[2024-01-24 13:45:58,846] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:58,850] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:58,850] [INFO] DQC Reference Directory: /var/lib/cwl/stg7cf8ed08-a827-407a-b726-b80a44ee8f09/dqc_reference
[2024-01-24 13:46:00,118] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:00,119] [INFO] Task started: Prodigal
[2024-01-24 13:46:00,119] [INFO] Running command: gunzip -c /var/lib/cwl/stg66f75a7d-b313-4572-a38a-3f15f7ba14ad/GCF_014656055.1_ASM1465605v1_genomic.fna.gz | prodigal -d GCF_014656055.1_ASM1465605v1_genomic.fna/cds.fna -a GCF_014656055.1_ASM1465605v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:24,655] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:24,656] [INFO] Task started: HMMsearch
[2024-01-24 13:46:24,656] [INFO] Running command: hmmsearch --tblout GCF_014656055.1_ASM1465605v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7cf8ed08-a827-407a-b726-b80a44ee8f09/dqc_reference/reference_markers.hmm GCF_014656055.1_ASM1465605v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:25,141] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:25,143] [INFO] Found 6/6 markers.
[2024-01-24 13:46:25,229] [INFO] Query marker FASTA was written to GCF_014656055.1_ASM1465605v1_genomic.fna/markers.fasta
[2024-01-24 13:46:25,230] [INFO] Task started: Blastn
[2024-01-24 13:46:25,230] [INFO] Running command: blastn -query GCF_014656055.1_ASM1465605v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cf8ed08-a827-407a-b726-b80a44ee8f09/dqc_reference/reference_markers.fasta -out GCF_014656055.1_ASM1465605v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:26,788] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:26,792] [INFO] Selected 24 target genomes.
[2024-01-24 13:46:26,793] [INFO] Target genome list was writen to GCF_014656055.1_ASM1465605v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:26,811] [INFO] Task started: fastANI
[2024-01-24 13:46:26,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg66f75a7d-b313-4572-a38a-3f15f7ba14ad/GCF_014656055.1_ASM1465605v1_genomic.fna.gz --refList GCF_014656055.1_ASM1465605v1_genomic.fna/target_genomes.txt --output GCF_014656055.1_ASM1465605v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:27,598] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:27,599] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7cf8ed08-a827-407a-b726-b80a44ee8f09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:27,600] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7cf8ed08-a827-407a-b726-b80a44ee8f09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:27,623] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:27,624] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:27,624] [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 griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	100.0	2713	2715	95	conclusive
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	86.1161	1803	2715	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	86.0991	1815	2715	95	below_threshold
Streptomyces longwoodensis	strain=DSM 41677	GCA_001514125.1	68231	68231	type	True	86.0126	1845	2715	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	85.896	1532	2715	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.8027	1794	2715	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.7579	1795	2715	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	85.6473	1783	2715	95	below_threshold
Streptomyces fumigatiscleroticus	strain=JCM 3101	GCA_014647975.1	66371	66371	type	True	85.645	1803	2715	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	85.6288	1766	2715	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	85.5807	1596	2715	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	85.5562	1842	2715	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	85.5058	1790	2715	95	below_threshold
Streptomyces viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	85.4677	1377	2715	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.4241	1509	2715	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	85.4023	1808	2715	95	below_threshold
Streptomyces rubradiris	strain=NBRC 14000	GCA_016860525.1	285531	285531	type	True	85.3441	1776	2715	95	below_threshold
Streptomyces carpinensis	strain=NRRL B-16921	GCA_002154505.1	66369	66369	type	True	85.3288	1580	2715	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	85.2506	1799	2715	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	85.227	1496	2715	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	85.0542	1780	2715	95	below_threshold
Streptomyces tailanensis	strain=TRM68348	GCA_008386495.1	2569858	2569858	type	True	83.708	1592	2715	95	below_threshold
Streptomyces capitiformicae	strain=CGMCC 4.7403	GCA_014653855.1	2014920	2014920	type	True	83.5623	1671	2715	95	below_threshold
Streptomyces capitiformicae	strain=1H-SSA4	GCA_002214185.1	2014920	2014920	type	True	83.4615	1682	2715	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:27,626] [INFO] DFAST Taxonomy check result was written to GCF_014656055.1_ASM1465605v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:27,626] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:27,626] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:27,627] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7cf8ed08-a827-407a-b726-b80a44ee8f09/dqc_reference/checkm_data
[2024-01-24 13:47:27,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:27,705] [INFO] Task started: CheckM
[2024-01-24 13:47:27,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014656055.1_ASM1465605v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014656055.1_ASM1465605v1_genomic.fna/checkm_input GCF_014656055.1_ASM1465605v1_genomic.fna/checkm_result
[2024-01-24 13:49:16,168] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:16,170] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:16,191] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:16,191] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:16,191] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014656055.1_ASM1465605v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:16,191] [INFO] Task started: Blastn
[2024-01-24 13:49:16,192] [INFO] Running command: blastn -query GCF_014656055.1_ASM1465605v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cf8ed08-a827-407a-b726-b80a44ee8f09/dqc_reference/reference_markers_gtdb.fasta -out GCF_014656055.1_ASM1465605v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:18,333] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:18,337] [INFO] Selected 20 target genomes.
[2024-01-24 13:49:18,337] [INFO] Target genome list was writen to GCF_014656055.1_ASM1465605v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:18,373] [INFO] Task started: fastANI
[2024-01-24 13:49:18,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg66f75a7d-b313-4572-a38a-3f15f7ba14ad/GCF_014656055.1_ASM1465605v1_genomic.fna.gz --refList GCF_014656055.1_ASM1465605v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014656055.1_ASM1465605v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:04,738] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:04,758] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:04,759] [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_014656055.1	s__Streptomyces griseosporeus	100.0	2713	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.70	98.69	0.95	0.95	3	conclusive
GCF_016921115.1	s__Streptomyces actuosus_A	87.2819	1759	2715	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	87.2713	1901	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280195.1	s__Streptomyces galbus	86.1453	1799	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.53	0.96	0.94	3	-
GCF_011193355.1	s__Streptomyces sp011193355	86.0908	1768	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002128465.1	s__Streptomyces pharetrae	86.053	1657	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514125.1	s__Streptomyces longwoodensis	86.0353	1841	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.95	95.95	0.86	0.86	2	-
GCF_000761215.1	s__Streptomyces glaucescens	85.8565	1754	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647975.1	s__Streptomyces fumigatiscleroticus	85.6077	1809	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001013905.1	s__Streptomyces leeuwenhoekii	85.5311	1724	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.603	99.67	99.36	0.97	0.94	3	-
GCF_018070565.1	s__Streptomyces sp018070565	85.5304	1717	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000931445.1	s__Streptomyces cyaneogriseus	85.5155	1709	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.603	N/A	N/A	N/A	N/A	1	-
GCF_000716535.1	s__Streptomyces flaveolus_A	85.499	1875	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.84	0.94	0.91	9	-
GCF_000383935.1	s__Streptomyces sp000383935	85.439	1715	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.62	97.70	0.92	0.84	4	-
GCF_015160855.1	s__Streptomyces ferrugineus	85.397	1808	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343515.1	s__Streptomyces sp004343515	85.3312	1865	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.56	96.56	0.86	0.86	2	-
GCF_001866665.1	s__Streptomyces monashensis	85.0643	1778	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.09	95.09	0.78	0.78	2	-
GCF_007896895.1	s__Streptomyces misionensis_A	84.8874	1589	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920635.1	s__Streptomyces sp002920635	84.7383	1624	2715	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	83.6963	1594	2715	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 13:50:04,762] [INFO] GTDB search result was written to GCF_014656055.1_ASM1465605v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:04,763] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:04,776] [INFO] DFAST_QC result json was written to GCF_014656055.1_ASM1465605v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:04,776] [INFO] DFAST_QC completed!
[2024-01-24 13:50:04,776] [INFO] Total running time: 0h4m6s