[2024-01-24 12:43:54,222] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:43:54,224] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:43:54,225] [INFO] DQC Reference Directory: /var/lib/cwl/stgd978474f-40f3-4888-9936-640b5d757ecf/dqc_reference
[2024-01-24 12:43:59,335] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:43:59,337] [INFO] Task started: Prodigal
[2024-01-24 12:43:59,337] [INFO] Running command: gunzip -c /var/lib/cwl/stg9fab4888-9b5c-4226-b609-2eff94bf406c/GCF_009931355.1_ASM993135v1_genomic.fna.gz | prodigal -d GCF_009931355.1_ASM993135v1_genomic.fna/cds.fna -a GCF_009931355.1_ASM993135v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:18,157] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:18,157] [INFO] Task started: HMMsearch
[2024-01-24 12:44:18,158] [INFO] Running command: hmmsearch --tblout GCF_009931355.1_ASM993135v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd978474f-40f3-4888-9936-640b5d757ecf/dqc_reference/reference_markers.hmm GCF_009931355.1_ASM993135v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:18,459] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:18,461] [INFO] Found 6/6 markers.
[2024-01-24 12:44:18,515] [INFO] Query marker FASTA was written to GCF_009931355.1_ASM993135v1_genomic.fna/markers.fasta
[2024-01-24 12:44:18,516] [INFO] Task started: Blastn
[2024-01-24 12:44:18,516] [INFO] Running command: blastn -query GCF_009931355.1_ASM993135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd978474f-40f3-4888-9936-640b5d757ecf/dqc_reference/reference_markers.fasta -out GCF_009931355.1_ASM993135v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:19,767] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:19,777] [INFO] Selected 12 target genomes.
[2024-01-24 12:44:19,777] [INFO] Target genome list was writen to GCF_009931355.1_ASM993135v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:19,792] [INFO] Task started: fastANI
[2024-01-24 12:44:19,792] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fab4888-9b5c-4226-b609-2eff94bf406c/GCF_009931355.1_ASM993135v1_genomic.fna.gz --refList GCF_009931355.1_ASM993135v1_genomic.fna/target_genomes.txt --output GCF_009931355.1_ASM993135v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:36,550] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:36,551] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd978474f-40f3-4888-9936-640b5d757ecf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:36,551] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd978474f-40f3-4888-9936-640b5d757ecf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:36,561] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:44:36,562] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:36,562] [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 monacense	strain=DSM 44395	GCA_009931355.1	85693	85693	type	True	100.0	2005	2006	95	conclusive
Mycolicibacterium monacense	strain=JCM 15658	GCA_010731575.1	85693	85693	type	True	99.9985	2000	2006	95	conclusive
Mycolicibacterium monacense	strain=DSM 44395	GCA_002086655.1	85693	85693	type	True	99.967	1939	2006	95	conclusive
Mycobacterium doricum	strain=DSM 44339	GCA_002102115.1	126673	126673	type	True	87.7104	1021	2006	95	below_threshold
Mycobacterium doricum	strain=JCM 12405	GCA_010728155.1	126673	126673	type	True	87.6133	1047	2006	95	below_threshold
Mycolicibacterium litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	86.7781	1480	2006	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	86.724	1478	2006	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	86.5838	1424	2006	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	86.5695	1416	2006	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	80.1409	935	2006	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	80.0991	971	2006	95	below_threshold
Mycolicibacterium mengxianglii	strain=Z-34	GCA_015710575.2	2736649	2736649	type	True	79.6192	896	2006	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:36,564] [INFO] DFAST Taxonomy check result was written to GCF_009931355.1_ASM993135v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:36,564] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:36,564] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:36,565] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd978474f-40f3-4888-9936-640b5d757ecf/dqc_reference/checkm_data
[2024-01-24 12:44:36,565] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:36,623] [INFO] Task started: CheckM
[2024-01-24 12:44:36,623] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009931355.1_ASM993135v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009931355.1_ASM993135v1_genomic.fna/checkm_input GCF_009931355.1_ASM993135v1_genomic.fna/checkm_result
[2024-01-24 12:45:57,012] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:57,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:57,042] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:57,042] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:57,043] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009931355.1_ASM993135v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:57,043] [INFO] Task started: Blastn
[2024-01-24 12:45:57,044] [INFO] Running command: blastn -query GCF_009931355.1_ASM993135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd978474f-40f3-4888-9936-640b5d757ecf/dqc_reference/reference_markers_gtdb.fasta -out GCF_009931355.1_ASM993135v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:59,071] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:59,075] [INFO] Selected 15 target genomes.
[2024-01-24 12:45:59,075] [INFO] Target genome list was writen to GCF_009931355.1_ASM993135v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:59,086] [INFO] Task started: fastANI
[2024-01-24 12:45:59,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fab4888-9b5c-4226-b609-2eff94bf406c/GCF_009931355.1_ASM993135v1_genomic.fna.gz --refList GCF_009931355.1_ASM993135v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009931355.1_ASM993135v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:21,046] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:21,069] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:21,069] [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_010731575.1	s__Mycobacterium monacense	99.9985	2000	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.29	98.82	0.95	0.89	9	conclusive
GCF_001499995.1	s__Mycobacterium sp001499995	89.4091	1531	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001500125.1	s__Mycobacterium sp001500125	89.1242	1521	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010728155.1	s__Mycobacterium doricum	87.6259	1046	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010731695.1	s__Mycobacterium litorale	86.7531	1483	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016313185.1	s__Mycobacterium sp016313185	86.6096	1423	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.68	97.36	0.93	0.85	3	-
GCF_014218295.1	s__Mycobacterium litorale_B	86.5145	1451	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499965.1	s__Mycobacterium sp001499965	86.094	1507	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570325.1	s__Mycobacterium sp004570325	83.8025	1300	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665575.1	s__Mycobacterium sp001665575	82.7557	1092	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352375.1	s__Mycobacterium sp017352375	82.5041	1219	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570485.1	s__Mycobacterium novocastrense	80.9952	1075	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.10	95.11	0.87	0.87	5	-
GCF_001722355.1	s__Mycobacterium holsaticum	80.7744	968	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284965.1	s__Mycobacterium sp003284965	80.5593	966	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002592005.1	s__Mycobacterium palauense	80.1595	928	2006	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 12:46:21,071] [INFO] GTDB search result was written to GCF_009931355.1_ASM993135v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:21,072] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:21,075] [INFO] DFAST_QC result json was written to GCF_009931355.1_ASM993135v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:21,075] [INFO] DFAST_QC completed!
[2024-01-24 12:46:21,076] [INFO] Total running time: 0h2m27s