[2024-01-24 14:06:02,950] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:02,952] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:02,952] [INFO] DQC Reference Directory: /var/lib/cwl/stge90ff2f4-f5aa-421d-8b1b-03a0c5ec4e93/dqc_reference
[2024-01-24 14:06:04,173] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:04,174] [INFO] Task started: Prodigal
[2024-01-24 14:06:04,174] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d50a47f-9c43-446c-81c1-8eb5d8a6fc36/GCF_014205085.1_ASM1420508v1_genomic.fna.gz | prodigal -d GCF_014205085.1_ASM1420508v1_genomic.fna/cds.fna -a GCF_014205085.1_ASM1420508v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:27,989] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:27,989] [INFO] Task started: HMMsearch
[2024-01-24 14:06:27,990] [INFO] Running command: hmmsearch --tblout GCF_014205085.1_ASM1420508v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge90ff2f4-f5aa-421d-8b1b-03a0c5ec4e93/dqc_reference/reference_markers.hmm GCF_014205085.1_ASM1420508v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:28,475] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:28,476] [INFO] Found 6/6 markers.
[2024-01-24 14:06:28,535] [INFO] Query marker FASTA was written to GCF_014205085.1_ASM1420508v1_genomic.fna/markers.fasta
[2024-01-24 14:06:28,536] [INFO] Task started: Blastn
[2024-01-24 14:06:28,536] [INFO] Running command: blastn -query GCF_014205085.1_ASM1420508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge90ff2f4-f5aa-421d-8b1b-03a0c5ec4e93/dqc_reference/reference_markers.fasta -out GCF_014205085.1_ASM1420508v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:29,971] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:29,974] [INFO] Selected 22 target genomes.
[2024-01-24 14:06:29,974] [INFO] Target genome list was writen to GCF_014205085.1_ASM1420508v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:30,029] [INFO] Task started: fastANI
[2024-01-24 14:06:30,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d50a47f-9c43-446c-81c1-8eb5d8a6fc36/GCF_014205085.1_ASM1420508v1_genomic.fna.gz --refList GCF_014205085.1_ASM1420508v1_genomic.fna/target_genomes.txt --output GCF_014205085.1_ASM1420508v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:19,241] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:19,241] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge90ff2f4-f5aa-421d-8b1b-03a0c5ec4e93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:19,241] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge90ff2f4-f5aa-421d-8b1b-03a0c5ec4e93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:19,257] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:07:19,258] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:07:19,258] [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
Actinomadura hallensis	strain=DSM 45043	GCA_006716765.1	337895	337895	type	True	88.9728	1907	2734	95	below_threshold
Actinomadura latina	strain=ATCC BAA-277	GCA_012396395.1	163603	163603	type	True	86.3886	1829	2734	95	below_threshold
Actinomadura latina	strain=NBRC 106108	GCA_001552195.1	163603	163603	type	True	86.3821	1873	2734	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	86.1193	1916	2734	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	85.9359	1904	2734	95	below_threshold
Actinomadura darangshiensis	strain=DSM 45941	GCA_004349235.1	705336	705336	type	True	85.8915	1735	2734	95	below_threshold
Actinomadura mexicana	strain=DSM 44485	GCA_900188105.1	134959	134959	type	True	85.8693	1786	2734	95	below_threshold
Actinomadura formosensis	strain=NBRC 14204	GCA_001552155.1	60706	60706	type	True	85.8591	1492	2734	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	85.7933	1630	2734	95	below_threshold
Actinomadura citrea	strain=DSM 43461	GCA_013409045.1	46158	46158	type	True	85.7652	1830	2734	95	below_threshold
Actinomadura citrea	strain=JCM 3295	GCA_014648455.1	46158	46158	type	True	85.6644	1825	2734	95	below_threshold
Actinomadura chibensis	strain=JCM 14158	GCA_008085895.1	392828	392828	type	True	84.9121	1735	2734	95	below_threshold
Actinomadura chibensis	strain=NBRC 106107	GCA_001552135.1	392828	392828	type	True	84.8839	1707	2734	95	below_threshold
Actinomadura syzygii	strain=GKU157	GCA_008085905.1	1427538	1427538	type	True	84.8746	1712	2734	95	below_threshold
Actinomadura decatromicini	strain=CYP1-5	GCA_008121305.1	2604572	2604572	type	True	84.7751	1756	2734	95	below_threshold
Actinomadura pelletieri	strain=DSM 43383	GCA_003634705.1	111805	111805	type	True	84.6866	1495	2734	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	84.5695	1542	2734	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	84.0594	1799	2734	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	83.7228	1562	2734	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	81.3932	1414	2734	95	below_threshold
Actinomadura oligospora	strain=ATCC 43269	GCA_000518265.1	111804	111804	type	True	80.8205	1361	2734	95	below_threshold
Actinoallomurus purpureus	strain=KCTC 19541	GCA_024055795.1	478114	478114	type	True	78.4645	993	2734	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:19,262] [INFO] DFAST Taxonomy check result was written to GCF_014205085.1_ASM1420508v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:19,263] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:19,263] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:19,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge90ff2f4-f5aa-421d-8b1b-03a0c5ec4e93/dqc_reference/checkm_data
[2024-01-24 14:07:19,265] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:19,343] [INFO] Task started: CheckM
[2024-01-24 14:07:19,343] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014205085.1_ASM1420508v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014205085.1_ASM1420508v1_genomic.fna/checkm_input GCF_014205085.1_ASM1420508v1_genomic.fna/checkm_result
[2024-01-24 14:08:42,678] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:42,680] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.48%
Strain heterogeneity: 83.33%
--------------------------------------------------------------------------------
[2024-01-24 14:08:42,705] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:42,706] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:42,706] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014205085.1_ASM1420508v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:42,706] [INFO] Task started: Blastn
[2024-01-24 14:08:42,707] [INFO] Running command: blastn -query GCF_014205085.1_ASM1420508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge90ff2f4-f5aa-421d-8b1b-03a0c5ec4e93/dqc_reference/reference_markers_gtdb.fasta -out GCF_014205085.1_ASM1420508v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:44,825] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:44,829] [INFO] Selected 12 target genomes.
[2024-01-24 14:08:44,829] [INFO] Target genome list was writen to GCF_014205085.1_ASM1420508v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:44,838] [INFO] Task started: fastANI
[2024-01-24 14:08:44,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d50a47f-9c43-446c-81c1-8eb5d8a6fc36/GCF_014205085.1_ASM1420508v1_genomic.fna.gz --refList GCF_014205085.1_ASM1420508v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014205085.1_ASM1420508v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:09:13,194] [INFO] Task succeeded: fastANI
[2024-01-24 14:09:13,205] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:09:13,205] [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_014648675.1	s__Spirillospora livida	99.9702	2692	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	98.54	97.09	0.95	0.91	3	conclusive
GCF_004349245.1	s__Spirillospora sp004349245	94.1082	2084	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348665.1	s__Spirillospora sp004348665	92.5	1798	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716765.1	s__Spirillospora hallensis	88.989	1903	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348425.1	s__Spirillospora sp004348425	88.3165	1937	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348515.1	s__Spirillospora sp004348515	88.1486	1719	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115095.1	s__Spirillospora madurae	86.1108	1918	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.34	99.27	0.95	0.95	3	-
GCF_004348735.1	s__Spirillospora sp004348735	85.9186	1655	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349235.1	s__Spirillospora darangshiensis	85.8827	1736	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008327685.1	s__Spirillospora sp008327685	85.6478	1879	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006547145.1	s__Spirillospora sp006547145	85.4722	1884	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003432485.1	s__Spirillospora sp003432485	84.5967	1537	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:09:13,207] [INFO] GTDB search result was written to GCF_014205085.1_ASM1420508v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:09:13,208] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:09:13,212] [INFO] DFAST_QC result json was written to GCF_014205085.1_ASM1420508v1_genomic.fna/dqc_result.json
[2024-01-24 14:09:13,212] [INFO] DFAST_QC completed!
[2024-01-24 14:09:13,213] [INFO] Total running time: 0h3m10s