[2024-01-25 20:04:35,778] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:04:35,779] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:04:35,780] [INFO] DQC Reference Directory: /var/lib/cwl/stg70112e7c-d424-4301-b693-3ecf4ef62db1/dqc_reference
[2024-01-25 20:04:36,923] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:04:36,924] [INFO] Task started: Prodigal
[2024-01-25 20:04:36,924] [INFO] Running command: gunzip -c /var/lib/cwl/stgca6bf147-dc94-4a0f-bc95-788f48ae1aa9/GCF_011045025.1_ASM1104502v1_genomic.fna.gz | prodigal -d GCF_011045025.1_ASM1104502v1_genomic.fna/cds.fna -a GCF_011045025.1_ASM1104502v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:02,082] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:02,082] [INFO] Task started: HMMsearch
[2024-01-25 20:05:02,082] [INFO] Running command: hmmsearch --tblout GCF_011045025.1_ASM1104502v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70112e7c-d424-4301-b693-3ecf4ef62db1/dqc_reference/reference_markers.hmm GCF_011045025.1_ASM1104502v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:02,462] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:02,463] [INFO] Found 6/6 markers.
[2024-01-25 20:05:02,541] [INFO] Query marker FASTA was written to GCF_011045025.1_ASM1104502v1_genomic.fna/markers.fasta
[2024-01-25 20:05:02,541] [INFO] Task started: Blastn
[2024-01-25 20:05:02,541] [INFO] Running command: blastn -query GCF_011045025.1_ASM1104502v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70112e7c-d424-4301-b693-3ecf4ef62db1/dqc_reference/reference_markers.fasta -out GCF_011045025.1_ASM1104502v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:03,737] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:03,739] [INFO] Selected 26 target genomes.
[2024-01-25 20:05:03,740] [INFO] Target genome list was writen to GCF_011045025.1_ASM1104502v1_genomic.fna/target_genomes.txt
[2024-01-25 20:05:03,759] [INFO] Task started: fastANI
[2024-01-25 20:05:03,759] [INFO] Running command: fastANI --query /var/lib/cwl/stgca6bf147-dc94-4a0f-bc95-788f48ae1aa9/GCF_011045025.1_ASM1104502v1_genomic.fna.gz --refList GCF_011045025.1_ASM1104502v1_genomic.fna/target_genomes.txt --output GCF_011045025.1_ASM1104502v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:05:59,984] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:59,984] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70112e7c-d424-4301-b693-3ecf4ef62db1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:05:59,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70112e7c-d424-4301-b693-3ecf4ef62db1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:05:59,999] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:05:59,999] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:06:00,000] [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 scabichelini	strain=HC44	GCA_011045015.1	2711217	2711217	type	True	89.6896	2134	3240	95	below_threshold
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_005768555.2	2315329	2315329	type	True	87.4293	2053	3240	95	below_threshold
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_003568675.1	2315329	2315329	type	True	87.4177	2056	3240	95	below_threshold
Streptomyces montanus	strain=NEAU-C151	GCA_005786655.1	2580423	2580423	type	True	87.3802	2010	3240	95	below_threshold
Streptomyces phaeochromogenes	strain=NRRL B-1248	GCA_001418655.1	1923	1923	type	True	85.7169	1839	3240	95	below_threshold
Streptomyces umbrinus	strain=JCM 4521	GCA_014650195.1	67370	67370	type	True	85.5993	2015	3240	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	84.8711	1536	3240	95	below_threshold
Streptomyces dengpaensis	strain=XZHG99	GCA_002946835.1	2049881	2049881	type	True	84.5093	1577	3240	95	below_threshold
Streptomyces mirabilis	strain=JCM 4551	GCA_014650275.1	68239	68239	suspected-type	True	84.0473	1793	3240	95	below_threshold
Streptomyces olivochromogenes	strain=DSM 40451	GCA_001514115.1	1963	1963	type	True	83.9068	1789	3240	95	below_threshold
Streptomyces swartbergensis	strain=HMC13	GCA_002148965.1	487165	487165	type	True	83.7964	1615	3240	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	83.7146	1559	3240	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	83.7123	1649	3240	95	below_threshold
Streptomyces lanatus	strain=JCM 4588	GCA_014655715.1	66900	66900	type	True	83.467	1864	3240	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	83.3865	1826	3240	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	83.2538	1841	3240	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	82.8751	1530	3240	95	below_threshold
Streptomyces humi	strain=MUSC 119	GCA_001005085.2	1428620	1428620	type	True	82.3379	1653	3240	95	below_threshold
Streptomyces thermodiastaticus	strain=JCM 4840	GCA_014656135.1	44061	44061	type	True	82.0639	1180	3240	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	81.9727	1203	3240	95	below_threshold
Streptomyces hydrogenans	strain=JCM 4771	GCA_014656075.1	1873719	1873719	type	True	80.6984	1267	3240	95	below_threshold
Streptomyces hydrogenans	strain=NBRC 13475	GCA_020521255.1	1873719	1873719	type	True	80.6742	1283	3240	95	below_threshold
Streptomyces toxytricini	strain=JCM 4421	GCA_014649915.1	67369	67369	type	True	80.3009	1119	3240	95	below_threshold
Kitasatospora paracochleata	strain=DSM 41656	GCA_024172095.1	58354	58354	type	True	78.3223	941	3240	95	below_threshold
Kitasatospora setae	strain=NRRL B-16185	GCA_000716965.1	2066	2066	type	True	77.9069	935	3240	95	below_threshold
Kitasatospora setae	strain=KM-6054	GCA_000269985.1	2066	2066	type	True	77.8432	967	3240	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:06:00,001] [INFO] DFAST Taxonomy check result was written to GCF_011045025.1_ASM1104502v1_genomic.fna/tc_result.tsv
[2024-01-25 20:06:00,002] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:06:00,002] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:06:00,002] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70112e7c-d424-4301-b693-3ecf4ef62db1/dqc_reference/checkm_data
[2024-01-25 20:06:00,003] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:06:00,097] [INFO] Task started: CheckM
[2024-01-25 20:06:00,097] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011045025.1_ASM1104502v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011045025.1_ASM1104502v1_genomic.fna/checkm_input GCF_011045025.1_ASM1104502v1_genomic.fna/checkm_result
[2024-01-25 20:07:28,227] [INFO] Task succeeded: CheckM
[2024-01-25 20:07:28,228] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-25 20:07:28,249] [INFO] ===== Completeness check finished =====
[2024-01-25 20:07:28,249] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:07:28,250] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011045025.1_ASM1104502v1_genomic.fna/markers.fasta)
[2024-01-25 20:07:28,250] [INFO] Task started: Blastn
[2024-01-25 20:07:28,250] [INFO] Running command: blastn -query GCF_011045025.1_ASM1104502v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70112e7c-d424-4301-b693-3ecf4ef62db1/dqc_reference/reference_markers_gtdb.fasta -out GCF_011045025.1_ASM1104502v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:30,199] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:30,202] [INFO] Selected 17 target genomes.
[2024-01-25 20:07:30,202] [INFO] Target genome list was writen to GCF_011045025.1_ASM1104502v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:07:30,215] [INFO] Task started: fastANI
[2024-01-25 20:07:30,216] [INFO] Running command: fastANI --query /var/lib/cwl/stgca6bf147-dc94-4a0f-bc95-788f48ae1aa9/GCF_011045025.1_ASM1104502v1_genomic.fna.gz --refList GCF_011045025.1_ASM1104502v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011045025.1_ASM1104502v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:08:08,853] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:08,864] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:08:08,864] [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_011045025.1	s__Streptomyces ureilyticus	100.0	3220	3240	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_014647675.1	s__Streptomyces flaveus	92.6444	2351	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.63	96.63	0.83	0.83	2	-
GCF_011045015.1	s__Streptomyces scabichelini	89.6992	2133	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005768555.2	s__Streptomyces sporangiiformans	87.4017	2058	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.93	95.85	0.91	0.82	3	-
GCF_008905045.1	s__Streptomyces albicerus	86.7669	2115	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007050945.1	s__Streptomyces sp007050945	85.772	2034	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418655.1	s__Streptomyces phaeochromogenes	85.6712	1849	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.97	95.89	0.88	0.87	3	-
GCF_014650275.1	s__Streptomyces mirabilis	84.0577	1791	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2382	96.82	96.27	0.84	0.80	23	-
GCF_012273535.1	s__Streptomyces sp002846625	83.8438	1871	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.4492	97.43	96.23	0.83	0.78	4	-
GCF_002148965.1	s__Streptomyces swartbergensis	83.7812	1618	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596915.1	s__Streptomyces sp014596915	83.5674	1705	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813405.1	s__Streptomyces sp002813405	82.9518	1531	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905385.1	s__Streptomyces sp001905385	82.8799	1545	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.01	96.01	0.83	0.83	2	-
GCF_014655295.1	s__Streptomyces fumanus	82.5837	1486	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004010275.1	s__Streptomyces huasconensis	82.2202	1367	3240	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	80.932	1357	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.86	99.72	0.99	0.98	3	-
GCF_014207445.1	s__Streptomyces candidus	80.7674	1169	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:08:08,866] [INFO] GTDB search result was written to GCF_011045025.1_ASM1104502v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:08:08,866] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:08:08,870] [INFO] DFAST_QC result json was written to GCF_011045025.1_ASM1104502v1_genomic.fna/dqc_result.json
[2024-01-25 20:08:08,870] [INFO] DFAST_QC completed!
[2024-01-25 20:08:08,870] [INFO] Total running time: 0h3m33s