[2024-01-24 13:58:55,646] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:55,648] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:55,648] [INFO] DQC Reference Directory: /var/lib/cwl/stg04b590a9-5a93-4e92-aec2-c4a98b476c24/dqc_reference
[2024-01-24 13:58:56,948] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:56,949] [INFO] Task started: Prodigal
[2024-01-24 13:58:56,949] [INFO] Running command: gunzip -c /var/lib/cwl/stgce5c77b8-b418-4426-9771-54a2916da04d/GCF_000425065.1_ASM42506v1_genomic.fna.gz | prodigal -d GCF_000425065.1_ASM42506v1_genomic.fna/cds.fna -a GCF_000425065.1_ASM42506v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:59:18,453] [INFO] Task succeeded: Prodigal
[2024-01-24 13:59:18,453] [INFO] Task started: HMMsearch
[2024-01-24 13:59:18,453] [INFO] Running command: hmmsearch --tblout GCF_000425065.1_ASM42506v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04b590a9-5a93-4e92-aec2-c4a98b476c24/dqc_reference/reference_markers.hmm GCF_000425065.1_ASM42506v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:59:18,829] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:59:18,830] [INFO] Found 6/6 markers.
[2024-01-24 13:59:18,897] [INFO] Query marker FASTA was written to GCF_000425065.1_ASM42506v1_genomic.fna/markers.fasta
[2024-01-24 13:59:18,897] [INFO] Task started: Blastn
[2024-01-24 13:59:18,897] [INFO] Running command: blastn -query GCF_000425065.1_ASM42506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04b590a9-5a93-4e92-aec2-c4a98b476c24/dqc_reference/reference_markers.fasta -out GCF_000425065.1_ASM42506v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:20,175] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:20,179] [INFO] Selected 17 target genomes.
[2024-01-24 13:59:20,179] [INFO] Target genome list was writen to GCF_000425065.1_ASM42506v1_genomic.fna/target_genomes.txt
[2024-01-24 13:59:20,188] [INFO] Task started: fastANI
[2024-01-24 13:59:20,188] [INFO] Running command: fastANI --query /var/lib/cwl/stgce5c77b8-b418-4426-9771-54a2916da04d/GCF_000425065.1_ASM42506v1_genomic.fna.gz --refList GCF_000425065.1_ASM42506v1_genomic.fna/target_genomes.txt --output GCF_000425065.1_ASM42506v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:00:04,945] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:04,946] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04b590a9-5a93-4e92-aec2-c4a98b476c24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:00:04,947] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04b590a9-5a93-4e92-aec2-c4a98b476c24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:00:04,974] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:00:04,974] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:00:04,974] [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 rifamycini	strain=DSM 43936	GCA_000425065.1	31962	31962	type	True	100.0	2756	2761	95	conclusive
Actinomadura cremea	strain=JCM 3308	GCA_014648495.1	1991	1991	type	True	90.7078	2281	2761	95	below_threshold
Actinomadura algeriensis	strain=DSM 46744	GCA_014873935.1	1679523	1679523	type	True	90.4213	2197	2761	95	below_threshold
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	83.8873	1566	2761	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	83.805	1747	2761	95	below_threshold
Actinomadura latina	strain=NBRC 106108	GCA_001552195.1	163603	163603	type	True	83.7678	1642	2761	95	below_threshold
Actinomadura latina	strain=ATCC BAA-277	GCA_012396395.1	163603	163603	type	True	83.7638	1596	2761	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	83.5757	1886	2761	95	below_threshold
Actinomadura darangshiensis	strain=DSM 45941	GCA_004349235.1	705336	705336	type	True	83.5282	1648	2761	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	83.4884	1887	2761	95	below_threshold
Actinomadura citrea	strain=JCM 3295	GCA_014648455.1	46158	46158	type	True	83.438	1724	2761	95	below_threshold
Actinomadura citrea	strain=DSM 43461	GCA_013409045.1	46158	46158	type	True	83.3769	1741	2761	95	below_threshold
Actinomadura litoris	strain=NEAU-AAG5	GCA_009733595.1	2678616	2678616	type	True	82.6765	1602	2761	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	82.4274	1580	2761	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	82.2868	1440	2761	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	81.1527	1528	2761	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	80.7051	1497	2761	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:00:04,976] [INFO] DFAST Taxonomy check result was written to GCF_000425065.1_ASM42506v1_genomic.fna/tc_result.tsv
[2024-01-24 14:00:04,977] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:00:04,977] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:00:04,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04b590a9-5a93-4e92-aec2-c4a98b476c24/dqc_reference/checkm_data
[2024-01-24 14:00:04,978] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:00:05,053] [INFO] Task started: CheckM
[2024-01-24 14:00:05,054] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000425065.1_ASM42506v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000425065.1_ASM42506v1_genomic.fna/checkm_input GCF_000425065.1_ASM42506v1_genomic.fna/checkm_result
[2024-01-24 14:01:39,014] [INFO] Task succeeded: CheckM
[2024-01-24 14:01:39,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:01:39,042] [INFO] ===== Completeness check finished =====
[2024-01-24 14:01:39,042] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:01:39,042] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000425065.1_ASM42506v1_genomic.fna/markers.fasta)
[2024-01-24 14:01:39,043] [INFO] Task started: Blastn
[2024-01-24 14:01:39,043] [INFO] Running command: blastn -query GCF_000425065.1_ASM42506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04b590a9-5a93-4e92-aec2-c4a98b476c24/dqc_reference/reference_markers_gtdb.fasta -out GCF_000425065.1_ASM42506v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:01:41,095] [INFO] Task succeeded: Blastn
[2024-01-24 14:01:41,100] [INFO] Selected 9 target genomes.
[2024-01-24 14:01:41,100] [INFO] Target genome list was writen to GCF_000425065.1_ASM42506v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:01:41,155] [INFO] Task started: fastANI
[2024-01-24 14:01:41,156] [INFO] Running command: fastANI --query /var/lib/cwl/stgce5c77b8-b418-4426-9771-54a2916da04d/GCF_000425065.1_ASM42506v1_genomic.fna.gz --refList GCF_000425065.1_ASM42506v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000425065.1_ASM42506v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:02:09,346] [INFO] Task succeeded: fastANI
[2024-01-24 14:02:09,356] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:02:09,357] [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_000425065.1	s__Spirillospora rifamycini	100.0	2756	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.13	99.13	0.92	0.92	2	conclusive
GCF_014648495.1	s__Spirillospora cremea	90.6922	2283	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873935.1	s__Spirillospora algeriensis	90.43	2197	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008824145.1	s__Spirillospora sp008824145	90.0528	2199	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001942465.1	s__Spirillospora sp001942465	89.916	2049	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348335.1	s__Spirillospora bangladeshensis	83.8815	1568	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552195.1	s__Spirillospora latina	83.8087	1635	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.98	99.98	0.98	0.98	2	-
GCF_013211575.1	s__Spirillospora verrucosospora	83.6689	1889	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.82	95.82	0.89	0.89	2	-
GCF_017573545.1	s__Spirillospora nitritigenes	83.4415	1897	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.12	95.12	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:02:09,358] [INFO] GTDB search result was written to GCF_000425065.1_ASM42506v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:02:09,359] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:02:09,362] [INFO] DFAST_QC result json was written to GCF_000425065.1_ASM42506v1_genomic.fna/dqc_result.json
[2024-01-24 14:02:09,362] [INFO] DFAST_QC completed!
[2024-01-24 14:02:09,363] [INFO] Total running time: 0h3m14s