[2024-01-24 12:22:34,050] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:34,054] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:34,054] [INFO] DQC Reference Directory: /var/lib/cwl/stg1bc32ab0-d002-4cc8-890c-a76143012d26/dqc_reference
[2024-01-24 12:22:35,712] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:35,713] [INFO] Task started: Prodigal
[2024-01-24 12:22:35,713] [INFO] Running command: gunzip -c /var/lib/cwl/stgb254641e-6804-4ac4-b0be-332ffc744a29/GCF_014656095.1_ASM1465609v1_genomic.fna.gz | prodigal -d GCF_014656095.1_ASM1465609v1_genomic.fna/cds.fna -a GCF_014656095.1_ASM1465609v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:59,208] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:59,208] [INFO] Task started: HMMsearch
[2024-01-24 12:22:59,208] [INFO] Running command: hmmsearch --tblout GCF_014656095.1_ASM1465609v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1bc32ab0-d002-4cc8-890c-a76143012d26/dqc_reference/reference_markers.hmm GCF_014656095.1_ASM1465609v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:59,523] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:59,524] [INFO] Found 6/6 markers.
[2024-01-24 12:22:59,587] [INFO] Query marker FASTA was written to GCF_014656095.1_ASM1465609v1_genomic.fna/markers.fasta
[2024-01-24 12:22:59,588] [INFO] Task started: Blastn
[2024-01-24 12:22:59,588] [INFO] Running command: blastn -query GCF_014656095.1_ASM1465609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bc32ab0-d002-4cc8-890c-a76143012d26/dqc_reference/reference_markers.fasta -out GCF_014656095.1_ASM1465609v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:00,815] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:00,818] [INFO] Selected 16 target genomes.
[2024-01-24 12:23:00,819] [INFO] Target genome list was writen to GCF_014656095.1_ASM1465609v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:00,828] [INFO] Task started: fastANI
[2024-01-24 12:23:00,828] [INFO] Running command: fastANI --query /var/lib/cwl/stgb254641e-6804-4ac4-b0be-332ffc744a29/GCF_014656095.1_ASM1465609v1_genomic.fna.gz --refList GCF_014656095.1_ASM1465609v1_genomic.fna/target_genomes.txt --output GCF_014656095.1_ASM1465609v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:40,882] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:40,883] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1bc32ab0-d002-4cc8-890c-a76143012d26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:40,883] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1bc32ab0-d002-4cc8-890c-a76143012d26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:40,894] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:40,894] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:40,894] [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 longispororuber	strain=JCM 4784	GCA_014656095.1	68230	68230	type	True	100.0	2844	2857	95	conclusive
Streptomyces spectabilis	strain=ATCC 27465	GCA_008704795.1	68270	68270	type	True	88.5787	2162	2857	95	below_threshold
Streptomyces spectabilis	strain=JCM 4308	GCA_014649235.1	68270	68270	type	True	88.5276	2153	2857	95	below_threshold
Streptomyces spectabilis	strain=CECT 3146	GCA_014203475.1	68270	68270	type	True	88.5251	2159	2857	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	88.5132	2155	2857	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	83.2946	1790	2857	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	82.3993	1350	2857	95	below_threshold
Streptomyces kebangsaanensis	strain=SUK12	GCA_001906585.1	864058	864058	type	True	82.3486	1369	2857	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	82.3374	1544	2857	95	below_threshold
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	82.2872	1509	2857	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	82.2867	1506	2857	95	below_threshold
Streptomyces fumigatiscleroticus	strain=JCM 3101	GCA_014647975.1	66371	66371	type	True	82.2069	1540	2857	95	below_threshold
Streptomyces coeruleorubidus	strain=ATCC 13740	GCA_008705135.1	116188	116188	suspected-type	True	82.2004	1567	2857	95	below_threshold
Streptomyces djakartensis	strain=JCM 4957	GCA_014651075.1	68193	68193	type	True	82.1941	1416	2857	95	below_threshold
Streptomyces iakyrus	strain=NRRL ISP-5482	GCA_000717055.1	68219	68219	type	True	82.1678	1536	2857	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	81.8747	1507	2857	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:40,896] [INFO] DFAST Taxonomy check result was written to GCF_014656095.1_ASM1465609v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:40,897] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:40,897] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:40,897] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1bc32ab0-d002-4cc8-890c-a76143012d26/dqc_reference/checkm_data
[2024-01-24 12:23:40,898] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:40,979] [INFO] Task started: CheckM
[2024-01-24 12:23:40,980] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014656095.1_ASM1465609v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014656095.1_ASM1465609v1_genomic.fna/checkm_input GCF_014656095.1_ASM1465609v1_genomic.fna/checkm_result
[2024-01-24 12:25:37,019] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:37,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:37,035] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:37,035] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:37,035] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014656095.1_ASM1465609v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:37,036] [INFO] Task started: Blastn
[2024-01-24 12:25:37,036] [INFO] Running command: blastn -query GCF_014656095.1_ASM1465609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bc32ab0-d002-4cc8-890c-a76143012d26/dqc_reference/reference_markers_gtdb.fasta -out GCF_014656095.1_ASM1465609v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:38,992] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:38,995] [INFO] Selected 13 target genomes.
[2024-01-24 12:25:38,995] [INFO] Target genome list was writen to GCF_014656095.1_ASM1465609v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:39,018] [INFO] Task started: fastANI
[2024-01-24 12:25:39,018] [INFO] Running command: fastANI --query /var/lib/cwl/stgb254641e-6804-4ac4-b0be-332ffc744a29/GCF_014656095.1_ASM1465609v1_genomic.fna.gz --refList GCF_014656095.1_ASM1465609v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014656095.1_ASM1465609v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:26:11,104] [INFO] Task succeeded: fastANI
[2024-01-24 12:26:11,112] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:26:11,112] [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_014656095.1	s__Streptomyces longispororuber	100.0	2844	2857	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_000720325.1	s__Streptomyces sp000720325	88.6295	2117	2857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704795.1	s__Streptomyces spectabilis	88.56	2166	2857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.73	96.21	0.96	0.90	4	-
GCF_006088715.1	s__Streptomyces sp006088715	88.5585	2133	2857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.04	98.04	0.88	0.88	2	-
GCF_014649395.1	s__Streptomyces aureoverticillatus	86.3361	2045	2857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000414115.1	s__Streptomyces aurantiacus_A	86.2011	1818	2857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716675.1	s__Streptomyces alboflavus	85.9432	2002	2857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.12	98.24	0.94	0.89	5	-
GCF_000720475.1	s__Streptomyces aureocirculatus	85.5878	1975	2857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001906585.1	s__Streptomyces kebangsaanensis	82.3139	1375	2857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717875.1	s__Streptomyces sp000717875	82.234	1430	2857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.70	99.70	0.96	0.96	2	-
GCF_014202475.1	s__Streptomyces paradoxus	82.1825	1541	2857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717055.1	s__Streptomyces iakyrus	82.1759	1533	2857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	96.00	95.60	0.85	0.85	3	-
GCF_014651075.1	s__Streptomyces djakartensis	82.1536	1424	2857	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 12:26:11,114] [INFO] GTDB search result was written to GCF_014656095.1_ASM1465609v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:26:11,114] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:26:11,117] [INFO] DFAST_QC result json was written to GCF_014656095.1_ASM1465609v1_genomic.fna/dqc_result.json
[2024-01-24 12:26:11,117] [INFO] DFAST_QC completed!
[2024-01-24 12:26:11,117] [INFO] Total running time: 0h3m37s