[2024-01-24 10:47:11,673] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:11,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:11,710] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa100e86-4f85-48f6-9cf8-74852f549b4f/dqc_reference
[2024-01-24 10:47:16,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:16,945] [INFO] Task started: Prodigal
[2024-01-24 10:47:16,946] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7da8f4a-4a8b-4ba2-aead-abd80d2b9356/GCF_014651135.1_ASM1465113v1_genomic.fna.gz | prodigal -d GCF_014651135.1_ASM1465113v1_genomic.fna/cds.fna -a GCF_014651135.1_ASM1465113v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:40,572] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:40,572] [INFO] Task started: HMMsearch
[2024-01-24 10:47:40,573] [INFO] Running command: hmmsearch --tblout GCF_014651135.1_ASM1465113v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa100e86-4f85-48f6-9cf8-74852f549b4f/dqc_reference/reference_markers.hmm GCF_014651135.1_ASM1465113v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:40,907] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:40,909] [INFO] Found 6/6 markers.
[2024-01-24 10:47:40,975] [INFO] Query marker FASTA was written to GCF_014651135.1_ASM1465113v1_genomic.fna/markers.fasta
[2024-01-24 10:47:40,976] [INFO] Task started: Blastn
[2024-01-24 10:47:40,976] [INFO] Running command: blastn -query GCF_014651135.1_ASM1465113v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa100e86-4f85-48f6-9cf8-74852f549b4f/dqc_reference/reference_markers.fasta -out GCF_014651135.1_ASM1465113v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:42,366] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:42,370] [INFO] Selected 24 target genomes.
[2024-01-24 10:47:42,370] [INFO] Target genome list was writen to GCF_014651135.1_ASM1465113v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:42,380] [INFO] Task started: fastANI
[2024-01-24 10:47:42,380] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7da8f4a-4a8b-4ba2-aead-abd80d2b9356/GCF_014651135.1_ASM1465113v1_genomic.fna.gz --refList GCF_014651135.1_ASM1465113v1_genomic.fna/target_genomes.txt --output GCF_014651135.1_ASM1465113v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:29,517] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:29,518] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa100e86-4f85-48f6-9cf8-74852f549b4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:29,518] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa100e86-4f85-48f6-9cf8-74852f549b4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:29,537] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:29,537] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:29,537] [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 echinoruber	strain=JCM 5016	GCA_014651135.1	68898	68898	type	True	100.0	2390	2398	95	conclusive
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	85.2064	1475	2398	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	85.2062	1638	2398	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	85.1101	1540	2398	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.0909	1537	2398	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	85.0785	1571	2398	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.0763	1359	2398	95	below_threshold
Streptomyces leeuwenhoekii	strain=C34	GCA_000696595.1	1437453	1437453	type	True	85.0506	1371	2398	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	85.0107	1560	2398	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	84.9665	1582	2398	95	below_threshold
Streptomyces carpinensis	strain=NRRL B-16921	GCA_002154505.1	66369	66369	type	True	84.9421	1452	2398	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	84.9249	1498	2398	95	below_threshold
Streptomyces leeuwenhoekii	strain=C34 (= DSM 42122 = NRRL B-24963)	GCA_001013905.1	1437453	1437453	type	True	84.9165	1519	2398	95	below_threshold
Streptomyces lomondensis	strain=JCM 4866	GCA_014651035.1	68229	68229	type	True	84.9069	1612	2398	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	84.9012	1324	2398	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	84.8597	1379	2398	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	84.6362	1581	2398	95	below_threshold
Streptomyces canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	84.6358	1630	2398	95	below_threshold
Streptomyces olivaceoviridis	strain=JCM 4499	GCA_014650115.1	1921	1921	type	True	84.6186	1615	2398	95	below_threshold
Streptomyces chromofuscus	strain=JCM 4354	GCA_014649435.1	42881	42881	type	True	84.5581	1558	2398	95	below_threshold
Streptomyces fodineus	strain=TW1S1	GCA_001735805.1	1904616	1904616	type	True	84.3991	1593	2398	95	below_threshold
Streptomyces misionensis	strain=DSM 40306	GCA_900104815.1	67331	67331	type	True	84.3249	1535	2398	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	84.2479	1575	2398	95	below_threshold
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	83.7383	1484	2398	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:29,539] [INFO] DFAST Taxonomy check result was written to GCF_014651135.1_ASM1465113v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:29,539] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:29,540] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:29,540] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa100e86-4f85-48f6-9cf8-74852f549b4f/dqc_reference/checkm_data
[2024-01-24 10:48:29,541] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:29,609] [INFO] Task started: CheckM
[2024-01-24 10:48:29,609] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651135.1_ASM1465113v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651135.1_ASM1465113v1_genomic.fna/checkm_input GCF_014651135.1_ASM1465113v1_genomic.fna/checkm_result
[2024-01-24 10:50:09,062] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:09,064] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:09,094] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:09,094] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:09,094] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651135.1_ASM1465113v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:09,095] [INFO] Task started: Blastn
[2024-01-24 10:50:09,095] [INFO] Running command: blastn -query GCF_014651135.1_ASM1465113v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa100e86-4f85-48f6-9cf8-74852f549b4f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651135.1_ASM1465113v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:11,362] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:11,371] [INFO] Selected 23 target genomes.
[2024-01-24 10:50:11,372] [INFO] Target genome list was writen to GCF_014651135.1_ASM1465113v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:11,912] [INFO] Task started: fastANI
[2024-01-24 10:50:11,912] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7da8f4a-4a8b-4ba2-aead-abd80d2b9356/GCF_014651135.1_ASM1465113v1_genomic.fna.gz --refList GCF_014651135.1_ASM1465113v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651135.1_ASM1465113v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:58,046] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:58,073] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:58,074] [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_014651135.1	s__Streptomyces echinoruber	100.0	2390	2398	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_902506575.1	s__Streptomyces mexicanus	85.4119	1545	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.95	96.19	0.87	0.78	3	-
GCF_014650655.1	s__Streptomyces anandii	85.3556	1621	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650575.1	s__Streptomyces naganishii	85.3369	1619	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920535.1	s__Streptomyces sp002920535	85.2957	1550	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009852415.1	s__Streptomyces sp009852415	85.2141	1612	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656055.1	s__Streptomyces griseosporeus	85.1973	1639	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.70	98.69	0.95	0.95	3	-
GCF_000931445.1	s__Streptomyces cyaneogriseus	85.1309	1519	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.603	N/A	N/A	N/A	N/A	1	-
GCF_014534645.1	s__Streptomyces sp014534645	85.1	1536	2398	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	85.0632	1574	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.88	99.76	0.99	0.98	3	-
GCF_000383935.1	s__Streptomyces sp000383935	85.0484	1586	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.62	97.70	0.92	0.84	4	-
GCF_005280195.1	s__Streptomyces galbus	84.9798	1561	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.53	0.96	0.94	3	-
GCF_001013905.1	s__Streptomyces leeuwenhoekii	84.9348	1517	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.603	99.67	99.36	0.97	0.94	3	-
GCF_014651035.1	s__Streptomyces lomondensis	84.9153	1610	2398	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	84.905	1568	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017526105.1	s__Streptomyces cyanogenus	84.8844	1617	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000761215.1	s__Streptomyces glaucescens	84.8321	1539	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155905.1	s__Streptomyces tricolor	84.7585	1348	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	98.00	0.86	0.72	5	-
GCF_000716535.1	s__Streptomyces flaveolus_A	84.7288	1634	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.84	0.94	0.91	9	-
GCF_012034205.1	s__Streptomyces sp012034205	84.639	1458	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636945.1	s__Streptomyces sp001636945	84.4772	1534	2398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015160855.1	s__Streptomyces ferrugineus	84.2864	1569	2398	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	84.1894	1591	2398	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 10:50:58,075] [INFO] GTDB search result was written to GCF_014651135.1_ASM1465113v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:58,077] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:58,082] [INFO] DFAST_QC result json was written to GCF_014651135.1_ASM1465113v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:58,083] [INFO] DFAST_QC completed!
[2024-01-24 10:50:58,083] [INFO] Total running time: 0h3m46s