[2024-01-24 13:27:55,381] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:55,383] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:55,383] [INFO] DQC Reference Directory: /var/lib/cwl/stge57738e5-0057-4932-8e9c-896cb29eacca/dqc_reference
[2024-01-24 13:27:56,720] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:56,721] [INFO] Task started: Prodigal
[2024-01-24 13:27:56,722] [INFO] Running command: gunzip -c /var/lib/cwl/stg422c7207-3733-424d-931b-5177bc83be0d/GCF_000719255.1_ASM71925v1_genomic.fna.gz | prodigal -d GCF_000719255.1_ASM71925v1_genomic.fna/cds.fna -a GCF_000719255.1_ASM71925v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:21,265] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:21,266] [INFO] Task started: HMMsearch
[2024-01-24 13:28:21,266] [INFO] Running command: hmmsearch --tblout GCF_000719255.1_ASM71925v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge57738e5-0057-4932-8e9c-896cb29eacca/dqc_reference/reference_markers.hmm GCF_000719255.1_ASM71925v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:21,728] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:21,730] [INFO] Found 6/6 markers.
[2024-01-24 13:28:21,800] [INFO] Query marker FASTA was written to GCF_000719255.1_ASM71925v1_genomic.fna/markers.fasta
[2024-01-24 13:28:21,800] [INFO] Task started: Blastn
[2024-01-24 13:28:21,801] [INFO] Running command: blastn -query GCF_000719255.1_ASM71925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge57738e5-0057-4932-8e9c-896cb29eacca/dqc_reference/reference_markers.fasta -out GCF_000719255.1_ASM71925v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:23,145] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:23,161] [INFO] Selected 22 target genomes.
[2024-01-24 13:28:23,162] [INFO] Target genome list was writen to GCF_000719255.1_ASM71925v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:23,190] [INFO] Task started: fastANI
[2024-01-24 13:28:23,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg422c7207-3733-424d-931b-5177bc83be0d/GCF_000719255.1_ASM71925v1_genomic.fna.gz --refList GCF_000719255.1_ASM71925v1_genomic.fna/target_genomes.txt --output GCF_000719255.1_ASM71925v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:07,977] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:07,977] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge57738e5-0057-4932-8e9c-896cb29eacca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:07,978] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge57738e5-0057-4932-8e9c-896cb29eacca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:08,006] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:29:08,007] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:08,007] [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 varsoviensis	strain=NRRL B-3589	GCA_000719255.1	67373	67373	type	True	100.0	2803	2805	95	conclusive
Streptomyces varsoviensis	strain=NRRL ISP-5346	GCA_000718635.1	67373	67373	type	True	99.9915	2790	2805	95	conclusive
Streptomyces syringium	strain=DSM 41480	GCA_017876625.1	76729	76729	type	True	83.1062	1452	2805	95	below_threshold
Streptomyces netropsis	strain=CECT 3265	GCA_014203545.1	55404	55404	type	True	82.9935	1476	2805	95	below_threshold
Streptomyces eurocidicus	strain=CECT 3259	GCA_014203505.1	66423	66423	type	True	82.8589	1464	2805	95	below_threshold
Streptomyces eurocidicus	strain=ATCC 27428	GCA_002891295.1	66423	66423	type	True	82.8173	1448	2805	95	below_threshold
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	82.7432	1382	2805	95	below_threshold
Streptomyces eurocidicus	strain=NRRL ISP-5604	GCA_015475845.1	66423	66423	type	True	82.7026	1462	2805	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	82.7025	1374	2805	95	below_threshold
Streptomyces albireticuli	strain=NRRL B-1670	GCA_002286695.1	1940	1940	type	True	82.6002	1342	2805	95	below_threshold
Streptomyces mashuensis	strain=JCM 4059	GCA_014654785.1	33904	33904	type	True	82.0792	1334	2805	95	below_threshold
Streptomyces huiliensis	strain=SCA2-4	GCA_020037025.1	2876027	2876027	type	True	81.949	1262	2805	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	81.9369	1609	2805	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	81.7843	1584	2805	95	below_threshold
Streptomyces hygroscopicus subsp. hygroscopicus	strain=NBRC 13472	GCA_001553455.1	68042	1912	type	True	81.54	1371	2805	95	below_threshold
Streptomyces platensis	strain=DSM 40041	GCA_002119195.1	58346	58346	type	True	81.4903	1356	2805	95	below_threshold
Streptomyces sabulosicollis	strain=PRKS01-29	GCA_016103465.1	2715963	2715963	type	True	81.4608	1298	2805	95	below_threshold
Streptomyces iranensis	strain=DSM 41954	GCA_017874715.1	576784	576784	type	True	81.286	1516	2805	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	81.0733	1534	2805	95	below_threshold
Streptomyces orinoci	strain=NRRL B-3379	GCA_003121295.1	67339	67339	type	True	80.9685	1240	2805	95	below_threshold
Actinacidiphila alni	strain=CGMCC 4.3510	GCA_900112845.1	380248	380248	type	True	80.1549	1247	2805	95	below_threshold
Streptomyces qinglanensis	strain=172205	GCA_003265665.1	943816	943816	type	True	79.8802	1148	2805	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:08,009] [INFO] DFAST Taxonomy check result was written to GCF_000719255.1_ASM71925v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:08,009] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:08,009] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:08,010] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge57738e5-0057-4932-8e9c-896cb29eacca/dqc_reference/checkm_data
[2024-01-24 13:29:08,011] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:08,088] [INFO] Task started: CheckM
[2024-01-24 13:29:08,088] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000719255.1_ASM71925v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000719255.1_ASM71925v1_genomic.fna/checkm_input GCF_000719255.1_ASM71925v1_genomic.fna/checkm_result
[2024-01-24 13:30:23,120] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:23,121] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:23,149] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:23,150] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:23,150] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000719255.1_ASM71925v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:23,151] [INFO] Task started: Blastn
[2024-01-24 13:30:23,151] [INFO] Running command: blastn -query GCF_000719255.1_ASM71925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge57738e5-0057-4932-8e9c-896cb29eacca/dqc_reference/reference_markers_gtdb.fasta -out GCF_000719255.1_ASM71925v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:25,238] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:25,242] [INFO] Selected 23 target genomes.
[2024-01-24 13:30:25,243] [INFO] Target genome list was writen to GCF_000719255.1_ASM71925v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:25,259] [INFO] Task started: fastANI
[2024-01-24 13:30:25,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg422c7207-3733-424d-931b-5177bc83be0d/GCF_000719255.1_ASM71925v1_genomic.fna.gz --refList GCF_000719255.1_ASM71925v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000719255.1_ASM71925v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:11,902] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:11,924] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:31:11,924] [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_000718635.1	s__Streptomyces varsoviensis	99.9915	2790	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_017876625.1	s__Streptomyces syringium	83.0944	1454	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.60	99.60	0.98	0.98	2	-
GCF_018614525.1	s__Streptomyces sp018614525	83.0196	1293	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203545.1	s__Streptomyces netropsis	82.9777	1480	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002891295.1	s__Streptomyces eurocidicus	82.8607	1440	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	3	-
GCF_002192455.1	s__Streptomyces albireticuli_B	82.7834	1493	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650495.1	s__Streptomyces cinnamoneus	82.7281	1358	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286695.1	s__Streptomyces albireticuli	82.6575	1331	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654785.1	s__Streptomyces mashuensis	82.0804	1331	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013055795.1	s__Streptomyces sp013055795	81.9772	1326	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007595705.1	s__Streptomyces sp007595705	81.7335	1392	2805	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	81.6304	1356	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001553455.1	s__Streptomyces hygroscopicus	81.5654	1366	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.24	98.00	0.92	0.90	7	-
GCF_008704855.1	s__Streptomyces platensis	81.5417	1358	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.55	95.21	0.91	0.87	7	-
GCF_013364155.1	s__Streptomyces sp013364155	81.4169	1416	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874715.1	s__Streptomyces iranensis	81.2901	1514	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.67	99.98	99.98	1.00	1.00	2	-
GCF_018138715.1	s__Streptomyces asiaticus	81.1685	1516	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	95.36	0.90	0.81	10	-
GCF_016741935.1	s__Streptomyces sp016741935	81.1539	1529	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0488	N/A	N/A	N/A	N/A	1	-
GCF_003675955.1	s__Streptomyces rapamycinicus	81.1003	1558	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.67	99.95	99.91	0.99	0.99	3	-
GCF_015689475.1	s__Streptomyces solisilvae	81.0773	1473	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.71	97.94	0.94	0.86	10	-
GCF_003121295.1	s__Streptomyces orinoci	80.9689	1240	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003999195.1	s__Streptomyces sp003999195	80.3652	1127	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112845.1	s__Streptomyces alni	80.1122	1256	2805	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 13:31:11,926] [INFO] GTDB search result was written to GCF_000719255.1_ASM71925v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:11,927] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:11,934] [INFO] DFAST_QC result json was written to GCF_000719255.1_ASM71925v1_genomic.fna/dqc_result.json
[2024-01-24 13:31:11,935] [INFO] DFAST_QC completed!
[2024-01-24 13:31:11,935] [INFO] Total running time: 0h3m17s