[2024-01-24 11:44:23,418] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,420] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,420] [INFO] DQC Reference Directory: /var/lib/cwl/stg8cffd8fc-a4d0-4657-9aab-9a8c64ee4fc9/dqc_reference
[2024-01-24 11:44:26,340] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,341] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,341] [INFO] Running command: gunzip -c /var/lib/cwl/stgabf3fe49-7ce7-46c4-9f3c-299728982e62/GCF_006716545.1_ASM671654v1_genomic.fna.gz | prodigal -d GCF_006716545.1_ASM671654v1_genomic.fna/cds.fna -a GCF_006716545.1_ASM671654v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:33,897] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:33,898] [INFO] Task started: HMMsearch
[2024-01-24 11:44:33,898] [INFO] Running command: hmmsearch --tblout GCF_006716545.1_ASM671654v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8cffd8fc-a4d0-4657-9aab-9a8c64ee4fc9/dqc_reference/reference_markers.hmm GCF_006716545.1_ASM671654v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:34,168] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:34,169] [INFO] Found 6/6 markers.
[2024-01-24 11:44:34,193] [INFO] Query marker FASTA was written to GCF_006716545.1_ASM671654v1_genomic.fna/markers.fasta
[2024-01-24 11:44:34,193] [INFO] Task started: Blastn
[2024-01-24 11:44:34,193] [INFO] Running command: blastn -query GCF_006716545.1_ASM671654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cffd8fc-a4d0-4657-9aab-9a8c64ee4fc9/dqc_reference/reference_markers.fasta -out GCF_006716545.1_ASM671654v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:35,255] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:35,260] [INFO] Selected 9 target genomes.
[2024-01-24 11:44:35,261] [INFO] Target genome list was writen to GCF_006716545.1_ASM671654v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:35,266] [INFO] Task started: fastANI
[2024-01-24 11:44:35,266] [INFO] Running command: fastANI --query /var/lib/cwl/stgabf3fe49-7ce7-46c4-9f3c-299728982e62/GCF_006716545.1_ASM671654v1_genomic.fna.gz --refList GCF_006716545.1_ASM671654v1_genomic.fna/target_genomes.txt --output GCF_006716545.1_ASM671654v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:40,566] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:40,567] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8cffd8fc-a4d0-4657-9aab-9a8c64ee4fc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:40,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8cffd8fc-a4d0-4657-9aab-9a8c64ee4fc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:40,577] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:44:40,577] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:40,577] [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
Microcella putealis	strain=DSM 19627	GCA_006716545.1	337005	337005	type	True	100.0	845	846	95	conclusive
Microcella putealis	strain=CV2	GCA_004216575.1	337005	337005	type	True	99.9941	835	846	95	conclusive
Microcella alkaliphila	strain=AC4r	GCA_004216855.1	279828	279828	type	True	85.5912	632	846	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_014200395.1	424758	424758	type	True	81.436	480	846	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_009664385.2	424758	424758	type	True	81.4211	468	846	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.7239	374	846	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	78.653	317	846	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	78.5159	333	846	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.5122	340	846	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:40,579] [INFO] DFAST Taxonomy check result was written to GCF_006716545.1_ASM671654v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:40,580] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:40,580] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:40,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8cffd8fc-a4d0-4657-9aab-9a8c64ee4fc9/dqc_reference/checkm_data
[2024-01-24 11:44:40,581] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:40,612] [INFO] Task started: CheckM
[2024-01-24 11:44:40,612] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006716545.1_ASM671654v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006716545.1_ASM671654v1_genomic.fna/checkm_input GCF_006716545.1_ASM671654v1_genomic.fna/checkm_result
[2024-01-24 11:45:08,264] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:08,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:08,289] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:08,290] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:08,290] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006716545.1_ASM671654v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:08,291] [INFO] Task started: Blastn
[2024-01-24 11:45:08,291] [INFO] Running command: blastn -query GCF_006716545.1_ASM671654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cffd8fc-a4d0-4657-9aab-9a8c64ee4fc9/dqc_reference/reference_markers_gtdb.fasta -out GCF_006716545.1_ASM671654v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:09,949] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:09,965] [INFO] Selected 10 target genomes.
[2024-01-24 11:45:09,965] [INFO] Target genome list was writen to GCF_006716545.1_ASM671654v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:09,975] [INFO] Task started: fastANI
[2024-01-24 11:45:09,976] [INFO] Running command: fastANI --query /var/lib/cwl/stgabf3fe49-7ce7-46c4-9f3c-299728982e62/GCF_006716545.1_ASM671654v1_genomic.fna.gz --refList GCF_006716545.1_ASM671654v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006716545.1_ASM671654v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:15,668] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:15,681] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:15,682] [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_004216575.1	s__Microcella putealis	99.9941	835	846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microcella	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_004216855.1	s__Microcella alkaliphila	85.6089	631	846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microcella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355395.1	s__Microcella alkaliphila_A	85.3818	634	846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microcella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014595885.1	s__Yonghaparkia alkaliphila_A	81.9126	533	846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001425665.1	s__Yonghaparkia sp001425665	81.7789	522	846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	99.25	99.25	0.97	0.97	2	-
GCA_012530535.1	s__Yonghaparkia sp012530535	81.7067	535	846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280615.1	s__Chryseoglobus sp002280615	81.651	294	846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200395.1	s__Chryseoglobus frigidaquae	81.4458	479	846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_005502445.1	s__Yonghaparkia sp005502445	81.3611	440	846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464255.1	s__Chryseoglobus sp001464255	81.3191	369	846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:15,684] [INFO] GTDB search result was written to GCF_006716545.1_ASM671654v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:15,684] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:15,687] [INFO] DFAST_QC result json was written to GCF_006716545.1_ASM671654v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:15,688] [INFO] DFAST_QC completed!
[2024-01-24 11:45:15,688] [INFO] Total running time: 0h0m52s