[2024-01-24 14:05:00,742] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:00,744] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:00,744] [INFO] DQC Reference Directory: /var/lib/cwl/stg7523664f-9929-43c3-bc52-4f5cce1e5a06/dqc_reference
[2024-01-24 14:05:01,886] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:01,887] [INFO] Task started: Prodigal
[2024-01-24 14:05:01,887] [INFO] Running command: gunzip -c /var/lib/cwl/stgb68aa9ef-fe6b-4eb4-ae42-5d584ffd21e1/GCF_010723135.1_ASM1072313v1_genomic.fna.gz | prodigal -d GCF_010723135.1_ASM1072313v1_genomic.fna/cds.fna -a GCF_010723135.1_ASM1072313v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:20,916] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:20,916] [INFO] Task started: HMMsearch
[2024-01-24 14:05:20,916] [INFO] Running command: hmmsearch --tblout GCF_010723135.1_ASM1072313v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7523664f-9929-43c3-bc52-4f5cce1e5a06/dqc_reference/reference_markers.hmm GCF_010723135.1_ASM1072313v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:21,158] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:21,159] [INFO] Found 6/6 markers.
[2024-01-24 14:05:21,204] [INFO] Query marker FASTA was written to GCF_010723135.1_ASM1072313v1_genomic.fna/markers.fasta
[2024-01-24 14:05:21,205] [INFO] Task started: Blastn
[2024-01-24 14:05:21,205] [INFO] Running command: blastn -query GCF_010723135.1_ASM1072313v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7523664f-9929-43c3-bc52-4f5cce1e5a06/dqc_reference/reference_markers.fasta -out GCF_010723135.1_ASM1072313v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:22,302] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:22,305] [INFO] Selected 13 target genomes.
[2024-01-24 14:05:22,305] [INFO] Target genome list was writen to GCF_010723135.1_ASM1072313v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:22,311] [INFO] Task started: fastANI
[2024-01-24 14:05:22,311] [INFO] Running command: fastANI --query /var/lib/cwl/stgb68aa9ef-fe6b-4eb4-ae42-5d584ffd21e1/GCF_010723135.1_ASM1072313v1_genomic.fna.gz --refList GCF_010723135.1_ASM1072313v1_genomic.fna/target_genomes.txt --output GCF_010723135.1_ASM1072313v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:40,152] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:40,152] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7523664f-9929-43c3-bc52-4f5cce1e5a06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:40,153] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7523664f-9929-43c3-bc52-4f5cce1e5a06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:40,164] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:05:40,164] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:40,165] [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 kubicae	strain=JCM 13573	GCA_010723135.1	120959	120959	type	True	100.0	2000	2003	95	conclusive
Mycobacterium kubicae	strain=JCM 13573	GCA_015689175.1	120959	120959	type	True	99.9944	1975	2003	95	conclusive
Mycobacterium kubicae	strain=CIP 106428	GCA_002101745.1	120959	120959	type	True	99.9526	1868	2003	95	conclusive
Mycobacterium heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	81.6357	993	2003	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	81.5596	1015	2003	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	81.5082	1096	2003	95	below_threshold
Mycobacterium angelicum	strain=DSM 45057	GCA_002086155.1	470074	470074	type	True	81.2148	1107	2003	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	81.1203	1027	2003	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	81.0848	1000	2003	95	below_threshold
Mycobacterium paragordonae	strain=49061	GCA_003614435.1	1389713	1389713	type	True	80.9765	1163	2003	95	below_threshold
Mycobacterium paragordonae	strain=JCM 18565	GCA_010723415.1	1389713	1389713	type	True	80.9641	1160	2003	95	below_threshold
Mycobacterium persicum	strain=AFPC-000227	GCA_002086675.1	1487726	1487726	type	True	80.5988	976	2003	95	below_threshold
Mycobacterium simulans	strain=FI-09026	GCA_900232995.1	627089	627089	type	True	80.4462	1025	2003	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:40,169] [INFO] DFAST Taxonomy check result was written to GCF_010723135.1_ASM1072313v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:40,170] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:40,170] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:40,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7523664f-9929-43c3-bc52-4f5cce1e5a06/dqc_reference/checkm_data
[2024-01-24 14:05:40,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:40,228] [INFO] Task started: CheckM
[2024-01-24 14:05:40,228] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010723135.1_ASM1072313v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010723135.1_ASM1072313v1_genomic.fna/checkm_input GCF_010723135.1_ASM1072313v1_genomic.fna/checkm_result
[2024-01-24 14:06:37,950] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:37,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:37,969] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:37,970] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:37,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010723135.1_ASM1072313v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:37,970] [INFO] Task started: Blastn
[2024-01-24 14:06:37,970] [INFO] Running command: blastn -query GCF_010723135.1_ASM1072313v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7523664f-9929-43c3-bc52-4f5cce1e5a06/dqc_reference/reference_markers_gtdb.fasta -out GCF_010723135.1_ASM1072313v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:39,670] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:39,673] [INFO] Selected 19 target genomes.
[2024-01-24 14:06:39,674] [INFO] Target genome list was writen to GCF_010723135.1_ASM1072313v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:39,713] [INFO] Task started: fastANI
[2024-01-24 14:06:39,714] [INFO] Running command: fastANI --query /var/lib/cwl/stgb68aa9ef-fe6b-4eb4-ae42-5d584ffd21e1/GCF_010723135.1_ASM1072313v1_genomic.fna.gz --refList GCF_010723135.1_ASM1072313v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010723135.1_ASM1072313v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:05,253] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:05,271] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:05,271] [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_015689175.1	s__Mycobacterium kubicae	99.9946	1971	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.05	97.98	0.96	0.92	7	conclusive
GCF_001673155.1	s__Mycobacterium sp001673155	86.2856	1389	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101815.1	s__Mycobacterium paraense	81.4958	1097	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_001673535.1	s__Mycobacterium sp001673535	81.3059	1036	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667015.1	s__Mycobacterium sp001667015	81.2866	1033	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102155.1	s__Mycobacterium europaeum	81.2461	1015	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.26	99.26	0.97	0.97	2	-
GCF_900078675.2	s__Mycobacterium interjectum	81.2057	1021	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900157385.1	s__Mycobacterium terramassiliense	81.1515	1072	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105755.1	s__Mycobacterium colombiense	81.1266	1026	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.60	97.75	0.94	0.91	4	-
GCF_010730055.1	s__Mycobacterium shinjukuense	81.1013	880	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001668675.1	s__Mycobacterium asiaticum_D	81.0061	1079	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673635.1	s__Mycobacterium asiaticum_C	81.0021	1113	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.07	99.07	0.94	0.94	2	-
GCF_001672755.1	s__Mycobacterium colombiense_C	80.9525	988	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003614435.1	s__Mycobacterium paragordonae	80.9522	1170	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.23	97.83	0.93	0.88	9	-
GCF_001417955.2	s__Mycobacterium gordonae_B	80.8966	1135	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613245.1	s__Mycobacterium asiaticum	80.7154	1136	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.95	98.52	0.95	0.93	5	-
GCF_002086675.1	s__Mycobacterium persicum	80.6293	971	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.71	99.58	0.97	0.95	12	-
GCF_900232995.1	s__Mycobacterium simulans	80.4463	1025	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.78	97.78	0.92	0.92	2	-
GCF_002104675.1	s__Mycobacterium decipiens	80.2913	945	2003	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 14:07:05,273] [INFO] GTDB search result was written to GCF_010723135.1_ASM1072313v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:05,277] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:05,281] [INFO] DFAST_QC result json was written to GCF_010723135.1_ASM1072313v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:05,282] [INFO] DFAST_QC completed!
[2024-01-24 14:07:05,282] [INFO] Total running time: 0h2m5s