[2024-01-24 11:35:07,271] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:07,273] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:07,273] [INFO] DQC Reference Directory: /var/lib/cwl/stg672471b2-d250-45b9-8253-6a9969ae706f/dqc_reference
[2024-01-24 11:35:08,513] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:08,514] [INFO] Task started: Prodigal
[2024-01-24 11:35:08,514] [INFO] Running command: gunzip -c /var/lib/cwl/stg584aed79-4dcc-4425-921e-f1a49ed2889b/GCF_025821945.1_ASM2582194v1_genomic.fna.gz | prodigal -d GCF_025821945.1_ASM2582194v1_genomic.fna/cds.fna -a GCF_025821945.1_ASM2582194v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:23,480] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:23,480] [INFO] Task started: HMMsearch
[2024-01-24 11:35:23,480] [INFO] Running command: hmmsearch --tblout GCF_025821945.1_ASM2582194v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg672471b2-d250-45b9-8253-6a9969ae706f/dqc_reference/reference_markers.hmm GCF_025821945.1_ASM2582194v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:23,789] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:23,790] [INFO] Found 6/6 markers.
[2024-01-24 11:35:23,839] [INFO] Query marker FASTA was written to GCF_025821945.1_ASM2582194v1_genomic.fna/markers.fasta
[2024-01-24 11:35:23,840] [INFO] Task started: Blastn
[2024-01-24 11:35:23,840] [INFO] Running command: blastn -query GCF_025821945.1_ASM2582194v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg672471b2-d250-45b9-8253-6a9969ae706f/dqc_reference/reference_markers.fasta -out GCF_025821945.1_ASM2582194v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:24,976] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:24,980] [INFO] Selected 13 target genomes.
[2024-01-24 11:35:24,980] [INFO] Target genome list was writen to GCF_025821945.1_ASM2582194v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:24,985] [INFO] Task started: fastANI
[2024-01-24 11:35:24,985] [INFO] Running command: fastANI --query /var/lib/cwl/stg584aed79-4dcc-4425-921e-f1a49ed2889b/GCF_025821945.1_ASM2582194v1_genomic.fna.gz --refList GCF_025821945.1_ASM2582194v1_genomic.fna/target_genomes.txt --output GCF_025821945.1_ASM2582194v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:43,092] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:43,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg672471b2-d250-45b9-8253-6a9969ae706f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:43,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg672471b2-d250-45b9-8253-6a9969ae706f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:43,105] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:43,105] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:43,105] [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 heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	99.988	1602	1604	95	conclusive
Mycobacterium heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	99.9518	1559	1604	95	conclusive
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	86.2543	1203	1604	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	85.8422	1144	1604	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	84.4539	1126	1604	95	below_threshold
Mycobacterium helveticum	strain=16-83	GCA_007714205.1	2592811	2592811	type	True	84.2957	1021	1604	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	84.2214	1144	1604	95	below_threshold
Mycobacterium intracellulare subsp. chimaera	strain=DSM 44623	GCA_002219285.1	222805	1767	type	True	84.1895	1123	1604	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	84.1615	1096	1604	95	below_threshold
Mycobacterium intracellulare subsp. yongonense	strain=05-1390	GCA_000418535.2	1203599	1767	type	True	84.1447	1147	1604	95	below_threshold
Mycobacterium lacus	strain=JCM 15657	GCA_010731535.1	169765	169765	type	True	83.1958	1034	1604	95	below_threshold
Mycobacterium angelicum	strain=DSM 45057	GCA_002086155.1	470074	470074	type	True	82.0538	1055	1604	95	below_threshold
Mycobacterium simiae	strain=JCM 12377	GCA_010727605.1	1784	1784	type	True	81.9269	1039	1604	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:43,108] [INFO] DFAST Taxonomy check result was written to GCF_025821945.1_ASM2582194v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:43,108] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:43,108] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:43,108] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg672471b2-d250-45b9-8253-6a9969ae706f/dqc_reference/checkm_data
[2024-01-24 11:35:43,109] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:43,158] [INFO] Task started: CheckM
[2024-01-24 11:35:43,158] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821945.1_ASM2582194v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821945.1_ASM2582194v1_genomic.fna/checkm_input GCF_025821945.1_ASM2582194v1_genomic.fna/checkm_result
[2024-01-24 11:36:27,712] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:27,713] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:27,736] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:27,736] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:27,737] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821945.1_ASM2582194v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:27,737] [INFO] Task started: Blastn
[2024-01-24 11:36:27,737] [INFO] Running command: blastn -query GCF_025821945.1_ASM2582194v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg672471b2-d250-45b9-8253-6a9969ae706f/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821945.1_ASM2582194v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:29,362] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:29,366] [INFO] Selected 17 target genomes.
[2024-01-24 11:36:29,366] [INFO] Target genome list was writen to GCF_025821945.1_ASM2582194v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:29,377] [INFO] Task started: fastANI
[2024-01-24 11:36:29,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg584aed79-4dcc-4425-921e-f1a49ed2889b/GCF_025821945.1_ASM2582194v1_genomic.fna.gz --refList GCF_025821945.1_ASM2582194v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821945.1_ASM2582194v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:52,508] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:52,528] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:52,528] [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_010730745.1	s__Mycobacterium heidelbergense	99.988	1602	1604	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_002086305.1	s__Mycobacterium malmoense_B	89.578	1330	1604	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	-
GCF_001667035.1	s__Mycobacterium sp001667035	86.399	1159	1604	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	86.1987	1230	1604	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673535.1	s__Mycobacterium sp001673535	86.1969	1165	1604	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667185.1	s__Mycobacterium sp001667185	86.1626	1184	1604	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078675.2	s__Mycobacterium interjectum	86.066	1182	1604	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672915.1	s__Mycobacterium sp001672915	86.0429	1166	1604	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	86.0072	1163	1604	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001668725.1	s__Mycobacterium sp001668725	86.0069	1196	1604	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.46	99.46	0.97	0.97	2	-
GCA_002102225.1	s__Mycobacterium interjectum_B	85.9531	1208	1604	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455205.1	s__Mycobacterium sp000455205	85.7455	1134	1604	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.16	95.96	0.85	0.84	3	-
GCF_002102155.1	s__Mycobacterium europaeum	84.5199	1129	1604	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.26	99.26	0.97	0.97	2	-
GCF_001053185.1	s__Mycobacterium bohemicum	84.1457	1098	1604	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_900157365.1	s__Mycobacterium numidiamassiliense	83.2178	1133	1604	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086155.1	s__Mycobacterium angelicum	82.0672	1053	1604	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727605.1	s__Mycobacterium simiae	81.9266	1039	1604	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	97.21	0.97	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:52,530] [INFO] GTDB search result was written to GCF_025821945.1_ASM2582194v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:52,531] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:52,539] [INFO] DFAST_QC result json was written to GCF_025821945.1_ASM2582194v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:52,539] [INFO] DFAST_QC completed!
[2024-01-24 11:36:52,539] [INFO] Total running time: 0h1m45s