[2024-01-24 13:40:43,505] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:43,507] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:43,507] [INFO] DQC Reference Directory: /var/lib/cwl/stg04da0f23-5d2e-4652-918a-ffad9acd6082/dqc_reference
[2024-01-24 13:40:44,841] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:44,842] [INFO] Task started: Prodigal
[2024-01-24 13:40:44,843] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c55b8f6-52b5-4b29-9163-1b4d0e83b47d/GCF_002102115.1_ASM210211v1_genomic.fna.gz | prodigal -d GCF_002102115.1_ASM210211v1_genomic.fna/cds.fna -a GCF_002102115.1_ASM210211v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:57,682] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:57,682] [INFO] Task started: HMMsearch
[2024-01-24 13:40:57,682] [INFO] Running command: hmmsearch --tblout GCF_002102115.1_ASM210211v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04da0f23-5d2e-4652-918a-ffad9acd6082/dqc_reference/reference_markers.hmm GCF_002102115.1_ASM210211v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:57,978] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:57,979] [INFO] Found 6/6 markers.
[2024-01-24 13:40:58,024] [INFO] Query marker FASTA was written to GCF_002102115.1_ASM210211v1_genomic.fna/markers.fasta
[2024-01-24 13:40:58,025] [INFO] Task started: Blastn
[2024-01-24 13:40:58,025] [INFO] Running command: blastn -query GCF_002102115.1_ASM210211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04da0f23-5d2e-4652-918a-ffad9acd6082/dqc_reference/reference_markers.fasta -out GCF_002102115.1_ASM210211v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:59,289] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:59,293] [INFO] Selected 13 target genomes.
[2024-01-24 13:40:59,293] [INFO] Target genome list was writen to GCF_002102115.1_ASM210211v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:59,297] [INFO] Task started: fastANI
[2024-01-24 13:40:59,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c55b8f6-52b5-4b29-9163-1b4d0e83b47d/GCF_002102115.1_ASM210211v1_genomic.fna.gz --refList GCF_002102115.1_ASM210211v1_genomic.fna/target_genomes.txt --output GCF_002102115.1_ASM210211v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:14,935] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:14,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04da0f23-5d2e-4652-918a-ffad9acd6082/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:14,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04da0f23-5d2e-4652-918a-ffad9acd6082/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:14,948] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:14,948] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:14,948] [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
Mycobacterium doricum	strain=DSM 44339	GCA_002102115.1	126673	126673	type	True	100.0	1277	1280	95	conclusive
Mycobacterium doricum	strain=JCM 12405	GCA_010728155.1	126673	126673	type	True	99.9976	1277	1280	95	conclusive
Mycolicibacterium monacense	strain=DSM 44395	GCA_009931355.1	85693	85693	type	True	87.9417	1005	1280	95	below_threshold
Mycolicibacterium monacense	strain=JCM 15658	GCA_010731575.1	85693	85693	type	True	87.9394	1014	1280	95	below_threshold
Mycolicibacterium monacense	strain=DSM 44395	GCA_002086655.1	85693	85693	type	True	87.9217	996	1280	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	85.5303	939	1280	95	below_threshold
Mycolicibacterium litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	85.4695	957	1280	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	85.2567	946	1280	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	85.1796	964	1280	95	below_threshold
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	80.4053	701	1280	95	below_threshold
Mycolicibacterium komanii	strain=GPK 1020	GCA_001050035.1	1566885	1566885	type	True	80.2767	710	1280	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	80.0036	692	1280	95	below_threshold
Mycolicibacterium alvei	strain=JCM 12272	GCA_010727325.1	67081	67081	type	True	79.7632	649	1280	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:14,950] [INFO] DFAST Taxonomy check result was written to GCF_002102115.1_ASM210211v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:14,951] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:14,951] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:14,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04da0f23-5d2e-4652-918a-ffad9acd6082/dqc_reference/checkm_data
[2024-01-24 13:41:14,952] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:14,999] [INFO] Task started: CheckM
[2024-01-24 13:41:14,999] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002102115.1_ASM210211v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002102115.1_ASM210211v1_genomic.fna/checkm_input GCF_002102115.1_ASM210211v1_genomic.fna/checkm_result
[2024-01-24 13:41:56,243] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:56,244] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:56,271] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:56,271] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:56,272] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002102115.1_ASM210211v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:56,272] [INFO] Task started: Blastn
[2024-01-24 13:41:56,272] [INFO] Running command: blastn -query GCF_002102115.1_ASM210211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04da0f23-5d2e-4652-918a-ffad9acd6082/dqc_reference/reference_markers_gtdb.fasta -out GCF_002102115.1_ASM210211v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:57,923] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:57,927] [INFO] Selected 12 target genomes.
[2024-01-24 13:41:57,927] [INFO] Target genome list was writen to GCF_002102115.1_ASM210211v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:57,942] [INFO] Task started: fastANI
[2024-01-24 13:41:57,942] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c55b8f6-52b5-4b29-9163-1b4d0e83b47d/GCF_002102115.1_ASM210211v1_genomic.fna.gz --refList GCF_002102115.1_ASM210211v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002102115.1_ASM210211v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:11,360] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:11,376] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:11,376] [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_010728155.1	s__Mycobacterium doricum	99.9976	1277	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001499995.1	s__Mycobacterium sp001499995	88.0089	962	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731575.1	s__Mycobacterium monacense	87.9145	1015	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.29	98.82	0.95	0.89	9	-
GCF_001500125.1	s__Mycobacterium sp001500125	87.493	965	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731695.1	s__Mycobacterium litorale	85.4579	959	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014218295.1	s__Mycobacterium litorale_B	85.3301	960	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016313185.1	s__Mycobacterium sp016313185	85.1684	965	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.68	97.36	0.93	0.85	3	-
GCF_001050015.1	s__Mycobacterium malmesburyense	80.3721	705	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010723735.1	s__Mycobacterium hippocampi_B	80.3565	733	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010726645.1	s__Mycobacterium duvalii	80.2957	695	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001050035.1	s__Mycobacterium komanii	80.2728	712	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727325.1	s__Mycobacterium alvei	79.7515	650	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:11,378] [INFO] GTDB search result was written to GCF_002102115.1_ASM210211v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:11,379] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:11,382] [INFO] DFAST_QC result json was written to GCF_002102115.1_ASM210211v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:11,383] [INFO] DFAST_QC completed!
[2024-01-24 13:42:11,383] [INFO] Total running time: 0h1m28s