[2024-01-24 11:20:34,468] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:34,469] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:34,469] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0dcf55b-4788-46d1-ab9b-f4386feef552/dqc_reference
[2024-01-24 11:20:35,700] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:35,701] [INFO] Task started: Prodigal
[2024-01-24 11:20:35,701] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1dc1f2c-4197-437a-b4e2-531342ceb1b4/GCF_014489615.1_ASM1448961v1_genomic.fna.gz | prodigal -d GCF_014489615.1_ASM1448961v1_genomic.fna/cds.fna -a GCF_014489615.1_ASM1448961v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:09,843] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:09,843] [INFO] Task started: HMMsearch
[2024-01-24 11:21:09,844] [INFO] Running command: hmmsearch --tblout GCF_014489615.1_ASM1448961v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0dcf55b-4788-46d1-ab9b-f4386feef552/dqc_reference/reference_markers.hmm GCF_014489615.1_ASM1448961v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:10,175] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:10,177] [INFO] Found 6/6 markers.
[2024-01-24 11:21:10,241] [INFO] Query marker FASTA was written to GCF_014489615.1_ASM1448961v1_genomic.fna/markers.fasta
[2024-01-24 11:21:10,242] [INFO] Task started: Blastn
[2024-01-24 11:21:10,242] [INFO] Running command: blastn -query GCF_014489615.1_ASM1448961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0dcf55b-4788-46d1-ab9b-f4386feef552/dqc_reference/reference_markers.fasta -out GCF_014489615.1_ASM1448961v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:11,568] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:11,572] [INFO] Selected 21 target genomes.
[2024-01-24 11:21:11,573] [INFO] Target genome list was writen to GCF_014489615.1_ASM1448961v1_genomic.fna/target_genomes.txt
[2024-01-24 11:21:11,587] [INFO] Task started: fastANI
[2024-01-24 11:21:11,588] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1dc1f2c-4197-437a-b4e2-531342ceb1b4/GCF_014489615.1_ASM1448961v1_genomic.fna.gz --refList GCF_014489615.1_ASM1448961v1_genomic.fna/target_genomes.txt --output GCF_014489615.1_ASM1448961v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:55,428] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:55,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0dcf55b-4788-46d1-ab9b-f4386feef552/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:55,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0dcf55b-4788-46d1-ab9b-f4386feef552/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:55,446] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:21:55,446] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:55,446] [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 genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	100.0	2725	2727	95	conclusive
Streptomyces zhihengii	strain=YIM T102	GCA_016919245.1	1818004	1818004	type	True	90.9707	2295	2727	95	below_threshold
Streptomyces kurssanovii	strain=JCM 4388	GCA_014649695.1	67312	67312	type	True	83.8868	1608	2727	95	below_threshold
Streptomyces xantholiticus	strain=JCM 4863	GCA_014651015.1	68285	68285	type	True	83.7217	1531	2727	95	below_threshold
Streptomyces purpureus	strain=JCM 3172	GCA_014648195.1	1951	1951	type	True	83.0978	1407	2727	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.986	1457	2727	95	below_threshold
Streptomyces cinereoruber	strain=JCM 4205	GCA_014649095.1	67260	67260	type	True	82.9613	1473	2727	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_021432215.1	54571	54571	type	True	82.9305	1219	2727	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_008639165.1	54571	54571	type	True	82.7829	1540	2727	95	below_threshold
Streptomyces vietnamensis	strain=GIM4.0001	GCA_000830005.1	362257	362257	type	True	82.6385	1509	2727	95	below_threshold
Streptomyces litmocidini	strain=JCM 4394	GCA_014649755.1	67318	67318	type	True	82.5659	1504	2727	95	below_threshold
Streptomyces tirandamycinicus	strain=HNM0039	GCA_003097515.1	2174846	2174846	type	True	82.5386	1400	2727	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.3999	1440	2727	95	below_threshold
Streptomyces kanasensis	strain=ZX01	GCA_001484625.1	936756	936756	type	True	82.3098	1348	2727	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	82.1773	1471	2727	95	below_threshold
Streptomyces violascens	strain=NBRC 12920	GCA_020521295.1	67381	67381	type	True	82.036	1369	2727	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	81.2637	1426	2727	95	below_threshold
Streptomyces hiroshimensis	strain=JCM 4586	GCA_014650335.1	66424	66424	type	True	81.0857	1216	2727	95	below_threshold
Streptomyces roseifaciens	strain=MBT76	GCA_001445655.1	1488406	1488406	type	True	81.02	1285	2727	95	below_threshold
Streptomyces klenkii	strain=KCTC 29202	GCA_003626645.1	1420899	1420899	type	True	80.8271	1271	2727	95	below_threshold
Planobispora takensis	strain=NBRC 109077	GCA_016863195.1	1367882	1367882	type	True	76.653	817	2727	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:55,448] [INFO] DFAST Taxonomy check result was written to GCF_014489615.1_ASM1448961v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:55,448] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:55,449] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:55,449] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0dcf55b-4788-46d1-ab9b-f4386feef552/dqc_reference/checkm_data
[2024-01-24 11:21:55,450] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:55,522] [INFO] Task started: CheckM
[2024-01-24 11:21:55,522] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014489615.1_ASM1448961v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014489615.1_ASM1448961v1_genomic.fna/checkm_input GCF_014489615.1_ASM1448961v1_genomic.fna/checkm_result
[2024-01-24 11:25:02,197] [INFO] Task succeeded: CheckM
[2024-01-24 11:25:02,199] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:25:02,223] [INFO] ===== Completeness check finished =====
[2024-01-24 11:25:02,223] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:25:02,224] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014489615.1_ASM1448961v1_genomic.fna/markers.fasta)
[2024-01-24 11:25:02,224] [INFO] Task started: Blastn
[2024-01-24 11:25:02,224] [INFO] Running command: blastn -query GCF_014489615.1_ASM1448961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0dcf55b-4788-46d1-ab9b-f4386feef552/dqc_reference/reference_markers_gtdb.fasta -out GCF_014489615.1_ASM1448961v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:25:04,314] [INFO] Task succeeded: Blastn
[2024-01-24 11:25:04,318] [INFO] Selected 14 target genomes.
[2024-01-24 11:25:04,318] [INFO] Target genome list was writen to GCF_014489615.1_ASM1448961v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:25:04,331] [INFO] Task started: fastANI
[2024-01-24 11:25:04,332] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1dc1f2c-4197-437a-b4e2-531342ceb1b4/GCF_014489615.1_ASM1448961v1_genomic.fna.gz --refList GCF_014489615.1_ASM1448961v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014489615.1_ASM1448961v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:25:31,834] [INFO] Task succeeded: fastANI
[2024-01-24 11:25:31,851] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:25:31,851] [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_014489615.1	s__Streptomyces sp014489615	100.0	2725	2727	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_016919245.1	s__Streptomyces zhihengii	90.9419	2294	2727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042045.1	s__Streptomyces sp008042045	90.5343	2122	2727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377145.1	s__Streptomyces sp000377145	85.4118	1597	2727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013387495.1	s__Streptomyces sp013387495	85.0072	1527	2727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018614575.1	s__Streptomyces sp018614575	84.7146	1510	2727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001278075.1	s__Streptomyces pristinaespiralis	84.1278	1714	2727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.86	99.72	0.99	0.98	3	-
GCF_014649695.1	s__Streptomyces kurssanovii	83.8549	1613	2727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716335.1	s__Streptomyces sp000716335	82.8251	1449	2727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905905.1	s__Streptomyces sp001905905	82.3543	1443	2727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.31	99.31	0.95	0.95	2	-
GCF_014596475.1	s__Streptomyces sp014596475	82.1704	1335	2727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863195.1	s__Planobispora takensis	76.6396	827	2727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_900105065.1	s__Friedmanniella luteola	76.1048	515	2727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882445.1	s__Palsa-744 sp017882445	75.3133	131	2727	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-744	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:25:31,853] [INFO] GTDB search result was written to GCF_014489615.1_ASM1448961v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:25:31,853] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:25:31,859] [INFO] DFAST_QC result json was written to GCF_014489615.1_ASM1448961v1_genomic.fna/dqc_result.json
[2024-01-24 11:25:31,859] [INFO] DFAST_QC completed!
[2024-01-24 11:25:31,859] [INFO] Total running time: 0h4m57s