[2024-01-25 18:00:51,049] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:00:51,054] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:00:51,054] [INFO] DQC Reference Directory: /var/lib/cwl/stge645c067-16fc-4ef9-bd36-7dc03a677dd3/dqc_reference
[2024-01-25 18:00:52,216] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:00:52,217] [INFO] Task started: Prodigal
[2024-01-25 18:00:52,217] [INFO] Running command: gunzip -c /var/lib/cwl/stgf80e353b-c54a-4ee0-932a-23a5e680983d/GCF_014648955.1_ASM1464895v1_genomic.fna.gz | prodigal -d GCF_014648955.1_ASM1464895v1_genomic.fna/cds.fna -a GCF_014648955.1_ASM1464895v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:01:07,604] [INFO] Task succeeded: Prodigal
[2024-01-25 18:01:07,605] [INFO] Task started: HMMsearch
[2024-01-25 18:01:07,605] [INFO] Running command: hmmsearch --tblout GCF_014648955.1_ASM1464895v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge645c067-16fc-4ef9-bd36-7dc03a677dd3/dqc_reference/reference_markers.hmm GCF_014648955.1_ASM1464895v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:01:07,884] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:01:07,885] [INFO] Found 6/6 markers.
[2024-01-25 18:01:07,944] [INFO] Query marker FASTA was written to GCF_014648955.1_ASM1464895v1_genomic.fna/markers.fasta
[2024-01-25 18:01:07,944] [INFO] Task started: Blastn
[2024-01-25 18:01:07,944] [INFO] Running command: blastn -query GCF_014648955.1_ASM1464895v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge645c067-16fc-4ef9-bd36-7dc03a677dd3/dqc_reference/reference_markers.fasta -out GCF_014648955.1_ASM1464895v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:09,205] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:09,208] [INFO] Selected 10 target genomes.
[2024-01-25 18:01:09,208] [INFO] Target genome list was writen to GCF_014648955.1_ASM1464895v1_genomic.fna/target_genomes.txt
[2024-01-25 18:01:09,219] [INFO] Task started: fastANI
[2024-01-25 18:01:09,219] [INFO] Running command: fastANI --query /var/lib/cwl/stgf80e353b-c54a-4ee0-932a-23a5e680983d/GCF_014648955.1_ASM1464895v1_genomic.fna.gz --refList GCF_014648955.1_ASM1464895v1_genomic.fna/target_genomes.txt --output GCF_014648955.1_ASM1464895v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:01:28,762] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:28,763] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge645c067-16fc-4ef9-bd36-7dc03a677dd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:01:28,763] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge645c067-16fc-4ef9-bd36-7dc03a677dd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:01:28,771] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 18:01:28,771] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:01:28,771] [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 gougerotii	strain=JCM 4136	GCA_014648955.1	53448	53448	suspected-type	True	100.0	2163	2166	95	inconclusive
Streptomyces gougerotii	strain=NBRC 13043	GCA_011170145.1	53448	53448	suspected-type	True	99.9825	2154	2166	95	inconclusive
Streptomyces diastaticus subsp. diastaticus	strain=JCM 4128	GCA_014648935.1	68040	1956	suspected-type	True	99.6192	2081	2166	95	inconclusive
Streptomyces diastaticus subsp. diastaticus	strain=NBRC 13412	GCA_011170125.1	68040	1956	suspected-type	True	99.6026	2094	2166	95	inconclusive
Streptomyces albidoflavus	strain=DSM 40455	GCA_004195735.1	1886	1886	type	True	92.1205	1799	2166	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	81.7234	1217	2166	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	81.6241	989	2166	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	81.5184	1034	2166	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	81.2388	1201	2166	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	81.0961	1207	2166	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:01:28,774] [INFO] DFAST Taxonomy check result was written to GCF_014648955.1_ASM1464895v1_genomic.fna/tc_result.tsv
[2024-01-25 18:01:28,775] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:01:28,775] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:01:28,775] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge645c067-16fc-4ef9-bd36-7dc03a677dd3/dqc_reference/checkm_data
[2024-01-25 18:01:28,776] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:01:28,839] [INFO] Task started: CheckM
[2024-01-25 18:01:28,839] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648955.1_ASM1464895v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648955.1_ASM1464895v1_genomic.fna/checkm_input GCF_014648955.1_ASM1464895v1_genomic.fna/checkm_result
[2024-01-25 18:02:53,832] [INFO] Task succeeded: CheckM
[2024-01-25 18:02:53,833] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:02:53,864] [INFO] ===== Completeness check finished =====
[2024-01-25 18:02:53,865] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:02:53,866] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648955.1_ASM1464895v1_genomic.fna/markers.fasta)
[2024-01-25 18:02:53,866] [INFO] Task started: Blastn
[2024-01-25 18:02:53,866] [INFO] Running command: blastn -query GCF_014648955.1_ASM1464895v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge645c067-16fc-4ef9-bd36-7dc03a677dd3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648955.1_ASM1464895v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:56,094] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:56,097] [INFO] Selected 23 target genomes.
[2024-01-25 18:02:56,097] [INFO] Target genome list was writen to GCF_014648955.1_ASM1464895v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:02:56,118] [INFO] Task started: fastANI
[2024-01-25 18:02:56,118] [INFO] Running command: fastANI --query /var/lib/cwl/stgf80e353b-c54a-4ee0-932a-23a5e680983d/GCF_014648955.1_ASM1464895v1_genomic.fna.gz --refList GCF_014648955.1_ASM1464895v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648955.1_ASM1464895v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:03:38,619] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:38,634] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:03:38,634] [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_011170125.1	s__Streptomyces diastaticus	99.6026	2094	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.51	98.72	0.93	0.90	11	conclusive
GCF_000719955.1	s__Streptomyces albidoflavus	92.1661	1800	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.27	95.93	0.92	0.84	100	-
GCF_018069565.1	s__Streptomyces sp018069565	81.9031	1293	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112555.1	s__Streptomyces coelicoflavus	81.8797	1311	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	97.03	0.90	0.86	6	-
GCF_900091845.1	s__Streptomyces sp900091845	81.8415	1269	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_010548465.1	s__Streptomyces sp010548465	81.8025	1043	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014655295.1	s__Streptomyces fumanus	81.7859	1308	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003268675.1	s__Streptomyces bacillaris	81.7643	1310	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.84	95.80	0.88	0.83	37	-
GCF_019090105.1	s__Streptomyces sp019090105	81.7284	1152	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004784465.1	s__Streptomyces griseoluteus	81.7173	1157	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3953	97.39	95.67	0.90	0.82	4	-
GCF_014648855.1	s__Streptomyces parvulus	81.6906	1292	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.39	95.93	0.93	0.87	4	-
GCF_004127445.1	s__Streptomyces alfalfae	81.6364	1268	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.46	98.55	0.94	0.88	8	-
GCF_014656095.1	s__Streptomyces longispororuber	81.518	1291	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649335.1	s__Streptomyces roseolilacinus	81.5176	1169	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018982965.1	s__Streptomyces sp018982965	81.5088	1265	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003671715.1	s__Streptomyces sp003671715	81.491	1252	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.92	95.92	0.81	0.81	2	-
GCF_007679425.1	s__Streptomyces incarnatus_A	81.3437	1202	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	99.00	0.97	0.94	3	-
GCF_000720835.1	s__Streptomyces achromogenes	81.3432	1231	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	N/A	N/A	N/A	N/A	1	-
GCF_001905885.1	s__Streptomyces sp001905885	81.3253	1222	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.05	96.05	0.87	0.87	2	-
GCF_002155905.1	s__Streptomyces tricolor	81.1381	1095	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	98.00	0.86	0.72	5	-
GCF_014649115.1	s__Streptomyces eurythermus	81.0785	1305	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	97.90	96.79	0.90	0.85	4	-
GCF_008974245.1	s__Streptomyces abyssomicinicus	80.9872	1207	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364195.1	s__Streptomyces sp013364195	80.9299	1147	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:03:38,638] [INFO] GTDB search result was written to GCF_014648955.1_ASM1464895v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:03:38,639] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:03:38,646] [INFO] DFAST_QC result json was written to GCF_014648955.1_ASM1464895v1_genomic.fna/dqc_result.json
[2024-01-25 18:03:38,647] [INFO] DFAST_QC completed!
[2024-01-25 18:03:38,647] [INFO] Total running time: 0h2m48s