[2024-01-24 12:21:57,679] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:57,681] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:57,681] [INFO] DQC Reference Directory: /var/lib/cwl/stg44db32fc-0b43-453d-95b9-1090b5f689f4/dqc_reference
[2024-01-24 12:21:59,044] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:59,045] [INFO] Task started: Prodigal
[2024-01-24 12:21:59,045] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ec40838-ba8f-4a1a-8777-dc7dcbaef382/GCF_004348985.1_ASM434898v1_genomic.fna.gz | prodigal -d GCF_004348985.1_ASM434898v1_genomic.fna/cds.fna -a GCF_004348985.1_ASM434898v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:38,616] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:38,617] [INFO] Task started: HMMsearch
[2024-01-24 12:22:38,617] [INFO] Running command: hmmsearch --tblout GCF_004348985.1_ASM434898v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44db32fc-0b43-453d-95b9-1090b5f689f4/dqc_reference/reference_markers.hmm GCF_004348985.1_ASM434898v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:39,005] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:39,006] [INFO] Found 6/6 markers.
[2024-01-24 12:22:39,077] [INFO] Query marker FASTA was written to GCF_004348985.1_ASM434898v1_genomic.fna/markers.fasta
[2024-01-24 12:22:39,078] [INFO] Task started: Blastn
[2024-01-24 12:22:39,078] [INFO] Running command: blastn -query GCF_004348985.1_ASM434898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44db32fc-0b43-453d-95b9-1090b5f689f4/dqc_reference/reference_markers.fasta -out GCF_004348985.1_ASM434898v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:40,435] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:40,439] [INFO] Selected 9 target genomes.
[2024-01-24 12:22:40,439] [INFO] Target genome list was writen to GCF_004348985.1_ASM434898v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:40,443] [INFO] Task started: fastANI
[2024-01-24 12:22:40,443] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ec40838-ba8f-4a1a-8777-dc7dcbaef382/GCF_004348985.1_ASM434898v1_genomic.fna.gz --refList GCF_004348985.1_ASM434898v1_genomic.fna/target_genomes.txt --output GCF_004348985.1_ASM434898v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:02,482] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:02,482] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44db32fc-0b43-453d-95b9-1090b5f689f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:02,483] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44db32fc-0b43-453d-95b9-1090b5f689f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:02,492] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:02,492] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:02,492] [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 elongata	strain=7K502	GCA_004348985.1	2530387	2530387	type	True	100.0	3289	3305	95	conclusive
Saccharopolyspora shandongensis	strain=CGMCC 4.3530	GCA_900106995.1	418495	418495	type	True	94.6248	2583	3305	95	below_threshold
Saccharopolyspora spinosa	strain=DSM 44228	GCA_002846475.1	60894	60894	type	True	88.2387	1783	3305	95	below_threshold
Saccharopolyspora spinosa	strain=NRRL 18395	GCA_000194155.1	60894	60894	type	True	88.2251	1777	3305	95	below_threshold
Saccharopolyspora phatthalungensis	strain=DSM 45584	GCA_014203395.1	664693	664693	type	True	86.3205	1524	3305	95	below_threshold
Saccharopolyspora hirsuta	strain=VKM Ac-666	GCA_008630535.1	1837	1837	type	True	85.6611	1792	3305	95	below_threshold
Saccharopolyspora kobensis	strain=ATCC 20501	GCA_900108315.1	146035	146035	type	True	85.3669	1808	3305	95	below_threshold
Saccharopolyspora subtropica	strain=CGMCC 4.7206	GCA_014646075.1	1530170	1530170	type	True	84.8493	1341	3305	95	below_threshold
Saccharopolyspora dendranthemae	strain=DSM 46699	GCA_007829955.1	1181886	1181886	type	True	82.1927	1284	3305	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:02,494] [INFO] DFAST Taxonomy check result was written to GCF_004348985.1_ASM434898v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:02,494] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:02,495] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:02,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44db32fc-0b43-453d-95b9-1090b5f689f4/dqc_reference/checkm_data
[2024-01-24 12:23:02,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:02,588] [INFO] Task started: CheckM
[2024-01-24 12:23:02,588] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004348985.1_ASM434898v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004348985.1_ASM434898v1_genomic.fna/checkm_input GCF_004348985.1_ASM434898v1_genomic.fna/checkm_result
[2024-01-24 12:24:54,451] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:54,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:54,475] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:54,476] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:54,476] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004348985.1_ASM434898v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:54,476] [INFO] Task started: Blastn
[2024-01-24 12:24:54,476] [INFO] Running command: blastn -query GCF_004348985.1_ASM434898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44db32fc-0b43-453d-95b9-1090b5f689f4/dqc_reference/reference_markers_gtdb.fasta -out GCF_004348985.1_ASM434898v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:56,562] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:56,565] [INFO] Selected 9 target genomes.
[2024-01-24 12:24:56,565] [INFO] Target genome list was writen to GCF_004348985.1_ASM434898v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:56,573] [INFO] Task started: fastANI
[2024-01-24 12:24:56,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ec40838-ba8f-4a1a-8777-dc7dcbaef382/GCF_004348985.1_ASM434898v1_genomic.fna.gz --refList GCF_004348985.1_ASM434898v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004348985.1_ASM434898v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:17,832] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:17,840] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:17,841] [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_004348985.1	s__Saccharopolyspora sp004348985	100.0	3289	3305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900106995.1	s__Saccharopolyspora shandongensis	94.6447	2581	3305	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	88.3554	1866	3305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	95.67	95.67	0.80	0.80	2	-
GCF_000194155.1	s__Saccharopolyspora spinosa	88.2174	1778	3305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	99.78	99.78	0.99	0.98	3	-
GCF_014203395.1	s__Saccharopolyspora phatthalungensis	86.3121	1526	3305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	99.57	99.57	0.93	0.93	2	-
GCF_008630535.1	s__Saccharopolyspora hirsuta	85.6506	1792	3305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112555.1	s__Saccharopolyspora jiangxiensis	85.3448	1819	3305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	96.3257	100.00	99.99	1.00	1.00	3	-
GCF_014646075.1	s__Saccharopolyspora subtropica	84.8362	1342	3305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829955.1	s__Saccharopolyspora dendranthemae	82.2653	1270	3305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:17,842] [INFO] GTDB search result was written to GCF_004348985.1_ASM434898v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:17,843] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:17,846] [INFO] DFAST_QC result json was written to GCF_004348985.1_ASM434898v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:17,846] [INFO] DFAST_QC completed!
[2024-01-24 12:25:17,846] [INFO] Total running time: 0h3m20s