[2024-01-24 13:55:15,062] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:15,063] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:15,064] [INFO] DQC Reference Directory: /var/lib/cwl/stg78867126-7884-4e52-be87-f8e5af73105c/dqc_reference
[2024-01-24 13:55:16,435] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:16,436] [INFO] Task started: Prodigal
[2024-01-24 13:55:16,436] [INFO] Running command: gunzip -c /var/lib/cwl/stg93988354-e801-485a-9014-317483497643/GCF_014649535.1_ASM1464953v1_genomic.fna.gz | prodigal -d GCF_014649535.1_ASM1464953v1_genomic.fna/cds.fna -a GCF_014649535.1_ASM1464953v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:38,795] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:38,795] [INFO] Task started: HMMsearch
[2024-01-24 13:55:38,795] [INFO] Running command: hmmsearch --tblout GCF_014649535.1_ASM1464953v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78867126-7884-4e52-be87-f8e5af73105c/dqc_reference/reference_markers.hmm GCF_014649535.1_ASM1464953v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:39,211] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:39,212] [INFO] Found 6/6 markers.
[2024-01-24 13:55:39,280] [INFO] Query marker FASTA was written to GCF_014649535.1_ASM1464953v1_genomic.fna/markers.fasta
[2024-01-24 13:55:39,281] [INFO] Task started: Blastn
[2024-01-24 13:55:39,281] [INFO] Running command: blastn -query GCF_014649535.1_ASM1464953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78867126-7884-4e52-be87-f8e5af73105c/dqc_reference/reference_markers.fasta -out GCF_014649535.1_ASM1464953v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:40,727] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:40,731] [INFO] Selected 21 target genomes.
[2024-01-24 13:55:40,732] [INFO] Target genome list was writen to GCF_014649535.1_ASM1464953v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:40,755] [INFO] Task started: fastANI
[2024-01-24 13:55:40,756] [INFO] Running command: fastANI --query /var/lib/cwl/stg93988354-e801-485a-9014-317483497643/GCF_014649535.1_ASM1464953v1_genomic.fna.gz --refList GCF_014649535.1_ASM1464953v1_genomic.fna/target_genomes.txt --output GCF_014649535.1_ASM1464953v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:17,104] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:17,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78867126-7884-4e52-be87-f8e5af73105c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:17,105] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78867126-7884-4e52-be87-f8e5af73105c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:17,128] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:17,128] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:17,128] [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 gelaticus	strain=JCM 4376	GCA_014649535.1	285446	285446	type	True	100.0	2530	2535	95	conclusive
Streptomyces atratus	strain=JCM 3386	GCA_014648655.1	1893	1893	suspected-type	True	89.8874	2011	2535	95	below_threshold
Streptomyces brevispora	strain=DSM 42059	GCA_007829885.1	887462	887462	type	True	86.9211	1651	2535	95	below_threshold
Streptomyces poriferorum	strain=P01-B04	GCA_019399235.1	2798799	2798799	type	True	86.4322	1533	2535	95	below_threshold
Streptomyces fulvorobeus	strain=DSM 41455	GCA_013409565.1	284028	284028	type	True	85.1741	1311	2535	95	below_threshold
Streptomyces fulvorobeus	strain=NBRC 15897	GCA_013167895.1	284028	284028	type	True	85.0965	1326	2535	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	84.9724	1253	2535	95	below_threshold
Streptomyces microflavus	strain=JCM 4496	GCA_014650075.1	1919	1919	type	True	84.9641	1532	2535	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	84.8564	1607	2535	95	below_threshold
Streptomyces griseus	strain=NCTC13033	GCA_900460065.1	1911	1911	type	True	84.6952	1554	2535	95	below_threshold
Streptomyces griseus	strain=DSM 40236	GCA_900105705.1	1911	1911	type	True	84.6824	1584	2535	95	below_threshold
Streptomyces griseolus	strain=NRRL B-2925	GCA_000721185.1	1909	1909	type	True	84.6186	1459	2535	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	84.506	1467	2535	95	below_threshold
Streptomyces nitrosporeus	strain=ATCC 12769	GCA_008704555.1	28894	28894	type	True	84.1692	1441	2535	95	below_threshold
Streptomyces chryseus	strain=DSM 40420	GCA_005981935.1	68186	68186	type	True	83.3607	1041	2535	95	below_threshold
Streptomyces albidochromogenes	strain=DSM 41800	GCA_005981925.1	329524	329524	type	True	83.16	1172	2535	95	below_threshold
Streptomyces chryseus	strain=JCM 4737	GCA_014650755.1	68186	68186	type	True	83.1586	1311	2535	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.9242	1389	2535	95	below_threshold
Streptomyces flavidovirens	strain=DSM 40150	GCA_000429085.1	67298	67298	type	True	82.9224	1318	2535	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	82.0238	1006	2535	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	81.309	1258	2535	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:17,130] [INFO] DFAST Taxonomy check result was written to GCF_014649535.1_ASM1464953v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:17,131] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:17,131] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:17,131] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78867126-7884-4e52-be87-f8e5af73105c/dqc_reference/checkm_data
[2024-01-24 13:56:17,132] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:17,202] [INFO] Task started: CheckM
[2024-01-24 13:56:17,202] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649535.1_ASM1464953v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649535.1_ASM1464953v1_genomic.fna/checkm_input GCF_014649535.1_ASM1464953v1_genomic.fna/checkm_result
[2024-01-24 13:58:04,097] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:04,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:04,119] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:04,119] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:04,120] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649535.1_ASM1464953v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:04,120] [INFO] Task started: Blastn
[2024-01-24 13:58:04,120] [INFO] Running command: blastn -query GCF_014649535.1_ASM1464953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78867126-7884-4e52-be87-f8e5af73105c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649535.1_ASM1464953v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:06,308] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:06,313] [INFO] Selected 8 target genomes.
[2024-01-24 13:58:06,313] [INFO] Target genome list was writen to GCF_014649535.1_ASM1464953v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:06,324] [INFO] Task started: fastANI
[2024-01-24 13:58:06,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg93988354-e801-485a-9014-317483497643/GCF_014649535.1_ASM1464953v1_genomic.fna.gz --refList GCF_014649535.1_ASM1464953v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649535.1_ASM1464953v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:26,066] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:26,075] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:26,075] [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_014649535.1	s__Streptomyces gelaticus	100.0	2530	2535	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_900119365.1	s__Streptomyces atratus_B	93.952	2100	2535	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091725.1	s__Streptomyces sp900091725	92.0964	2016	2535	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003846175.1	s__Streptomyces sp003846175	91.7269	2121	2535	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648655.1	s__Streptomyces atratus	89.8215	2020	2535	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.41	98.41	0.88	0.88	2	-
GCF_900091955.1	s__Streptomyces sp900091955	89.7582	1957	2535	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008120935.1	s__Streptomyces sp008120935	89.5925	1991	2535	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116325.1	s__Streptomyces sp900116325	87.0978	1595	2535	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.66	95.15	0.89	0.84	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:26,077] [INFO] GTDB search result was written to GCF_014649535.1_ASM1464953v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:26,078] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:26,082] [INFO] DFAST_QC result json was written to GCF_014649535.1_ASM1464953v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:26,082] [INFO] DFAST_QC completed!
[2024-01-24 13:58:26,082] [INFO] Total running time: 0h3m11s