[2024-01-25 20:01:35,519] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:01:35,521] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:01:35,521] [INFO] DQC Reference Directory: /var/lib/cwl/stg63d1a167-196c-4517-a70a-3d1b17427f6d/dqc_reference
[2024-01-25 20:01:36,629] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:01:36,630] [INFO] Task started: Prodigal
[2024-01-25 20:01:36,630] [INFO] Running command: gunzip -c /var/lib/cwl/stg72caf6a4-acd9-4eff-b5c6-c84b3d01e763/GCF_000559085.1_ASM55908v2_genomic.fna.gz | prodigal -d GCF_000559085.1_ASM55908v2_genomic.fna/cds.fna -a GCF_000559085.1_ASM55908v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:01:54,763] [INFO] Task succeeded: Prodigal
[2024-01-25 20:01:54,764] [INFO] Task started: HMMsearch
[2024-01-25 20:01:54,764] [INFO] Running command: hmmsearch --tblout GCF_000559085.1_ASM55908v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63d1a167-196c-4517-a70a-3d1b17427f6d/dqc_reference/reference_markers.hmm GCF_000559085.1_ASM55908v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:01:55,073] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:01:55,074] [INFO] Found 6/6 markers.
[2024-01-25 20:01:55,125] [INFO] Query marker FASTA was written to GCF_000559085.1_ASM55908v2_genomic.fna/markers.fasta
[2024-01-25 20:01:55,125] [INFO] Task started: Blastn
[2024-01-25 20:01:55,125] [INFO] Running command: blastn -query GCF_000559085.1_ASM55908v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg63d1a167-196c-4517-a70a-3d1b17427f6d/dqc_reference/reference_markers.fasta -out GCF_000559085.1_ASM55908v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:56,338] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:56,341] [INFO] Selected 9 target genomes.
[2024-01-25 20:01:56,341] [INFO] Target genome list was writen to GCF_000559085.1_ASM55908v2_genomic.fna/target_genomes.txt
[2024-01-25 20:01:56,348] [INFO] Task started: fastANI
[2024-01-25 20:01:56,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg72caf6a4-acd9-4eff-b5c6-c84b3d01e763/GCF_000559085.1_ASM55908v2_genomic.fna.gz --refList GCF_000559085.1_ASM55908v2_genomic.fna/target_genomes.txt --output GCF_000559085.1_ASM55908v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:02:10,582] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:10,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63d1a167-196c-4517-a70a-3d1b17427f6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:02:10,583] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63d1a167-196c-4517-a70a-3d1b17427f6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:02:10,590] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:02:10,590] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:02:10,590] [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 aromaticivorans	strain=JS19b1	GCA_000559085.2	318425	318425	type	True	100.0	2092	2097	95	conclusive
Mycolicibacterium aichiense	strain=JCM 6376	GCA_010726245.1	1799	1799	type	True	91.4051	1602	2097	95	below_threshold
Mycolicibacterium aichiense	strain=NCTC10820	GCA_900453085.1	1799	1799	type	True	91.3985	1621	2097	95	below_threshold
Mycolicibacterium rhodesiae	strain=DSM 44223	GCA_002086695.1	36814	36814	type	True	91.1929	1629	2097	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	86.74	1565	2097	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	86.6986	1616	2097	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	84.5475	1462	2097	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	81.7683	1154	2097	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	79.2757	857	2097	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:02:10,591] [INFO] DFAST Taxonomy check result was written to GCF_000559085.1_ASM55908v2_genomic.fna/tc_result.tsv
[2024-01-25 20:02:10,592] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:02:10,592] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:02:10,592] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63d1a167-196c-4517-a70a-3d1b17427f6d/dqc_reference/checkm_data
[2024-01-25 20:02:10,593] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:02:10,650] [INFO] Task started: CheckM
[2024-01-25 20:02:10,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000559085.1_ASM55908v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000559085.1_ASM55908v2_genomic.fna/checkm_input GCF_000559085.1_ASM55908v2_genomic.fna/checkm_result
[2024-01-25 20:03:08,371] [INFO] Task succeeded: CheckM
[2024-01-25 20:03:08,372] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:03:08,394] [INFO] ===== Completeness check finished =====
[2024-01-25 20:03:08,394] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:03:08,395] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000559085.1_ASM55908v2_genomic.fna/markers.fasta)
[2024-01-25 20:03:08,395] [INFO] Task started: Blastn
[2024-01-25 20:03:08,395] [INFO] Running command: blastn -query GCF_000559085.1_ASM55908v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg63d1a167-196c-4517-a70a-3d1b17427f6d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000559085.1_ASM55908v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:10,436] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:10,438] [INFO] Selected 8 target genomes.
[2024-01-25 20:03:10,438] [INFO] Target genome list was writen to GCF_000559085.1_ASM55908v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:03:10,454] [INFO] Task started: fastANI
[2024-01-25 20:03:10,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg72caf6a4-acd9-4eff-b5c6-c84b3d01e763/GCF_000559085.1_ASM55908v2_genomic.fna.gz --refList GCF_000559085.1_ASM55908v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000559085.1_ASM55908v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:03:23,326] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:23,332] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:03:23,332] [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_000559085.1	s__Mycobacterium aromaticivorans	100.0	2093	2097	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002887815.1	s__Mycobacterium sp002887815	93.7349	1640	2097	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008329905.1	s__Mycobacterium sp008329905	91.5941	1633	2097	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010726245.1	s__Mycobacterium aichiense	91.4014	1603	2097	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002086695.1	s__Mycobacterium rhodesiae	91.183	1630	2097	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886515.1	s__Mycobacterium sp001886515	86.64	1564	2097	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.54	98.54	0.94	0.94	2	-
GCF_001021385.1	s__Mycobacterium sp001021385	86.2437	1537	2097	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362315.1	s__Mycobacterium sp004362315	84.5276	1478	2097	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.02	98.99	0.96	0.96	6	-
--------------------------------------------------------------------------------
[2024-01-25 20:03:23,333] [INFO] GTDB search result was written to GCF_000559085.1_ASM55908v2_genomic.fna/result_gtdb.tsv
[2024-01-25 20:03:23,334] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:03:23,336] [INFO] DFAST_QC result json was written to GCF_000559085.1_ASM55908v2_genomic.fna/dqc_result.json
[2024-01-25 20:03:23,336] [INFO] DFAST_QC completed!
[2024-01-25 20:03:23,336] [INFO] Total running time: 0h1m48s