648935.1	68040	1956	suspected-type	True	81.3371	1086	2313	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	81.3356	1050	2313	95	below_threshold
Streptomyces diastaticus subsp. diastaticus	strain=NBRC 13412	GCA_011170125.1	68040	1956	suspected-type	True	81.303	1100	2313	95	below_threshold
Streptomyces gougerotii	strain=NBRC 13043	GCA_011170145.1	53448	53448	suspected-type	True	81.293	1085	2313	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	81.0548	919	2313	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:28,574] [INFO] DFAST Taxonomy check result was written to GCF_009739465.1_ASM973946v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:28,575] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:28,575] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:28,576] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb13d826e-35b6-4e6a-8a26-cb8b72b9693a/dqc_reference/checkm_data
[2024-01-24 12:23:28,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:28,645] [INFO] Task started: CheckM
[2024-01-24 12:23:28,645] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009739465.1_ASM973946v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009739465.1_ASM973946v1_genomic.fna/checkm_input GCF_009739465.1_ASM973946v1_genomic.fna/checkm_result
[2024-01-24 12:24:28,755] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:28,756] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 30.21%
Strain heterogeneity: 93.33%
--------------------------------------------------------------------------------
[2024-01-24 12:24:28,795] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:28,796] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:28,796] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009739465.1_ASM973946v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:28,797] [INFO] Task started: Blastn
[2024-01-24 12:24:28,797] [INFO] Running command: blastn -query GCF_009739465.1_ASM973946v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb13d826e-35b6-4e6a-8a26-cb8b72b9693a/dqc_reference/reference_markers_gtdb.fasta -out GCF_009739465.1_ASM973946v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:30,836] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:30,841] [INFO] Selected 27 target genomes.
[2024-01-24 12:24:30,842] [INFO] Target genome list was writen to GCF_009739465.1_ASM973946v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:30,878] [INFO] Task started: fastANI
[2024-01-24 12:24:30,878] [INFO] Running command: fastANI --query /var/lib/cwl/stg67d69919-1724-442f-9d02-ac4b1bf5f20a/GCF_009739465.1_ASM973946v1_genomic.fna.gz --refList GCF_009739465.1_ASM973946v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009739465.1_ASM973946v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:22,481] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:22,506] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:22,506] [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_009739465.1	s__Streptomyces sp009739465	100.0	2256	2313	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_009908195.1	s__Streptomyces boluensis	83.1956	1178	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001419745.1	s__Streptomyces silaceus	82.7018	1196	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.58	99.58	0.96	0.96	2	-
GCF_016905445.1	s__Streptomyces sp016905445	82.5247	1228	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684775.1	s__Streptomyces sp004684775	82.429	1247	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002556545.1	s__Streptomyces formicae	82.4241	1364	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003429565.1	s__Streptomyces triticagri	82.4065	1232	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100315.1	s__Streptomyces indicus	82.3911	1319	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769735.1	s__Streptomyces sp009769735	82.3079	1362	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650815.1	s__Streptomyces flavofungini	82.147	1355	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003403055.1	s__Streptomyces sp003403055	82.1287	1322	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650875.1	s__Streptomyces minutiscleroticus	82.0537	1236	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	98.56	0.90	0.90	2	-
GCF_018614055.1	s__Streptomyces sp018614055	82.0119	1248	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002803065.1	s__Streptomyces sp002803065	81.9186	1320	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649875.1	s__Streptomyces rubiginosohelvolus	81.859	1205	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.09	96.67	0.91	0.87	22	-
GCF_014647975.1	s__Streptomyces fumigatiscleroticus	81.817	1225	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000349325.1	s__Streptomyces davaonensis	81.7886	1292	2313	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	81.7489	1211	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.53	0.96	0.94	3	-
GCF_000444875.1	s__Streptomyces collinus_A	81.7206	1246	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.10	97.10	0.84	0.84	2	-
GCF_014650675.1	s__Streptomyces anulatus	81.6899	1236	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.62	96.42	0.89	0.81	27	-
GCF_001514305.1	s__Streptomyces dysideae	81.64	1287	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001866665.1	s__Streptomyces monashensis	81.6387	1217	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.09	95.09	0.78	0.78	2	-
GCF_014650915.1	s__Streptomyces poonensis	81.6337	1234	2313	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	81.6129	1148	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000497445.1	s__Streptomyces roseochromogenus	81.6009	1242	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719955.1	s__Streptomyces albidoflavus	81.5154	1096	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.27	95.93	0.92	0.84	100	-
GCF_011170125.1	s__Streptomyces diastaticus	81.3149	1099	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.51	98.72	0.93	0.90	11	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:22,508] [INFO] GTDB search result was written to GCF_009739465.1_ASM973946v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:22,508] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:22,515] [INFO] DFAST_QC result json was written to GCF_009739465.1_ASM973946v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:22,515] [INFO] DFAST_QC completed!
[2024-01-24 12:25:22,515] [INFO] Total running time: 0h3m8s