[2024-01-25 19:55:05,433] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:55:05,435] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:55:05,435] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d8c0a7e-fd9e-4387-a595-058ae0baa78c/dqc_reference
[2024-01-25 19:55:06,572] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:55:06,573] [INFO] Task started: Prodigal
[2024-01-25 19:55:06,573] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9b56a06-2e6b-4e96-8c25-a7f84d7b457d/GCF_000062885.1_ASM6288v1_genomic.fna.gz | prodigal -d GCF_000062885.1_ASM6288v1_genomic.fna/cds.fna -a GCF_000062885.1_ASM6288v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:56:11,381] [INFO] Task succeeded: Prodigal
[2024-01-25 19:56:11,382] [INFO] Task started: HMMsearch
[2024-01-25 19:56:11,382] [INFO] Running command: hmmsearch --tblout GCF_000062885.1_ASM6288v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d8c0a7e-fd9e-4387-a595-058ae0baa78c/dqc_reference/reference_markers.hmm GCF_000062885.1_ASM6288v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:56:11,671] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:56:11,672] [INFO] Found 6/6 markers.
[2024-01-25 19:56:11,736] [INFO] Query marker FASTA was written to GCF_000062885.1_ASM6288v1_genomic.fna/markers.fasta
[2024-01-25 19:56:11,736] [INFO] Task started: Blastn
[2024-01-25 19:56:11,736] [INFO] Running command: blastn -query GCF_000062885.1_ASM6288v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d8c0a7e-fd9e-4387-a595-058ae0baa78c/dqc_reference/reference_markers.fasta -out GCF_000062885.1_ASM6288v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:12,993] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:12,996] [INFO] Selected 12 target genomes.
[2024-01-25 19:56:12,996] [INFO] Target genome list was writen to GCF_000062885.1_ASM6288v1_genomic.fna/target_genomes.txt
[2024-01-25 19:56:13,003] [INFO] Task started: fastANI
[2024-01-25 19:56:13,004] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9b56a06-2e6b-4e96-8c25-a7f84d7b457d/GCF_000062885.1_ASM6288v1_genomic.fna.gz --refList GCF_000062885.1_ASM6288v1_genomic.fna/target_genomes.txt --output GCF_000062885.1_ASM6288v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:56:36,668] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:36,669] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d8c0a7e-fd9e-4387-a595-058ae0baa78c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:56:36,669] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d8c0a7e-fd9e-4387-a595-058ae0baa78c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:56:36,678] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:56:36,678] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:56:36,678] [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
Saccharopolyspora erythraea	strain=NRRL 2338	GCA_000062885.1	1836	1836	type	True	100.0	2736	2737	95	conclusive
Saccharopolyspora erythraea	strain=DSM 40517	GCA_002564065.1	1836	1836	type	True	99.9991	2736	2737	95	conclusive
Saccharopolyspora erythraea	strain=NRRL 2338	GCA_000171635.1	1836	1836	type	True	99.9289	2574	2737	95	conclusive
Saccharopolyspora hordei	strain=DSM 44065	GCA_013410345.1	1838	1838	type	True	82.5324	1290	2737	95	below_threshold
Saccharopolyspora hirsuta	strain=VKM Ac-666	GCA_008630535.1	1837	1837	type	True	82.4391	1478	2737	95	below_threshold
Saccharopolyspora subtropica	strain=CGMCC 4.7206	GCA_014646075.1	1530170	1530170	type	True	82.3579	1189	2737	95	below_threshold
Saccharopolyspora antimicrobica	strain=DSM 45119	GCA_003635025.1	455193	455193	type	True	82.0262	1433	2737	95	below_threshold
Saccharopolyspora kobensis	strain=ATCC 20501	GCA_900108315.1	146035	146035	type	True	82.0239	1423	2737	95	below_threshold
Saccharopolyspora elongata	strain=7K502	GCA_004348985.1	2530387	2530387	type	True	82.0085	1500	2737	95	below_threshold
Saccharopolyspora shandongensis	strain=CGMCC 4.3530	GCA_900106995.1	418495	418495	type	True	81.8609	1494	2737	95	below_threshold
Saccharopolyspora flava	strain=DSM 44771	GCA_900116135.1	95161	95161	type	True	81.7123	1234	2737	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	78.7718	903	2737	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:56:36,679] [INFO] DFAST Taxonomy check result was written to GCF_000062885.1_ASM6288v1_genomic.fna/tc_result.tsv
[2024-01-25 19:56:36,680] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:56:36,680] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:56:36,680] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d8c0a7e-fd9e-4387-a595-058ae0baa78c/dqc_reference/checkm_data
[2024-01-25 19:56:36,681] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:56:36,762] [INFO] Task started: CheckM
[2024-01-25 19:56:36,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000062885.1_ASM6288v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000062885.1_ASM6288v1_genomic.fna/checkm_input GCF_000062885.1_ASM6288v1_genomic.fna/checkm_result
[2024-01-25 20:00:54,669] [INFO] Task succeeded: CheckM
[2024-01-25 20:00:54,670] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:00:54,691] [INFO] ===== Completeness check finished =====
[2024-01-25 20:00:54,691] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:00:54,692] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000062885.1_ASM6288v1_genomic.fna/markers.fasta)
[2024-01-25 20:00:54,692] [INFO] Task started: Blastn
[2024-01-25 20:00:54,692] [INFO] Running command: blastn -query GCF_000062885.1_ASM6288v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d8c0a7e-fd9e-4387-a595-058ae0baa78c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000062885.1_ASM6288v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:56,628] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:56,630] [INFO] Selected 14 target genomes.
[2024-01-25 20:00:56,630] [INFO] Target genome list was writen to GCF_000062885.1_ASM6288v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:00:56,643] [INFO] Task started: fastANI
[2024-01-25 20:00:56,643] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9b56a06-2e6b-4e96-8c25-a7f84d7b457d/GCF_000062885.1_ASM6288v1_genomic.fna.gz --refList GCF_000062885.1_ASM6288v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000062885.1_ASM6288v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:01:23,845] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:23,855] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:01:23,855] [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_000062885.1	s__Saccharopolyspora_D erythraea	100.0	2735	2737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora_D	95.0	99.99	99.99	1.00	1.00	5	conclusive
GCF_018141105.1	s__Saccharopolyspora_D erythraea_A	94.6119	2331	2737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410345.1	s__Saccharopolyspora hordei	82.5233	1297	2737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630535.1	s__Saccharopolyspora hirsuta	82.4348	1479	2737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646075.1	s__Saccharopolyspora subtropica	82.312	1196	2737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003635025.1	s__Saccharopolyspora antimicrobica	82.0556	1424	2737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	96.3257	100.00	100.00	1.00	1.00	2	-
GCF_900112555.1	s__Saccharopolyspora jiangxiensis	82.0242	1424	2737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	96.3257	100.00	99.99	1.00	1.00	3	-
GCF_004348985.1	s__Saccharopolyspora sp004348985	82.0118	1500	2737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106995.1	s__Saccharopolyspora shandongensis	81.8783	1491	2737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116135.1	s__Saccharopolyspora flava	81.6941	1235	2737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014697215.1	s__Saccharopolyspora pogona	81.6709	1339	2737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	95.67	95.67	0.80	0.80	2	-
GCF_014203395.1	s__Saccharopolyspora phatthalungensis	81.4257	1207	2737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	99.57	99.57	0.93	0.93	2	-
GCF_009664835.1	s__Allosaccharopolyspora coralli	79.8726	824	2737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Allosaccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129375.1	s__Streptoalloteichus hindustanus	78.7935	899	2737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Streptoalloteichus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:01:23,856] [INFO] GTDB search result was written to GCF_000062885.1_ASM6288v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:01:23,857] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:01:23,860] [INFO] DFAST_QC result json was written to GCF_000062885.1_ASM6288v1_genomic.fna/dqc_result.json
[2024-01-25 20:01:23,860] [INFO] DFAST_QC completed!
[2024-01-25 20:01:23,860] [INFO] Total running time: 0h6m18s