[2024-01-24 10:57:21,429] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:21,431] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:21,431] [INFO] DQC Reference Directory: /var/lib/cwl/stgb658bbef-7285-42c6-89b4-89467b6b423b/dqc_reference
[2024-01-24 10:57:22,673] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:22,674] [INFO] Task started: Prodigal
[2024-01-24 10:57:22,674] [INFO] Running command: gunzip -c /var/lib/cwl/stg3bc8c1f1-08b4-43ef-addb-b277ee66e2a0/GCF_004348435.1_ASM434843v1_genomic.fna.gz | prodigal -d GCF_004348435.1_ASM434843v1_genomic.fna/cds.fna -a GCF_004348435.1_ASM434843v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:40,681] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:40,681] [INFO] Task started: HMMsearch
[2024-01-24 10:57:40,682] [INFO] Running command: hmmsearch --tblout GCF_004348435.1_ASM434843v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb658bbef-7285-42c6-89b4-89467b6b423b/dqc_reference/reference_markers.hmm GCF_004348435.1_ASM434843v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:41,037] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:41,038] [INFO] Found 6/6 markers.
[2024-01-24 10:57:41,099] [INFO] Query marker FASTA was written to GCF_004348435.1_ASM434843v1_genomic.fna/markers.fasta
[2024-01-24 10:57:41,101] [INFO] Task started: Blastn
[2024-01-24 10:57:41,101] [INFO] Running command: blastn -query GCF_004348435.1_ASM434843v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb658bbef-7285-42c6-89b4-89467b6b423b/dqc_reference/reference_markers.fasta -out GCF_004348435.1_ASM434843v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:42,461] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:42,464] [INFO] Selected 9 target genomes.
[2024-01-24 10:57:42,465] [INFO] Target genome list was writen to GCF_004348435.1_ASM434843v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:42,468] [INFO] Task started: fastANI
[2024-01-24 10:57:42,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bc8c1f1-08b4-43ef-addb-b277ee66e2a0/GCF_004348435.1_ASM434843v1_genomic.fna.gz --refList GCF_004348435.1_ASM434843v1_genomic.fna/target_genomes.txt --output GCF_004348435.1_ASM434843v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:00,807] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:00,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb658bbef-7285-42c6-89b4-89467b6b423b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:00,808] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb658bbef-7285-42c6-89b4-89467b6b423b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:00,817] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 10:58:00,817] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 10:58:00,818] [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 terrae	strain=16K309	GCA_004348435.1	2530384	2530384	type	True	100.0	2129	2137	95	inconclusive
Saccharopolyspora endophytica	strain=KCTC 19397	GCA_018070075.1	543886	543886	type	True	96.7139	1869	2137	95	inconclusive
Saccharopolyspora karakumensis	strain=5K548	GCA_004349225.1	2530386	2530386	type	True	95.6823	1840	2137	95	inconclusive
Saccharopolyspora aridisoli	strain=16K404	GCA_004348445.1	2530385	2530385	type	True	94.2505	1688	2137	95	below_threshold
Saccharopolyspora flava	strain=DSM 44771	GCA_900116135.1	95161	95161	type	True	89.3107	1623	2137	95	below_threshold
Saccharopolyspora rhizosphaerae	strain=H219	GCA_003931915.1	2492662	2492662	type	True	88.428	1577	2137	95	below_threshold
Saccharopolyspora antimicrobica	strain=DSM 45119	GCA_003635025.1	455193	455193	type	True	83.3703	1301	2137	95	below_threshold
Saccharopolyspora hordei	strain=DSM 44065	GCA_013410345.1	1838	1838	type	True	83.3475	1219	2137	95	below_threshold
Saccharopolyspora shandongensis	strain=CGMCC 4.3530	GCA_900106995.1	418495	418495	type	True	82.9191	1311	2137	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:00,820] [INFO] DFAST Taxonomy check result was written to GCF_004348435.1_ASM434843v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:00,820] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:00,821] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:00,821] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb658bbef-7285-42c6-89b4-89467b6b423b/dqc_reference/checkm_data
[2024-01-24 10:58:00,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:00,891] [INFO] Task started: CheckM
[2024-01-24 10:58:00,891] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004348435.1_ASM434843v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004348435.1_ASM434843v1_genomic.fna/checkm_input GCF_004348435.1_ASM434843v1_genomic.fna/checkm_result
[2024-01-24 10:59:31,120] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:31,121] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:31,144] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:31,145] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:31,145] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004348435.1_ASM434843v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:31,145] [INFO] Task started: Blastn
[2024-01-24 10:59:31,145] [INFO] Running command: blastn -query GCF_004348435.1_ASM434843v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb658bbef-7285-42c6-89b4-89467b6b423b/dqc_reference/reference_markers_gtdb.fasta -out GCF_004348435.1_ASM434843v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:33,013] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:33,015] [INFO] Selected 9 target genomes.
[2024-01-24 10:59:33,015] [INFO] Target genome list was writen to GCF_004348435.1_ASM434843v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:33,021] [INFO] Task started: fastANI
[2024-01-24 10:59:33,022] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bc8c1f1-08b4-43ef-addb-b277ee66e2a0/GCF_004348435.1_ASM434843v1_genomic.fna.gz --refList GCF_004348435.1_ASM434843v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004348435.1_ASM434843v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:49,096] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:49,105] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:49,106] [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_018070075.1	s__Saccharopolyspora endophytica	96.7139	1869	2137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	96.33	95.95	0.87	0.87	3	conclusive
GCF_004348445.1	s__Saccharopolyspora sp004348445	94.2505	1688	2137	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	89.3547	1691	2137	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	89.3029	1624	2137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003931915.1	s__Saccharopolyspora rhizosphaerae	88.4279	1577	2137	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	83.3796	1299	2137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	96.3257	100.00	100.00	1.00	1.00	2	-
GCF_013410345.1	s__Saccharopolyspora hordei	83.3552	1219	2137	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	82.9599	1306	2137	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	82.6965	1168	2137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	95.67	95.67	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:49,107] [INFO] GTDB search result was written to GCF_004348435.1_ASM434843v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:49,108] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:49,111] [INFO] DFAST_QC result json was written to GCF_004348435.1_ASM434843v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:49,111] [INFO] DFAST_QC completed!
[2024-01-24 10:59:49,111] [INFO] Total running time: 0h2m28s