[2024-01-24 14:55:25,764] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:25,767] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:25,767] [INFO] DQC Reference Directory: /var/lib/cwl/stg1037198a-db19-44f3-9d11-3d374a29e4ce/dqc_reference
[2024-01-24 14:55:27,027] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:27,028] [INFO] Task started: Prodigal
[2024-01-24 14:55:27,029] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d01cefa-11c4-4daf-b174-637a8374bddf/GCF_014873875.1_ASM1487387v1_genomic.fna.gz | prodigal -d GCF_014873875.1_ASM1487387v1_genomic.fna/cds.fna -a GCF_014873875.1_ASM1487387v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:58,965] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:58,965] [INFO] Task started: HMMsearch
[2024-01-24 14:55:58,965] [INFO] Running command: hmmsearch --tblout GCF_014873875.1_ASM1487387v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1037198a-db19-44f3-9d11-3d374a29e4ce/dqc_reference/reference_markers.hmm GCF_014873875.1_ASM1487387v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:59,356] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:59,357] [INFO] Found 6/6 markers.
[2024-01-24 14:55:59,439] [INFO] Query marker FASTA was written to GCF_014873875.1_ASM1487387v1_genomic.fna/markers.fasta
[2024-01-24 14:55:59,439] [INFO] Task started: Blastn
[2024-01-24 14:55:59,439] [INFO] Running command: blastn -query GCF_014873875.1_ASM1487387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1037198a-db19-44f3-9d11-3d374a29e4ce/dqc_reference/reference_markers.fasta -out GCF_014873875.1_ASM1487387v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:00,541] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:00,545] [INFO] Selected 14 target genomes.
[2024-01-24 14:56:00,545] [INFO] Target genome list was writen to GCF_014873875.1_ASM1487387v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:00,551] [INFO] Task started: fastANI
[2024-01-24 14:56:00,551] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d01cefa-11c4-4daf-b174-637a8374bddf/GCF_014873875.1_ASM1487387v1_genomic.fna.gz --refList GCF_014873875.1_ASM1487387v1_genomic.fna/target_genomes.txt --output GCF_014873875.1_ASM1487387v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:23,608] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:23,609] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1037198a-db19-44f3-9d11-3d374a29e4ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:23,609] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1037198a-db19-44f3-9d11-3d374a29e4ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:23,621] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:56:23,621] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:23,622] [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
Actinopolymorpha pittospori	strain=DSM 45354	GCA_014873875.1	648752	648752	type	True	100.0	3520	3520	95	conclusive
Actinopolymorpha rutila	strain=DSM 18448	GCA_013407855.1	446787	446787	type	True	81.3193	1417	3520	95	below_threshold
Actinopolymorpha cephalotaxi	strain=DSM 45117	GCA_013408535.1	504797	504797	type	True	81.1705	1433	3520	95	below_threshold
Actinopolymorpha singaporensis	strain=DSM 22024	GCA_900104745.1	117157	117157	type	True	81.1238	1377	3520	95	below_threshold
Actinopolymorpha alba	strain=DSM 45243	GCA_000373925.1	533267	533267	type	True	79.8773	1251	3520	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	76.7445	541	3520	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	76.4903	420	3520	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	76.4184	421	3520	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	76.2266	489	3520	95	below_threshold
Jiangella endophytica	strain=KE2-3	GCA_003427025.1	1623398	1623398	type	True	76.2219	678	3520	95	below_threshold
Streptomyces verrucosisporus	strain=CPB1-1	GCA_017114865.1	1695161	1695161	type	True	76.1544	455	3520	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	76.0975	463	3520	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	76.0592	415	3520	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	76.0161	536	3520	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:23,623] [INFO] DFAST Taxonomy check result was written to GCF_014873875.1_ASM1487387v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:23,624] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:23,624] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:23,624] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1037198a-db19-44f3-9d11-3d374a29e4ce/dqc_reference/checkm_data
[2024-01-24 14:56:23,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:23,721] [INFO] Task started: CheckM
[2024-01-24 14:56:23,721] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014873875.1_ASM1487387v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014873875.1_ASM1487387v1_genomic.fna/checkm_input GCF_014873875.1_ASM1487387v1_genomic.fna/checkm_result
[2024-01-24 14:58:26,868] [INFO] Task succeeded: CheckM
[2024-01-24 14:58:26,869] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 12.50%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:58:26,893] [INFO] ===== Completeness check finished =====
[2024-01-24 14:58:26,894] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:58:26,894] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014873875.1_ASM1487387v1_genomic.fna/markers.fasta)
[2024-01-24 14:58:26,895] [INFO] Task started: Blastn
[2024-01-24 14:58:26,895] [INFO] Running command: blastn -query GCF_014873875.1_ASM1487387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1037198a-db19-44f3-9d11-3d374a29e4ce/dqc_reference/reference_markers_gtdb.fasta -out GCF_014873875.1_ASM1487387v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:58:28,544] [INFO] Task succeeded: Blastn
[2024-01-24 14:58:28,547] [INFO] Selected 9 target genomes.
[2024-01-24 14:58:28,547] [INFO] Target genome list was writen to GCF_014873875.1_ASM1487387v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:58:28,554] [INFO] Task started: fastANI
[2024-01-24 14:58:28,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d01cefa-11c4-4daf-b174-637a8374bddf/GCF_014873875.1_ASM1487387v1_genomic.fna.gz --refList GCF_014873875.1_ASM1487387v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014873875.1_ASM1487387v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:58:45,280] [INFO] Task succeeded: fastANI
[2024-01-24 14:58:45,288] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:58:45,288] [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_014873875.1	s__Actinopolymorpha pittospori	100.0	3520	3520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013407855.1	s__Actinopolymorpha rutila	81.3075	1416	3520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408535.1	s__Actinopolymorpha cephalotaxi	81.1832	1432	3520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900104745.1	s__Actinopolymorpha singaporensis	81.1175	1379	3520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373925.1	s__Actinopolymorpha alba	79.8617	1254	3520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718255.1	s__Spirillospora albida	76.2351	506	3520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003427025.1	s__Jiangella endophytica	76.2242	677	3520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017114865.1	s__Streptomyces verrucosisporus	76.1666	452	3520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.1585	N/A	N/A	N/A	N/A	1	-
GCF_000383935.1	s__Streptomyces sp000383935	75.9994	586	3520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.62	97.70	0.92	0.84	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:58:45,290] [INFO] GTDB search result was written to GCF_014873875.1_ASM1487387v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:58:45,291] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:58:45,297] [INFO] DFAST_QC result json was written to GCF_014873875.1_ASM1487387v1_genomic.fna/dqc_result.json
[2024-01-24 14:58:45,297] [INFO] DFAST_QC completed!
[2024-01-24 14:58:45,297] [INFO] Total running time: 0h3m20s