[2024-01-24 13:57:16,666] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:16,671] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:16,672] [INFO] DQC Reference Directory: /var/lib/cwl/stg966abcc1-9c0d-4dbe-9422-79383f36ee4b/dqc_reference
[2024-01-24 13:57:18,029] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:18,030] [INFO] Task started: Prodigal
[2024-01-24 13:57:18,030] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc9a36f1-14a0-41f5-96e2-f2067a38c4bc/GCF_000427885.1_ASM42788v1_genomic.fna.gz | prodigal -d GCF_000427885.1_ASM42788v1_genomic.fna/cds.fna -a GCF_000427885.1_ASM42788v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:33,369] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:33,370] [INFO] Task started: HMMsearch
[2024-01-24 13:57:33,370] [INFO] Running command: hmmsearch --tblout GCF_000427885.1_ASM42788v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg966abcc1-9c0d-4dbe-9422-79383f36ee4b/dqc_reference/reference_markers.hmm GCF_000427885.1_ASM42788v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:33,675] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:33,676] [INFO] Found 6/6 markers.
[2024-01-24 13:57:33,731] [INFO] Query marker FASTA was written to GCF_000427885.1_ASM42788v1_genomic.fna/markers.fasta
[2024-01-24 13:57:33,731] [INFO] Task started: Blastn
[2024-01-24 13:57:33,732] [INFO] Running command: blastn -query GCF_000427885.1_ASM42788v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg966abcc1-9c0d-4dbe-9422-79383f36ee4b/dqc_reference/reference_markers.fasta -out GCF_000427885.1_ASM42788v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:34,932] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:34,941] [INFO] Selected 10 target genomes.
[2024-01-24 13:57:34,941] [INFO] Target genome list was writen to GCF_000427885.1_ASM42788v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:34,950] [INFO] Task started: fastANI
[2024-01-24 13:57:34,950] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc9a36f1-14a0-41f5-96e2-f2067a38c4bc/GCF_000427885.1_ASM42788v1_genomic.fna.gz --refList GCF_000427885.1_ASM42788v1_genomic.fna/target_genomes.txt --output GCF_000427885.1_ASM42788v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:49,988] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:49,989] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg966abcc1-9c0d-4dbe-9422-79383f36ee4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:49,989] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg966abcc1-9c0d-4dbe-9422-79383f36ee4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:49,999] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:49,999] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:50,000] [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
Glycomyces tenuis	strain=DSM 44171	GCA_000427885.1	58116	58116	type	True	100.0	1889	1890	95	conclusive
Glycomyces tenuis	strain=NRRL B-16895	GCA_000715885.1	58116	58116	type	True	99.768	1858	1890	95	conclusive
Glycomyces arizonensis	strain=DSM 44726	GCA_000482705.1	256035	256035	type	True	89.4188	1298	1890	95	below_threshold
Glycomyces xiaoerkulensis	strain=TRM 41368	GCA_002798405.1	2038139	2038139	type	True	83.9261	1020	1890	95	below_threshold
Glycomyces salinus	strain=YIM 93776	GCA_016428645.1	980294	980294	type	True	83.8423	1108	1890	95	below_threshold
Glycomyces buryatensis	strain=18	GCA_004912275.1	2570927	2570927	type	True	83.372	1089	1890	95	below_threshold
Glycomyces terrestris	strain=YIM 121974	GCA_003933745.1	2493553	2493553	type	True	83.3328	1132	1890	95	below_threshold
Glycomyces paridis	strain=CPCC 204357	GCA_004912155.1	2126555	2126555	type	True	83.2535	1102	1890	95	below_threshold
Glycomyces dulcitolivorans	strain=SJ-25	GCA_003265355.1	2200759	2200759	type	True	83.1068	1037	1890	95	below_threshold
Glycomyces albidus	strain=NEAU-7082	GCA_009451885.1	2656774	2656774	type	True	83.0668	1168	1890	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:50,001] [INFO] DFAST Taxonomy check result was written to GCF_000427885.1_ASM42788v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:50,002] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:50,002] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:50,002] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg966abcc1-9c0d-4dbe-9422-79383f36ee4b/dqc_reference/checkm_data
[2024-01-24 13:57:50,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:50,059] [INFO] Task started: CheckM
[2024-01-24 13:57:50,060] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000427885.1_ASM42788v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000427885.1_ASM42788v1_genomic.fna/checkm_input GCF_000427885.1_ASM42788v1_genomic.fna/checkm_result
[2024-01-24 13:58:58,317] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:58,319] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:58,346] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:58,347] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:58,347] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000427885.1_ASM42788v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:58,348] [INFO] Task started: Blastn
[2024-01-24 13:58:58,348] [INFO] Running command: blastn -query GCF_000427885.1_ASM42788v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg966abcc1-9c0d-4dbe-9422-79383f36ee4b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000427885.1_ASM42788v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:00,078] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:00,082] [INFO] Selected 12 target genomes.
[2024-01-24 13:59:00,082] [INFO] Target genome list was writen to GCF_000427885.1_ASM42788v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:00,095] [INFO] Task started: fastANI
[2024-01-24 13:59:00,095] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc9a36f1-14a0-41f5-96e2-f2067a38c4bc/GCF_000427885.1_ASM42788v1_genomic.fna.gz --refList GCF_000427885.1_ASM42788v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000427885.1_ASM42788v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:16,947] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:16,960] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:16,960] [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_000427885.1	s__Glycomyces tenuis	100.0	1889	1890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000482705.1	s__Glycomyces arizonensis	89.4054	1299	1890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002798405.1	s__Glycomyces xiaoerkulensis	83.8668	1027	1890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428645.1	s__Glycomyces sp016428645	83.8155	1111	1890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101745.1	s__Glycomyces harbinensis	83.4908	1181	1890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719515.1	s__Glycomyces sp000719515	83.4779	1080	1890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003933745.1	s__Glycomyces terrestris	83.3607	1128	1890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004912275.1	s__Glycomyces buryatensis	83.3549	1091	1890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004912155.1	s__Glycomyces paridis	83.2794	1098	1890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003265355.1	s__Glycomyces dulcitolivorans	83.0823	1040	1890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009451885.1	s__Glycomyces albidus	83.0504	1172	1890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002955.1	s__Glycomyces artemisiae	82.8208	1139	1890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	97.80	97.80	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:16,961] [INFO] GTDB search result was written to GCF_000427885.1_ASM42788v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:16,962] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:16,965] [INFO] DFAST_QC result json was written to GCF_000427885.1_ASM42788v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:16,965] [INFO] DFAST_QC completed!
[2024-01-24 13:59:16,965] [INFO] Total running time: 0h2m0s