[2024-01-24 14:05:00,692] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:00,695] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:00,695] [INFO] DQC Reference Directory: /var/lib/cwl/stg50d08cdb-78bc-4d6b-867f-91dd2fe5df34/dqc_reference
[2024-01-24 14:05:01,874] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:01,875] [INFO] Task started: Prodigal
[2024-01-24 14:05:01,875] [INFO] Running command: gunzip -c /var/lib/cwl/stg252c2704-f7d1-494f-856b-e83a3fd45f97/GCF_014649935.1_ASM1464993v1_genomic.fna.gz | prodigal -d GCF_014649935.1_ASM1464993v1_genomic.fna/cds.fna -a GCF_014649935.1_ASM1464993v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:21,498] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:21,498] [INFO] Task started: HMMsearch
[2024-01-24 14:05:21,498] [INFO] Running command: hmmsearch --tblout GCF_014649935.1_ASM1464993v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50d08cdb-78bc-4d6b-867f-91dd2fe5df34/dqc_reference/reference_markers.hmm GCF_014649935.1_ASM1464993v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:21,760] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:21,762] [INFO] Found 6/6 markers.
[2024-01-24 14:05:21,814] [INFO] Query marker FASTA was written to GCF_014649935.1_ASM1464993v1_genomic.fna/markers.fasta
[2024-01-24 14:05:21,815] [INFO] Task started: Blastn
[2024-01-24 14:05:21,815] [INFO] Running command: blastn -query GCF_014649935.1_ASM1464993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50d08cdb-78bc-4d6b-867f-91dd2fe5df34/dqc_reference/reference_markers.fasta -out GCF_014649935.1_ASM1464993v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:23,098] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:23,101] [INFO] Selected 21 target genomes.
[2024-01-24 14:05:23,102] [INFO] Target genome list was writen to GCF_014649935.1_ASM1464993v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:23,110] [INFO] Task started: fastANI
[2024-01-24 14:05:23,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg252c2704-f7d1-494f-856b-e83a3fd45f97/GCF_014649935.1_ASM1464993v1_genomic.fna.gz --refList GCF_014649935.1_ASM1464993v1_genomic.fna/target_genomes.txt --output GCF_014649935.1_ASM1464993v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:04,014] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:04,015] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50d08cdb-78bc-4d6b-867f-91dd2fe5df34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:04,015] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50d08cdb-78bc-4d6b-867f-91dd2fe5df34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:04,031] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:04,031] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:04,031] [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 malachitofuscus	strain=JCM 4493	GCA_014650055.1	67322	67322	type	True	88.0014	1836	2422	95	below_threshold
Streptomyces capillispiralis	strain=DSM 41695	GCA_007829875.1	68182	68182	type	True	87.8233	1827	2422	95	below_threshold
Streptomyces capillispiralis	strain=JCM 5075	GCA_014656315.1	68182	68182	type	True	87.8161	1820	2422	95	below_threshold
Streptomyces pilosus	strain=JCM 4403	GCA_014649835.1	28893	28893	type	True	87.7895	1810	2422	95	below_threshold
Streptomyces griseoflavus	strain=JCM 4479	GCA_014649995.1	35619	35619	type	True	87.7303	1794	2422	95	below_threshold
Streptomyces calvus	strain=JCM 4326	GCA_014649315.1	67282	67282	type	True	87.7057	1839	2422	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	87.6692	1839	2422	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	87.4235	1820	2422	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	87.4072	1799	2422	95	below_threshold
Streptomyces viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	87.0337	1445	2422	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	85.4162	1662	2422	95	below_threshold
Streptomyces viridiviolaceus	strain=JCM 4855	GCA_014650995.1	68282	68282	type	True	85.406	1657	2422	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.3582	1686	2422	95	below_threshold
Streptomyces anthocyanicus	strain=JCM 5058	GCA_014651155.1	68174	68174	type	True	85.1904	1690	2422	95	below_threshold
Streptomyces mutabilis	strain=JCM 4400	GCA_014649815.1	67332	67332	type	True	85.1423	1612	2422	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	85.1377	1535	2422	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	85.0984	1638	2422	95	below_threshold
Streptomyces nigra	strain=452	GCA_003074055.1	1827580	1827580	type	True	84.947	1659	2422	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	84.8304	1419	2422	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	84.2887	1627	2422	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	83.4522	1560	2422	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:04,033] [INFO] DFAST Taxonomy check result was written to GCF_014649935.1_ASM1464993v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:04,033] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:04,034] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:04,034] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50d08cdb-78bc-4d6b-867f-91dd2fe5df34/dqc_reference/checkm_data
[2024-01-24 14:06:04,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:04,101] [INFO] Task started: CheckM
[2024-01-24 14:06:04,102] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649935.1_ASM1464993v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649935.1_ASM1464993v1_genomic.fna/checkm_input GCF_014649935.1_ASM1464993v1_genomic.fna/checkm_result
[2024-01-24 14:07:42,321] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:42,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:42,346] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:42,346] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:42,347] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649935.1_ASM1464993v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:42,347] [INFO] Task started: Blastn
[2024-01-24 14:07:42,347] [INFO] Running command: blastn -query GCF_014649935.1_ASM1464993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50d08cdb-78bc-4d6b-867f-91dd2fe5df34/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649935.1_ASM1464993v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:44,479] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:44,483] [INFO] Selected 6 target genomes.
[2024-01-24 14:07:44,483] [INFO] Target genome list was writen to GCF_014649935.1_ASM1464993v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:44,490] [INFO] Task started: fastANI
[2024-01-24 14:07:44,491] [INFO] Running command: fastANI --query /var/lib/cwl/stg252c2704-f7d1-494f-856b-e83a3fd45f97/GCF_014649935.1_ASM1464993v1_genomic.fna.gz --refList GCF_014649935.1_ASM1464993v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649935.1_ASM1464993v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:57,828] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:57,835] [INFO] Found 6 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 14:07:57,835] [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
GCA_014649575.1	s__Streptomyces griseoincarnatus	99.9876	2396	2422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.374	98.24	97.52	0.91	0.85	21	inconclusive
GCA_014649355.1	s__Streptomyces althioticus	95.3762	2056	2422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.374	98.43	96.72	0.91	0.83	9	inconclusive
GCA_014656175.1	s__Streptomyces werraensis	94.7443	2045	2422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014650475.1	s__Streptomyces albogriseolus	94.3432	2012	2422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.59	97.23	0.93	0.90	7	-
GCA_014655195.1	s__Streptomyces cellulosae	94.141	1983	2422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.05	95.87	0.87	0.85	11	-
GCA_002154585.1	s__Streptomyces pseudogriseolus	92.9799	1637	2422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.58	96.58	0.90	0.87	9	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:57,837] [INFO] GTDB search result was written to GCF_014649935.1_ASM1464993v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:57,838] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:57,843] [INFO] DFAST_QC result json was written to GCF_014649935.1_ASM1464993v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:57,843] [INFO] DFAST_QC completed!
[2024-01-24 14:07:57,843] [INFO] Total running time: 0h2m57s