[2024-01-24 12:36:35,530] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:35,534] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:35,534] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e8ca208-436d-4d93-937c-ba037a74540e/dqc_reference
[2024-01-24 12:36:36,739] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:36,740] [INFO] Task started: Prodigal
[2024-01-24 12:36:36,740] [INFO] Running command: gunzip -c /var/lib/cwl/stg27df2414-fbe5-4bae-9a30-516abd8192f8/GCF_025331195.1_ASM2533119v1_genomic.fna.gz | prodigal -d GCF_025331195.1_ASM2533119v1_genomic.fna/cds.fna -a GCF_025331195.1_ASM2533119v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:57,620] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:57,621] [INFO] Task started: HMMsearch
[2024-01-24 12:36:57,621] [INFO] Running command: hmmsearch --tblout GCF_025331195.1_ASM2533119v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e8ca208-436d-4d93-937c-ba037a74540e/dqc_reference/reference_markers.hmm GCF_025331195.1_ASM2533119v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:58,015] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:58,016] [INFO] Found 6/6 markers.
[2024-01-24 12:36:58,076] [INFO] Query marker FASTA was written to GCF_025331195.1_ASM2533119v1_genomic.fna/markers.fasta
[2024-01-24 12:36:58,077] [INFO] Task started: Blastn
[2024-01-24 12:36:58,077] [INFO] Running command: blastn -query GCF_025331195.1_ASM2533119v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e8ca208-436d-4d93-937c-ba037a74540e/dqc_reference/reference_markers.fasta -out GCF_025331195.1_ASM2533119v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:59,321] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:59,326] [INFO] Selected 14 target genomes.
[2024-01-24 12:36:59,326] [INFO] Target genome list was writen to GCF_025331195.1_ASM2533119v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:59,341] [INFO] Task started: fastANI
[2024-01-24 12:36:59,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg27df2414-fbe5-4bae-9a30-516abd8192f8/GCF_025331195.1_ASM2533119v1_genomic.fna.gz --refList GCF_025331195.1_ASM2533119v1_genomic.fna/target_genomes.txt --output GCF_025331195.1_ASM2533119v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:18,142] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:18,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e8ca208-436d-4d93-937c-ba037a74540e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:18,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e8ca208-436d-4d93-937c-ba037a74540e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:18,158] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:18,158] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:18,158] [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
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	99.9997	2182	2185	95	conclusive
Mycolicibacterium phocaicum	strain=DSM 45104	GCA_005670655.1	319706	319706	type	True	89.4399	1544	2185	95	below_threshold
Mycolicibacterium phocaicum	strain=JCM 15301	GCA_010731115.1	319706	319706	type	True	89.4198	1569	2185	95	below_threshold
Mycolicibacterium aubagnense	strain=DSM 45150	GCA_005670695.1	319707	319707	type	True	88.7929	1505	2185	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	80.6988	971	2185	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	80.6178	932	2185	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	80.0339	945	2185	95	below_threshold
Mycolicibacterium brumae	strain=ATCC 51384	GCA_025215495.1	85968	85968	type	True	79.8263	655	2185	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	79.8229	837	2185	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	79.7715	833	2185	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.6825	777	2185	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.5264	821	2185	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.48	800	2185	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.4648	782	2185	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:18,161] [INFO] DFAST Taxonomy check result was written to GCF_025331195.1_ASM2533119v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:18,161] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:18,161] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:18,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e8ca208-436d-4d93-937c-ba037a74540e/dqc_reference/checkm_data
[2024-01-24 12:37:18,162] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:18,226] [INFO] Task started: CheckM
[2024-01-24 12:37:18,226] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025331195.1_ASM2533119v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025331195.1_ASM2533119v1_genomic.fna/checkm_input GCF_025331195.1_ASM2533119v1_genomic.fna/checkm_result
[2024-01-24 12:38:23,455] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:23,457] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:23,483] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:23,483] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:23,484] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025331195.1_ASM2533119v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:23,484] [INFO] Task started: Blastn
[2024-01-24 12:38:23,484] [INFO] Running command: blastn -query GCF_025331195.1_ASM2533119v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e8ca208-436d-4d93-937c-ba037a74540e/dqc_reference/reference_markers_gtdb.fasta -out GCF_025331195.1_ASM2533119v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:25,428] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:25,431] [INFO] Selected 9 target genomes.
[2024-01-24 12:38:25,431] [INFO] Target genome list was writen to GCF_025331195.1_ASM2533119v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:25,447] [INFO] Task started: fastANI
[2024-01-24 12:38:25,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg27df2414-fbe5-4bae-9a30-516abd8192f8/GCF_025331195.1_ASM2533119v1_genomic.fna.gz --refList GCF_025331195.1_ASM2533119v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025331195.1_ASM2533119v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:39,298] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:39,306] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:39,307] [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_000878195.1	s__Mycobacterium llatzerense	96.5353	1696	2185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.29	97.98	0.87	0.81	4	conclusive
GCF_004363795.1	s__Mycobacterium sp004363795	94.6444	1617	2185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005670685.2	s__Mycobacterium mucogenicum_B	89.8421	1632	2185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.72	96.94	0.94	0.86	7	-
GCF_018326285.1	s__Mycobacterium sp018326285	89.4716	1604	2185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_010731115.1	s__Mycobacterium phocaicum	89.4161	1569	2185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.06	95.24	0.87	0.80	8	-
GCF_001905655.1	s__Mycobacterium sp001905655	89.301	1486	2185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009729075.1	s__Mycobacterium sp009729075	88.8017	1480	2185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010730955.1	s__Mycobacterium aubagnense	88.7751	1524	2185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_009729415.1	s__Mycobacterium sp009729415	86.6366	1441	2185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.10	96.08	0.81	0.80	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:39,311] [INFO] GTDB search result was written to GCF_025331195.1_ASM2533119v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:39,312] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:39,318] [INFO] DFAST_QC result json was written to GCF_025331195.1_ASM2533119v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:39,318] [INFO] DFAST_QC completed!
[2024-01-24 12:38:39,318] [INFO] Total running time: 0h2m4s