[2024-01-24 14:22:02,928] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:02,930] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:02,930] [INFO] DQC Reference Directory: /var/lib/cwl/stge6c1f822-28a7-4e07-a12b-06ec8fc07d21/dqc_reference
[2024-01-24 14:22:04,348] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:04,350] [INFO] Task started: Prodigal
[2024-01-24 14:22:04,350] [INFO] Running command: gunzip -c /var/lib/cwl/stgb52abecd-c060-40dc-8e5f-8cdb0114a388/GCF_000718015.1_ASM71801v1_genomic.fna.gz | prodigal -d GCF_000718015.1_ASM71801v1_genomic.fna/cds.fna -a GCF_000718015.1_ASM71801v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:24,548] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:24,548] [INFO] Task started: HMMsearch
[2024-01-24 14:22:24,548] [INFO] Running command: hmmsearch --tblout GCF_000718015.1_ASM71801v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6c1f822-28a7-4e07-a12b-06ec8fc07d21/dqc_reference/reference_markers.hmm GCF_000718015.1_ASM71801v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:24,927] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:24,928] [INFO] Found 6/6 markers.
[2024-01-24 14:22:24,986] [INFO] Query marker FASTA was written to GCF_000718015.1_ASM71801v1_genomic.fna/markers.fasta
[2024-01-24 14:22:24,987] [INFO] Task started: Blastn
[2024-01-24 14:22:24,987] [INFO] Running command: blastn -query GCF_000718015.1_ASM71801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6c1f822-28a7-4e07-a12b-06ec8fc07d21/dqc_reference/reference_markers.fasta -out GCF_000718015.1_ASM71801v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:26,429] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:26,437] [INFO] Selected 21 target genomes.
[2024-01-24 14:22:26,437] [INFO] Target genome list was writen to GCF_000718015.1_ASM71801v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:26,456] [INFO] Task started: fastANI
[2024-01-24 14:22:26,456] [INFO] Running command: fastANI --query /var/lib/cwl/stgb52abecd-c060-40dc-8e5f-8cdb0114a388/GCF_000718015.1_ASM71801v1_genomic.fna.gz --refList GCF_000718015.1_ASM71801v1_genomic.fna/target_genomes.txt --output GCF_000718015.1_ASM71801v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:07,979] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:07,980] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6c1f822-28a7-4e07-a12b-06ec8fc07d21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:07,980] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6c1f822-28a7-4e07-a12b-06ec8fc07d21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:08,001] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:08,001] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:08,001] [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 catenulae	strain=NRRL B-2342	GCA_000718015.1	66875	66875	type	True	100.0	2302	2309	95	conclusive
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	92.6105	1527	2309	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	85.9273	1646	2309	95	below_threshold
Streptomyces kronopolitis	strain=CGMCC 4.7323	GCA_014646275.1	1612435	1612435	type	True	84.7654	1427	2309	95	below_threshold
Streptomyces angustmyceticus	strain=JCM 4053	GCA_019933235.1	285578	285578	type	True	84.6138	1488	2309	95	below_threshold
Streptomyces angustmyceticus	strain=NBRC 3934	GCA_009176265.1	285578	285578	type	True	84.5819	1484	2309	95	below_threshold
Streptomyces tubercidicus	strain=NBRC 13090	GCA_009811635.1	47759	47759	type	True	84.3451	1438	2309	95	below_threshold
Streptomyces inhibens	strain=NEAU-D10	GCA_003389455.1	2293571	2293571	type	True	84.3423	1420	2309	95	below_threshold
Streptomyces piniterrae	strain=jys28	GCA_005048155.1	2571125	2571125	type	True	84.3304	1454	2309	95	below_threshold
Streptomyces albospinus	strain=JCM 3399	GCA_014648695.1	285515	285515	type	True	84.2731	1468	2309	95	below_threshold
Streptomyces caniferus	strain=NBRC 15389	GCA_009811555.1	285557	285557	type	True	84.2439	1534	2309	95	below_threshold
Streptomyces platensis	strain=ATCC 23948	GCA_008704855.1	58346	58346	type	True	84.2232	1493	2309	95	below_threshold
Streptomyces platensis	strain=DSM 40041	GCA_002119195.1	58346	58346	type	True	84.2039	1462	2309	95	below_threshold
Streptomyces glebosus	strain=NBRC 13786	GCA_009811575.1	249580	249580	type	True	84.1807	1507	2309	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	83.3416	1449	2309	95	below_threshold
Streptomyces albofaciens	strain=ATCC 23873	GCA_008634025.1	66866	66866	type	True	83.2377	1455	2309	95	below_threshold
Streptomyces fradiae	strain=NRRL B-1195	GCA_002154445.1	1906	1906	suspected-type	True	81.3193	754	2309	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	81.1482	1176	2309	95	below_threshold
Streptomyces apocyni	strain=TRM 66233	GCA_009739465.1	2654677	2654677	type	True	80.8737	1046	2309	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_008704425.1	1906	1906	suspected-type	True	80.7872	1161	2309	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_009834665.1	1906	1906	suspected-type	True	80.7597	1128	2309	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:08,003] [INFO] DFAST Taxonomy check result was written to GCF_000718015.1_ASM71801v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:08,004] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:08,004] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:08,004] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6c1f822-28a7-4e07-a12b-06ec8fc07d21/dqc_reference/checkm_data
[2024-01-24 14:23:08,005] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:08,080] [INFO] Task started: CheckM
[2024-01-24 14:23:08,080] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000718015.1_ASM71801v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000718015.1_ASM71801v1_genomic.fna/checkm_input GCF_000718015.1_ASM71801v1_genomic.fna/checkm_result
[2024-01-24 14:24:37,706] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:37,707] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:37,732] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:37,732] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:37,732] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000718015.1_ASM71801v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:37,733] [INFO] Task started: Blastn
[2024-01-24 14:24:37,733] [INFO] Running command: blastn -query GCF_000718015.1_ASM71801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6c1f822-28a7-4e07-a12b-06ec8fc07d21/dqc_reference/reference_markers_gtdb.fasta -out GCF_000718015.1_ASM71801v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:39,879] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:39,882] [INFO] Selected 22 target genomes.
[2024-01-24 14:24:39,882] [INFO] Target genome list was writen to GCF_000718015.1_ASM71801v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:39,918] [INFO] Task started: fastANI
[2024-01-24 14:24:39,919] [INFO] Running command: fastANI --query /var/lib/cwl/stgb52abecd-c060-40dc-8e5f-8cdb0114a388/GCF_000718015.1_ASM71801v1_genomic.fna.gz --refList GCF_000718015.1_ASM71801v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000718015.1_ASM71801v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:25:24,297] [INFO] Task succeeded: fastANI
[2024-01-24 14:25:24,326] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:25:24,327] [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_000718015.1	s__Streptomyces catenulae	100.0	2302	2309	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_007280575.1	s__Streptomyces sp007280575	92.6443	1524	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646275.1	s__Streptomyces kronopolitis	84.7268	1433	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176265.1	s__Streptomyces angustmyceticus	84.5748	1486	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	1.00	1.00	2	-
GCF_000717345.1	s__Streptomyces lydicus	84.4125	1494	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.39	95.38	0.95	0.89	6	-
GCF_005048155.1	s__Streptomyces piniterrae	84.3604	1449	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000805335.1	s__Streptomyces sp000805335	84.3519	1428	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003389455.1	s__Streptomyces inhibens	84.3348	1420	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811635.1	s__Streptomyces tubercidicus	84.3197	1442	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811555.1	s__Streptomyces caniferus	84.2557	1533	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648695.1	s__Streptomyces albospinus	84.2391	1474	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187385.1	s__Streptomyces sp900187385	84.2342	1464	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.51	0.98	0.96	9	-
GCF_008704855.1	s__Streptomyces platensis	84.2281	1492	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.55	95.21	0.91	0.87	7	-
GCF_000935125.1	s__Streptomyces natalensis	84.2134	1445	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0251	N/A	N/A	N/A	N/A	1	-
GCF_002082195.1	s__Streptomyces gilvosporeus	84.1463	1470	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0251	N/A	N/A	N/A	N/A	1	-
GCA_000963515.1	s__Streptomyces albulus_C	83.9061	1559	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.74	99.39	0.98	0.95	6	-
GCF_001590865.1	s__Streptomyces sp001590865	83.8156	1400	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008634025.1	s__Streptomyces albofaciens	83.2804	1447	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704655.1	s__Streptomyces rimosus	83.1962	1458	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.17	96.53	0.95	0.89	49	-
GCF_005517195.1	s__Streptomyces exfoliatus_B	81.2684	1168	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927245.1	s__Streptomyces sp012927245	81.2391	1218	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008704425.1	s__Streptomyces fradiae	80.8559	1149	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.82	99.37	0.98	0.97	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:25:24,328] [INFO] GTDB search result was written to GCF_000718015.1_ASM71801v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:25:24,329] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:25:24,333] [INFO] DFAST_QC result json was written to GCF_000718015.1_ASM71801v1_genomic.fna/dqc_result.json
[2024-01-24 14:25:24,333] [INFO] DFAST_QC completed!
[2024-01-24 14:25:24,334] [INFO] Total running time: 0h3m21s