[2024-01-25 19:38:20,540] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:38:20,542] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:38:20,542] [INFO] DQC Reference Directory: /var/lib/cwl/stg3cd4cebb-ac99-4337-ba30-e23a9166285f/dqc_reference
[2024-01-25 19:38:21,668] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:38:21,669] [INFO] Task started: Prodigal
[2024-01-25 19:38:21,669] [INFO] Running command: gunzip -c /var/lib/cwl/stgaea205b5-4ef1-491f-a517-52d3fb1c8b14/GCF_026274175.1_ASM2627417v1_genomic.fna.gz | prodigal -d GCF_026274175.1_ASM2627417v1_genomic.fna/cds.fna -a GCF_026274175.1_ASM2627417v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:38:37,636] [INFO] Task succeeded: Prodigal
[2024-01-25 19:38:37,637] [INFO] Task started: HMMsearch
[2024-01-25 19:38:37,637] [INFO] Running command: hmmsearch --tblout GCF_026274175.1_ASM2627417v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3cd4cebb-ac99-4337-ba30-e23a9166285f/dqc_reference/reference_markers.hmm GCF_026274175.1_ASM2627417v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:38:37,966] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:38:37,967] [INFO] Found 6/6 markers.
[2024-01-25 19:38:38,026] [INFO] Query marker FASTA was written to GCF_026274175.1_ASM2627417v1_genomic.fna/markers.fasta
[2024-01-25 19:38:38,027] [INFO] Task started: Blastn
[2024-01-25 19:38:38,027] [INFO] Running command: blastn -query GCF_026274175.1_ASM2627417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3cd4cebb-ac99-4337-ba30-e23a9166285f/dqc_reference/reference_markers.fasta -out GCF_026274175.1_ASM2627417v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:39,284] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:39,287] [INFO] Selected 32 target genomes.
[2024-01-25 19:38:39,287] [INFO] Target genome list was writen to GCF_026274175.1_ASM2627417v1_genomic.fna/target_genomes.txt
[2024-01-25 19:38:39,303] [INFO] Task started: fastANI
[2024-01-25 19:38:39,303] [INFO] Running command: fastANI --query /var/lib/cwl/stgaea205b5-4ef1-491f-a517-52d3fb1c8b14/GCF_026274175.1_ASM2627417v1_genomic.fna.gz --refList GCF_026274175.1_ASM2627417v1_genomic.fna/target_genomes.txt --output GCF_026274175.1_ASM2627417v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:39:38,607] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:38,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3cd4cebb-ac99-4337-ba30-e23a9166285f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:39:38,609] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3cd4cebb-ac99-4337-ba30-e23a9166285f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:39:38,626] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:39:38,626] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:39:38,626] [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 xanthii	strain=CRXT-Y-14	GCA_014621695.1	2768069	2768069	type	True	84.8362	1443	2146	95	below_threshold
Streptomyces alboniger	strain=NRRL B-1832	GCA_001418385.1	132473	132473	type	True	82.8929	1114	2146	95	below_threshold
Streptomyces alboniger	strain=ATCC 12461	GCA_008704395.1	132473	132473	type	True	82.8059	1256	2146	95	below_threshold
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	82.6229	1272	2146	95	below_threshold
Streptomyces dengpaensis	strain=XZHG99	GCA_002946835.1	2049881	2049881	type	True	82.5995	1216	2146	95	below_threshold
Streptomyces parvulus	strain=JCM 4068	GCA_014648855.1	146923	146923	type	True	82.5753	1213	2146	95	below_threshold
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	82.5719	1250	2146	95	below_threshold
Streptomyces longispororuber	strain=JCM 4784	GCA_014656095.1	68230	68230	type	True	82.5246	1274	2146	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	82.5152	1324	2146	95	below_threshold
Streptomyces ardesiacus	strain=NBRC 15402	GCA_003112575.1	285564	285564	type	True	82.4555	1243	2146	95	below_threshold
Streptomyces hyderabadensis	strain=JCM 17657	GCA_020404845.1	598549	598549	type	True	82.3895	1260	2146	95	below_threshold
Streptomyces poonensis	strain=JCM 4815	GCA_014650915.1	68255	68255	type	True	82.3643	1211	2146	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	82.3232	1298	2146	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	82.318	1321	2146	95	below_threshold
Streptomyces misionensis	strain=DSM 40306	GCA_900104815.1	67331	67331	type	True	82.2372	1270	2146	95	below_threshold
Streptomyces chartreusis	strain=ATCC 14922	GCA_008704715.1	1969	1969	suspected-type	True	82.1977	1330	2146	95	below_threshold
Streptomyces chartreusis	strain=JCM 4570	GCA_014650315.1	1969	1969	suspected-type	True	82.1786	1314	2146	95	below_threshold
Streptomyces phaeochromogenes	strain=NRRL B-1248	GCA_001418655.1	1923	1923	type	True	82.1025	1182	2146	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	82.0682	1356	2146	95	below_threshold
Streptomyces montanus	strain=NEAU-C151	GCA_005786655.1	2580423	2580423	type	True	82.0188	1217	2146	95	below_threshold
Streptomyces griseofuscus	strain=NRRL B-5429	GCA_000718315.1	146922	146922	type	True	82.0059	1252	2146	95	below_threshold
Streptomyces hokutonensis	strain=R1-NS-10	GCA_000376565.1	1306990	1306990	type	True	81.9716	1317	2146	95	below_threshold
Streptomyces prunicolor	strain=NBRC 13075	GCA_000367365.1	67348	67348	type	True	81.966	1291	2146	95	below_threshold
Streptomyces phaeolivaceus	strain=GY16	GCA_009184865.1	2653200	2653200	type	True	81.8773	1270	2146	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	81.8187	1319	2146	95	below_threshold
Streptomyces adelaidensis	strain=CAP261	GCA_016598475.1	2796465	2796465	type	True	81.8017	1248	2146	95	below_threshold
Streptomyces tailanensis	strain=TRM68348	GCA_008386495.1	2569858	2569858	type	True	81.7618	1232	2146	95	below_threshold
Streptomyces lavendofoliae	strain=JCM 4391	GCA_014649735.1	67314	67314	type	True	81.511	1151	2146	95	below_threshold
Streptomyces cavourensis	strain=DSM 41795	GCA_006788935.1	67258	67258	type	True	81.4971	1173	2146	95	below_threshold
Streptomyces cavourensis	strain=JCM 4298	GCA_014649215.1	67258	67258	type	True	81.4788	1152	2146	95	below_threshold
Streptomyces parvus	strain=NRRL B-1455	GCA_008632535.1	66428	66428	type	True	81.3633	1105	2146	95	below_threshold
Streptomyces gobiensis	strain=1_25	GCA_021216675.1	2875706	2875706	type	True	79.7436	758	2146	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:39:38,628] [INFO] DFAST Taxonomy check result was written to GCF_026274175.1_ASM2627417v1_genomic.fna/tc_result.tsv
[2024-01-25 19:39:38,629] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:39:38,629] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:39:38,629] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3cd4cebb-ac99-4337-ba30-e23a9166285f/dqc_reference/checkm_data
[2024-01-25 19:39:38,630] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:39:38,695] [INFO] Task started: CheckM
[2024-01-25 19:39:38,695] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026274175.1_ASM2627417v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026274175.1_ASM2627417v1_genomic.fna/checkm_input GCF_026274175.1_ASM2627417v1_genomic.fna/checkm_result
[2024-01-25 19:41:06,421] [INFO] Task succeeded: CheckM
[2024-01-25 19:41:06,422] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:41:06,441] [INFO] ===== Completeness check finished =====
[2024-01-25 19:41:06,441] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:41:06,442] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026274175.1_ASM2627417v1_genomic.fna/markers.fasta)
[2024-01-25 19:41:06,442] [INFO] Task started: Blastn
[2024-01-25 19:41:06,442] [INFO] Running command: blastn -query GCF_026274175.1_ASM2627417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3cd4cebb-ac99-4337-ba30-e23a9166285f/dqc_reference/reference_markers_gtdb.fasta -out GCF_026274175.1_ASM2627417v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:41:08,512] [INFO] Task succeeded: Blastn
[2024-01-25 19:41:08,515] [INFO] Selected 27 target genomes.
[2024-01-25 19:41:08,515] [INFO] Target genome list was writen to GCF_026274175.1_ASM2627417v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:41:08,563] [INFO] Task started: fastANI
[2024-01-25 19:41:08,563] [INFO] Running command: fastANI --query /var/lib/cwl/stgaea205b5-4ef1-491f-a517-52d3fb1c8b14/GCF_026274175.1_ASM2627417v1_genomic.fna.gz --refList GCF_026274175.1_ASM2627417v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026274175.1_ASM2627417v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:42:00,718] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:00,737] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:42:00,738] [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_017377775.1	s__Streptomyces sp017377775	85.1132	1523	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373565.1	s__Streptomyces sp000373565	85.0358	1478	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003259365.1	s__Streptomyces sp003259365	84.8531	1479	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014621695.1	s__Streptomyces sp014621695	84.8376	1444	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005495.1	s__Streptomyces sp004005495	83.5201	1363	2146	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	83.3992	1366	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003403055.1	s__Streptomyces sp003403055	83.3716	1406	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005565.1	s__Streptomyces sp002005565	82.7477	1231	2146	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	82.6468	1268	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	98.56	0.90	0.90	2	-
GCF_002946835.1	s__Streptomyces dengpaensis	82.6048	1215	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014648855.1	s__Streptomyces parvulus	82.5728	1214	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.39	95.93	0.93	0.87	4	-
GCF_001905385.1	s__Streptomyces sp001905385	82.5679	1262	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.01	96.01	0.83	0.83	2	-
GCA_002128465.1	s__Streptomyces pharetrae	82.5327	1202	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772045.1	s__Streptomyces sp000772045	82.4772	1264	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.88	95.78	0.85	0.82	9	-
GCF_014656095.1	s__Streptomyces longispororuber	82.4752	1282	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112575.1	s__Streptomyces ardesiacus	82.4324	1250	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.97	95.84	0.93	0.82	10	-
GCF_001484565.1	s__Streptomyces sp001484565	82.3757	1399	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104815.1	s__Streptomyces misionensis	82.187	1279	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.36	97.46	0.91	0.87	3	-
GCF_001418655.1	s__Streptomyces phaeochromogenes	82.1204	1180	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.97	95.89	0.88	0.87	3	-
GCF_001514305.1	s__Streptomyces dysideae	82.0705	1355	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018638295.1	s__Streptomyces sp018638295	82.0157	1117	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000367365.1	s__Streptomyces prunicolor	81.9373	1296	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184865.1	s__Streptomyces phaeolivaceus	81.8612	1272	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386495.1	s__Streptomyces tailanensis	81.761	1231	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598475.1	s__Streptomyces adelaidensis	81.7443	1259	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718455.1	s__Streptomyces globisporus_A	81.4911	1114	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2621	N/A	N/A	N/A	N/A	1	-
GCF_016862995.1	s__Acrocarpospora phusangensis	76.3476	511	2146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:42:00,739] [INFO] GTDB search result was written to GCF_026274175.1_ASM2627417v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:42:00,740] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:42:00,746] [INFO] DFAST_QC result json was written to GCF_026274175.1_ASM2627417v1_genomic.fna/dqc_result.json
[2024-01-25 19:42:00,746] [INFO] DFAST_QC completed!
[2024-01-25 19:42:00,746] [INFO] Total running time: 0h3m40s