[2024-01-24 14:32:33,911] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:32:33,913] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:32:33,914] [INFO] DQC Reference Directory: /var/lib/cwl/stg380868a7-a1ce-4a97-bd00-08c1f1cf62a9/dqc_reference
[2024-01-24 14:32:35,344] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:32:35,345] [INFO] Task started: Prodigal
[2024-01-24 14:32:35,345] [INFO] Running command: gunzip -c /var/lib/cwl/stg2fa2e3d8-2ecd-4638-a34d-3c3b873e8e9c/GCF_005876955.1_ASM587695v1_genomic.fna.gz | prodigal -d GCF_005876955.1_ASM587695v1_genomic.fna/cds.fna -a GCF_005876955.1_ASM587695v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:32:48,060] [INFO] Task succeeded: Prodigal
[2024-01-24 14:32:48,061] [INFO] Task started: HMMsearch
[2024-01-24 14:32:48,061] [INFO] Running command: hmmsearch --tblout GCF_005876955.1_ASM587695v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg380868a7-a1ce-4a97-bd00-08c1f1cf62a9/dqc_reference/reference_markers.hmm GCF_005876955.1_ASM587695v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:32:48,345] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:32:48,346] [INFO] Found 6/6 markers.
[2024-01-24 14:32:48,391] [INFO] Query marker FASTA was written to GCF_005876955.1_ASM587695v1_genomic.fna/markers.fasta
[2024-01-24 14:32:48,391] [INFO] Task started: Blastn
[2024-01-24 14:32:48,391] [INFO] Running command: blastn -query GCF_005876955.1_ASM587695v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg380868a7-a1ce-4a97-bd00-08c1f1cf62a9/dqc_reference/reference_markers.fasta -out GCF_005876955.1_ASM587695v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:49,554] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:49,559] [INFO] Selected 11 target genomes.
[2024-01-24 14:32:49,560] [INFO] Target genome list was writen to GCF_005876955.1_ASM587695v1_genomic.fna/target_genomes.txt
[2024-01-24 14:32:49,575] [INFO] Task started: fastANI
[2024-01-24 14:32:49,575] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fa2e3d8-2ecd-4638-a34d-3c3b873e8e9c/GCF_005876955.1_ASM587695v1_genomic.fna.gz --refList GCF_005876955.1_ASM587695v1_genomic.fna/target_genomes.txt --output GCF_005876955.1_ASM587695v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:32:59,181] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:59,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg380868a7-a1ce-4a97-bd00-08c1f1cf62a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:32:59,182] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg380868a7-a1ce-4a97-bd00-08c1f1cf62a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:32:59,194] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:32:59,194] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:32:59,195] [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
Sinomonas albida	strain=LC13	GCA_004919045.1	369942	369942	type	True	82.4294	778	1422	95	below_threshold
Sinomonas susongensis	strain=A31	GCA_005877005.1	1324851	1324851	type	True	81.937	786	1422	95	below_threshold
Sinomonas humi	strain=MUSC 117	GCA_000802235.1	1338436	1338436	type	True	81.8411	803	1422	95	below_threshold
Sinomonas mesophila	strain=MPKL 26	GCA_001999765.1	1531955	1531955	type	True	80.8022	644	1422	95	below_threshold
Sinomonas atrocyanea	strain=CGMCC 1.1891	GCA_014644475.1	37927	37927	type	True	80.775	709	1422	95	below_threshold
Sinomonas atrocyanea	strain=NBRC 12956	GCA_006539205.1	37927	37927	type	True	80.7619	725	1422	95	below_threshold
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	79.8165	582	1422	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	78.1759	288	1422	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	77.9467	319	1422	95	below_threshold
Arthrobacter cheniae	strain=Hz2	GCA_003602275.1	1258888	1258888	type	True	77.7354	260	1422	95	below_threshold
Arthrobacter ulcerisalmonis		GCA_900609065.1	2483813	2483813	type	True	77.6723	222	1422	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:32:59,196] [INFO] DFAST Taxonomy check result was written to GCF_005876955.1_ASM587695v1_genomic.fna/tc_result.tsv
[2024-01-24 14:32:59,197] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:32:59,198] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:32:59,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg380868a7-a1ce-4a97-bd00-08c1f1cf62a9/dqc_reference/checkm_data
[2024-01-24 14:32:59,200] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:32:59,245] [INFO] Task started: CheckM
[2024-01-24 14:32:59,245] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005876955.1_ASM587695v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005876955.1_ASM587695v1_genomic.fna/checkm_input GCF_005876955.1_ASM587695v1_genomic.fna/checkm_result
[2024-01-24 14:33:37,804] [INFO] Task succeeded: CheckM
[2024-01-24 14:33:37,806] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:33:37,827] [INFO] ===== Completeness check finished =====
[2024-01-24 14:33:37,827] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:33:37,828] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005876955.1_ASM587695v1_genomic.fna/markers.fasta)
[2024-01-24 14:33:37,828] [INFO] Task started: Blastn
[2024-01-24 14:33:37,828] [INFO] Running command: blastn -query GCF_005876955.1_ASM587695v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg380868a7-a1ce-4a97-bd00-08c1f1cf62a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_005876955.1_ASM587695v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:33:39,533] [INFO] Task succeeded: Blastn
[2024-01-24 14:33:39,542] [INFO] Selected 9 target genomes.
[2024-01-24 14:33:39,542] [INFO] Target genome list was writen to GCF_005876955.1_ASM587695v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:33:39,563] [INFO] Task started: fastANI
[2024-01-24 14:33:39,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fa2e3d8-2ecd-4638-a34d-3c3b873e8e9c/GCF_005876955.1_ASM587695v1_genomic.fna.gz --refList GCF_005876955.1_ASM587695v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005876955.1_ASM587695v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:47,621] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:47,636] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:47,637] [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_005876955.1	s__Sinomonas sp005876955	100.0	1421	1422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004919045.1	s__Sinomonas albida	82.4354	778	1422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005877005.1	s__Sinomonas susongensis	81.912	789	1422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000802235.1	s__Sinomonas humi	81.8494	803	1422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999765.1	s__Sinomonas mesophila	80.7865	646	1422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001577305.1	s__Sinomonas atrocyanea	80.744	735	1422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	99.98	99.98	1.00	1.00	3	-
GCF_014656475.1	s__Sinomonas sp014656475	80.47	636	1422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014651715.1	s__Zhihengliuella salsuginis	78.1842	298	1422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zhihengliuella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929375.1	s__Arthrobacter_D sp002929375	78.1001	332	1422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:47,639] [INFO] GTDB search result was written to GCF_005876955.1_ASM587695v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:47,639] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:47,642] [INFO] DFAST_QC result json was written to GCF_005876955.1_ASM587695v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:47,643] [INFO] DFAST_QC completed!
[2024-01-24 14:33:47,643] [INFO] Total running time: 0h1m14s