[2024-01-25 20:03:05,832] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:05,833] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:05,833] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b92bf59-5b69-4940-9fe8-a53f56fd8074/dqc_reference
[2024-01-25 20:03:06,983] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:06,983] [INFO] Task started: Prodigal
[2024-01-25 20:03:06,984] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9d8a1f1-c1cc-404e-94ee-76c80942afe2/GCF_016862495.1_ASM1686249v1_genomic.fna.gz | prodigal -d GCF_016862495.1_ASM1686249v1_genomic.fna/cds.fna -a GCF_016862495.1_ASM1686249v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:28,787] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:28,787] [INFO] Task started: HMMsearch
[2024-01-25 20:03:28,787] [INFO] Running command: hmmsearch --tblout GCF_016862495.1_ASM1686249v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b92bf59-5b69-4940-9fe8-a53f56fd8074/dqc_reference/reference_markers.hmm GCF_016862495.1_ASM1686249v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:29,107] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:29,109] [INFO] Found 6/6 markers.
[2024-01-25 20:03:29,175] [INFO] Query marker FASTA was written to GCF_016862495.1_ASM1686249v1_genomic.fna/markers.fasta
[2024-01-25 20:03:29,175] [INFO] Task started: Blastn
[2024-01-25 20:03:29,175] [INFO] Running command: blastn -query GCF_016862495.1_ASM1686249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b92bf59-5b69-4940-9fe8-a53f56fd8074/dqc_reference/reference_markers.fasta -out GCF_016862495.1_ASM1686249v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:30,278] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:30,280] [INFO] Selected 8 target genomes.
[2024-01-25 20:03:30,281] [INFO] Target genome list was writen to GCF_016862495.1_ASM1686249v1_genomic.fna/target_genomes.txt
[2024-01-25 20:03:30,284] [INFO] Task started: fastANI
[2024-01-25 20:03:30,284] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9d8a1f1-c1cc-404e-94ee-76c80942afe2/GCF_016862495.1_ASM1686249v1_genomic.fna.gz --refList GCF_016862495.1_ASM1686249v1_genomic.fna/target_genomes.txt --output GCF_016862495.1_ASM1686249v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:03:50,103] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:50,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b92bf59-5b69-4940-9fe8-a53f56fd8074/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:03:50,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b92bf59-5b69-4940-9fe8-a53f56fd8074/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:03:50,111] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:03:50,111] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:03:50,111] [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
Asanoa ferruginea	strain=NBRC 14496	GCA_016862495.1	53367	53367	type	True	100.0	2906	2914	95	conclusive
Asanoa ferruginea	strain=DSM 44099	GCA_003387075.1	53367	53367	type	True	99.9977	2912	2914	95	conclusive
Asanoa ishikariensis	strain=DSM 44718	GCA_900107455.1	137265	137265	type	True	86.1374	2149	2914	95	below_threshold
Asanoa ishikariensis	strain=NBRC 14551	GCA_016862535.1	137265	137265	type	True	86.0919	2142	2914	95	below_threshold
Asanoa iriomotensis	strain=NBRC 100142	GCA_016862515.1	234613	234613	type	True	85.8777	2012	2914	95	below_threshold
Asanoa hainanensis	strain=CGMCC 4.5593	GCA_900188485.1	560556	560556	type	True	85.863	2043	2914	95	below_threshold
Asanoa siamensis	strain=NBRC 107932	GCA_016862555.1	926357	926357	type	True	85.6145	1932	2914	95	below_threshold
Actinoplanes xinjiangensis	strain=DSM 45184	GCA_003148685.1	512350	512350	type	True	77.8263	1113	2914	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:03:50,112] [INFO] DFAST Taxonomy check result was written to GCF_016862495.1_ASM1686249v1_genomic.fna/tc_result.tsv
[2024-01-25 20:03:50,113] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:03:50,113] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:03:50,113] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b92bf59-5b69-4940-9fe8-a53f56fd8074/dqc_reference/checkm_data
[2024-01-25 20:03:50,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:03:50,192] [INFO] Task started: CheckM
[2024-01-25 20:03:50,192] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862495.1_ASM1686249v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862495.1_ASM1686249v1_genomic.fna/checkm_input GCF_016862495.1_ASM1686249v1_genomic.fna/checkm_result
[2024-01-25 20:04:56,979] [INFO] Task succeeded: CheckM
[2024-01-25 20:04:56,980] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:04:57,010] [INFO] ===== Completeness check finished =====
[2024-01-25 20:04:57,010] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:04:57,011] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862495.1_ASM1686249v1_genomic.fna/markers.fasta)
[2024-01-25 20:04:57,011] [INFO] Task started: Blastn
[2024-01-25 20:04:57,012] [INFO] Running command: blastn -query GCF_016862495.1_ASM1686249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b92bf59-5b69-4940-9fe8-a53f56fd8074/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862495.1_ASM1686249v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:58,704] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:58,707] [INFO] Selected 7 target genomes.
[2024-01-25 20:04:58,707] [INFO] Target genome list was writen to GCF_016862495.1_ASM1686249v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:04:58,715] [INFO] Task started: fastANI
[2024-01-25 20:04:58,715] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9d8a1f1-c1cc-404e-94ee-76c80942afe2/GCF_016862495.1_ASM1686249v1_genomic.fna.gz --refList GCF_016862495.1_ASM1686249v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862495.1_ASM1686249v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:05:15,549] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:15,554] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:05:15,555] [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_003387075.1	s__Asanoa ferruginea	99.9977	2912	2914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900107455.1	s__Asanoa ishikariensis	86.0876	2159	2914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016862515.1	s__Asanoa iriomotensis	85.9029	2007	2914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188485.1	s__Asanoa hainanensis	85.8741	2040	2914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862555.1	s__Asanoa siamensis	85.646	1925	2914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862395.1	s__Actinoplanes siamensis	78.221	1003	2914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148685.1	s__Actinoplanes xinjiangensis	77.8461	1104	2914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:05:15,556] [INFO] GTDB search result was written to GCF_016862495.1_ASM1686249v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:05:15,557] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:05:15,559] [INFO] DFAST_QC result json was written to GCF_016862495.1_ASM1686249v1_genomic.fna/dqc_result.json
[2024-01-25 20:05:15,559] [INFO] DFAST_QC completed!
[2024-01-25 20:05:15,560] [INFO] Total running time: 0h2m10s