[2024-01-24 10:47:08,450] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:08,452] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:08,452] [INFO] DQC Reference Directory: /var/lib/cwl/stga6da1db4-5f14-4696-bc15-129fc657d9c5/dqc_reference
[2024-01-24 10:47:11,830] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,931] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,931] [INFO] Running command: gunzip -c /var/lib/cwl/stg3624e5c1-3963-4677-9031-26c637764241/GCF_000802245.2_ASM80224v2_genomic.fna.gz | prodigal -d GCF_000802245.2_ASM80224v2_genomic.fna/cds.fna -a GCF_000802245.2_ASM80224v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:34,082] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:34,083] [INFO] Task started: HMMsearch
[2024-01-24 10:47:34,083] [INFO] Running command: hmmsearch --tblout GCF_000802245.2_ASM80224v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6da1db4-5f14-4696-bc15-129fc657d9c5/dqc_reference/reference_markers.hmm GCF_000802245.2_ASM80224v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:34,436] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:34,438] [INFO] Found 6/6 markers.
[2024-01-24 10:47:34,494] [INFO] Query marker FASTA was written to GCF_000802245.2_ASM80224v2_genomic.fna/markers.fasta
[2024-01-24 10:47:34,495] [INFO] Task started: Blastn
[2024-01-24 10:47:34,495] [INFO] Running command: blastn -query GCF_000802245.2_ASM80224v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga6da1db4-5f14-4696-bc15-129fc657d9c5/dqc_reference/reference_markers.fasta -out GCF_000802245.2_ASM80224v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:35,768] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:35,772] [INFO] Selected 25 target genomes.
[2024-01-24 10:47:35,772] [INFO] Target genome list was writen to GCF_000802245.2_ASM80224v2_genomic.fna/target_genomes.txt
[2024-01-24 10:47:37,064] [INFO] Task started: fastANI
[2024-01-24 10:47:37,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg3624e5c1-3963-4677-9031-26c637764241/GCF_000802245.2_ASM80224v2_genomic.fna.gz --refList GCF_000802245.2_ASM80224v2_genomic.fna/target_genomes.txt --output GCF_000802245.2_ASM80224v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:24,946] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:24,947] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6da1db4-5f14-4696-bc15-129fc657d9c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:24,947] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6da1db4-5f14-4696-bc15-129fc657d9c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:24,970] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:48:24,971] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:48:24,971] [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 fodineus	strain=TW1S1	GCA_001735805.1	1904616	1904616	type	True	86.4666	1712	2448	95	below_threshold
Streptomyces filipinensis	strain=JCM 4369	GCA_014649495.1	66887	66887	type	True	86.4161	1688	2448	95	below_threshold
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	86.4004	1662	2448	95	below_threshold
Streptomyces olivaceoviridis	strain=JCM 4499	GCA_014650115.1	1921	1921	type	True	86.385	1685	2448	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	86.3772	1673	2448	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	86.3635	1639	2448	95	below_threshold
Streptomyces echinatus	strain=CECT 3313	GCA_014203595.1	67293	67293	type	True	86.3567	1673	2448	95	below_threshold
Streptomyces echinatus	strain=JCM4574	GCA_020400685.1	67293	67293	type	True	86.3235	1634	2448	95	below_threshold
Streptomyces canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	86.2363	1682	2448	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	86.1433	1658	2448	95	below_threshold
Streptomyces yokosukanensis	strain=DSM 40224	GCA_001514035.1	67386	67386	type	True	86.0146	1708	2448	95	below_threshold
Streptomyces alanosinicus	strain=JCM 4714	GCA_014650595.1	68171	68171	type	True	85.8923	1659	2448	95	below_threshold
Streptomyces eurythermus	strain=JCM 4206	GCA_014649115.1	42237	42237	type	True	85.7872	1560	2448	95	below_threshold
Streptomyces rubradiris	strain=NBRC 14000	GCA_016860525.1	285531	285531	type	True	85.7527	1568	2448	95	below_threshold
Streptomyces rubradiris	strain=JCM 4955	GCA_014656255.1	285531	285531	type	True	85.7119	1566	2448	95	below_threshold
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	85.6533	1561	2448	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	85.6499	1682	2448	95	below_threshold
Streptomyces brasiliensis	strain=JCM 3086	GCA_014647875.1	1954	1954	type	True	84.1422	1523	2448	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	84.0145	1229	2448	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	83.8584	1592	2448	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	83.8372	1421	2448	95	below_threshold
Streptomyces colonosanans	strain=MUSC 93	GCA_001866645.1	1428652	1428652	type	True	83.0913	1199	2448	95	below_threshold
Streptomyces nodosus	strain=ATCC 14899	GCA_000819545.1	40318	40318	type	True	82.5546	1297	2448	95	below_threshold
Streptomyces nodosus	strain=DSM 40109	GCA_014205035.1	40318	40318	type	True	82.535	1307	2448	95	below_threshold
Streptomyces nodosus	strain=ATCC 14899	GCA_008704995.1	40318	40318	type	True	82.4616	1313	2448	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:24,973] [INFO] DFAST Taxonomy check result was written to GCF_000802245.2_ASM80224v2_genomic.fna/tc_result.tsv
[2024-01-24 10:48:24,974] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:24,975] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:24,975] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6da1db4-5f14-4696-bc15-129fc657d9c5/dqc_reference/checkm_data
[2024-01-24 10:48:24,977] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:25,050] [INFO] Task started: CheckM
[2024-01-24 10:48:25,050] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000802245.2_ASM80224v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000802245.2_ASM80224v2_genomic.fna/checkm_input GCF_000802245.2_ASM80224v2_genomic.fna/checkm_result
[2024-01-24 10:49:47,375] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:47,377] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:47,405] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:47,406] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:47,406] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000802245.2_ASM80224v2_genomic.fna/markers.fasta)
[2024-01-24 10:49:47,407] [INFO] Task started: Blastn
[2024-01-24 10:49:47,407] [INFO] Running command: blastn -query GCF_000802245.2_ASM80224v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga6da1db4-5f14-4696-bc15-129fc657d9c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000802245.2_ASM80224v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:49,338] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:49,344] [INFO] Selected 21 target genomes.
[2024-01-24 10:49:49,344] [INFO] Target genome list was writen to GCF_000802245.2_ASM80224v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:49,360] [INFO] Task started: fastANI
[2024-01-24 10:49:49,360] [INFO] Running command: fastANI --query /var/lib/cwl/stg3624e5c1-3963-4677-9031-26c637764241/GCF_000802245.2_ASM80224v2_genomic.fna.gz --refList GCF_000802245.2_ASM80224v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000802245.2_ASM80224v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:30,538] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:30,559] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:30,559] [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_000802245.2	s__Streptomyces pluripotens	100.0	2447	2448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.77	99.54	0.95	0.90	3	conclusive
GCF_900105245.1	s__Streptomyces sp900105245	86.5911	1669	2448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.80	95.98	0.93	0.89	5	-
GCF_014650035.1	s__Streptomyces lucensis	86.5708	1614	2448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001735805.1	s__Streptomyces fodineus	86.4757	1715	2448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716535.1	s__Streptomyces flaveolus_A	86.463	1660	2448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.84	0.94	0.91	9	-
GCF_017526105.1	s__Streptomyces cyanogenus	86.4604	1677	2448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920615.1	s__Streptomyces sp002920615	86.4436	1625	2448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.01	97.01	0.88	0.88	2	-
GCF_014650115.1	s__Streptomyces olivaceoviridis	86.379	1686	2448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.78	96.54	0.86	0.85	6	-
GCF_014203595.1	s__Streptomyces echinatus	86.3471	1674	2448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013046785.1	s__Streptomyces sp013046785	86.334	1644	2448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009604455.1	s__Streptomyces sp009604455	86.2896	1677	2448	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	86.2696	1375	2448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	98.00	0.86	0.72	5	-
GCF_001280015.1	s__Streptomyces sp001280015	86.2092	1670	2448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675325.1	s__Streptomyces sp003675325	86.1306	1604	2448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002242805.1	s__Streptomyces diastatochromogenes	86.0972	1671	2448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.15	97.09	0.86	0.86	5	-
GCF_000497445.1	s__Streptomyces roseochromogenus	86.0923	1707	2448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650595.1	s__Streptomyces alanosinicus	85.8745	1660	2448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007176755.1	s__Streptomyces sp007176755	85.3494	1564	2448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004124325.1	s__Streptomyces sp004124325	85.1609	1637	2448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647875.1	s__Streptomyces brasiliensis	84.1479	1521	2448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001417775.1	s__Streptomyces sp001417775	83.04	1388	2448	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 10:50:30,561] [INFO] GTDB search result was written to GCF_000802245.2_ASM80224v2_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:30,561] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:30,566] [INFO] DFAST_QC result json was written to GCF_000802245.2_ASM80224v2_genomic.fna/dqc_result.json
[2024-01-24 10:50:30,566] [INFO] DFAST_QC completed!
[2024-01-24 10:50:30,566] [INFO] Total running time: 0h3m22s