[2024-01-24 11:20:34,197] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:34,200] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:34,200] [INFO] DQC Reference Directory: /var/lib/cwl/stg6053f089-c943-4cb5-966b-bb26572be851/dqc_reference
[2024-01-24 11:20:35,400] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:35,401] [INFO] Task started: Prodigal
[2024-01-24 11:20:35,401] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ae06082-a413-4bd2-8c9b-e7fb91102bc2/GCF_004216855.1_ASM421685v1_genomic.fna.gz | prodigal -d GCF_004216855.1_ASM421685v1_genomic.fna/cds.fna -a GCF_004216855.1_ASM421685v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:43,230] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:43,230] [INFO] Task started: HMMsearch
[2024-01-24 11:20:43,230] [INFO] Running command: hmmsearch --tblout GCF_004216855.1_ASM421685v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6053f089-c943-4cb5-966b-bb26572be851/dqc_reference/reference_markers.hmm GCF_004216855.1_ASM421685v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:43,474] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:43,475] [INFO] Found 6/6 markers.
[2024-01-24 11:20:43,506] [INFO] Query marker FASTA was written to GCF_004216855.1_ASM421685v1_genomic.fna/markers.fasta
[2024-01-24 11:20:43,506] [INFO] Task started: Blastn
[2024-01-24 11:20:43,506] [INFO] Running command: blastn -query GCF_004216855.1_ASM421685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6053f089-c943-4cb5-966b-bb26572be851/dqc_reference/reference_markers.fasta -out GCF_004216855.1_ASM421685v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:44,556] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:44,559] [INFO] Selected 9 target genomes.
[2024-01-24 11:20:44,560] [INFO] Target genome list was writen to GCF_004216855.1_ASM421685v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:44,567] [INFO] Task started: fastANI
[2024-01-24 11:20:44,568] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ae06082-a413-4bd2-8c9b-e7fb91102bc2/GCF_004216855.1_ASM421685v1_genomic.fna.gz --refList GCF_004216855.1_ASM421685v1_genomic.fna/target_genomes.txt --output GCF_004216855.1_ASM421685v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:50,267] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:50,267] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6053f089-c943-4cb5-966b-bb26572be851/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:50,268] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6053f089-c943-4cb5-966b-bb26572be851/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:50,278] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:50,278] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:50,278] [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 alkaliphila	strain=AC4r	GCA_004216855.1	279828	279828	type	True	100.0	885	886	95	conclusive
Microcella putealis	strain=DSM 19627	GCA_006716545.1	337005	337005	type	True	85.5548	651	886	95	below_threshold
Microcella putealis	strain=CV2	GCA_004216575.1	337005	337005	type	True	85.497	656	886	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_014200395.1	424758	424758	type	True	81.0876	500	886	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_009664385.2	424758	424758	type	True	81.0817	494	886	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	78.6666	336	886	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.6534	345	886	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.6295	366	886	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	78.3238	309	886	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:50,280] [INFO] DFAST Taxonomy check result was written to GCF_004216855.1_ASM421685v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:50,280] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:50,280] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:50,280] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6053f089-c943-4cb5-966b-bb26572be851/dqc_reference/checkm_data
[2024-01-24 11:20:50,281] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:50,308] [INFO] Task started: CheckM
[2024-01-24 11:20:50,309] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004216855.1_ASM421685v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004216855.1_ASM421685v1_genomic.fna/checkm_input GCF_004216855.1_ASM421685v1_genomic.fna/checkm_result
[2024-01-24 11:21:17,681] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:17,683] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:17,700] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:17,701] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:17,701] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004216855.1_ASM421685v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:17,702] [INFO] Task started: Blastn
[2024-01-24 11:21:17,702] [INFO] Running command: blastn -query GCF_004216855.1_ASM421685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6053f089-c943-4cb5-966b-bb26572be851/dqc_reference/reference_markers_gtdb.fasta -out GCF_004216855.1_ASM421685v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:19,380] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:19,382] [INFO] Selected 11 target genomes.
[2024-01-24 11:21:19,383] [INFO] Target genome list was writen to GCF_004216855.1_ASM421685v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:19,396] [INFO] Task started: fastANI
[2024-01-24 11:21:19,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ae06082-a413-4bd2-8c9b-e7fb91102bc2/GCF_004216855.1_ASM421685v1_genomic.fna.gz --refList GCF_004216855.1_ASM421685v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004216855.1_ASM421685v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:26,000] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:26,019] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:26,020] [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_004216855.1	s__Microcella alkaliphila	100.0	885	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microcella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002355395.1	s__Microcella alkaliphila_A	93.9547	731	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microcella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216575.1	s__Microcella putealis	85.5028	656	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microcella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014595885.1	s__Yonghaparkia alkaliphila_A	81.882	524	886	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	81.4644	521	886	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	81.4339	526	886	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	81.4145	285	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464255.1	s__Chryseoglobus sp001464255	81.2662	352	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005502445.1	s__Yonghaparkia sp005502445	81.2056	452	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014137945.1	s__Yonghaparkia alkaliphila	80.8586	493	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009371975.2	s__Marinisubtilis pacificus	80.696	477	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marinisubtilis	95.0	97.81	97.81	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:26,022] [INFO] GTDB search result was written to GCF_004216855.1_ASM421685v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:26,023] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:26,026] [INFO] DFAST_QC result json was written to GCF_004216855.1_ASM421685v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:26,026] [INFO] DFAST_QC completed!
[2024-01-24 11:21:26,026] [INFO] Total running time: 0h0m52s