[2024-01-25 18:59:05,931] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:59:05,933] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:59:05,933] [INFO] DQC Reference Directory: /var/lib/cwl/stg3be8dea8-7c4c-4f52-a8f2-4019e9baa402/dqc_reference
[2024-01-25 18:59:07,095] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:59:07,096] [INFO] Task started: Prodigal
[2024-01-25 18:59:07,096] [INFO] Running command: gunzip -c /var/lib/cwl/stg7aa5a7b3-ff9f-40ac-9522-1aac3874e908/GCF_025823255.1_ASM2582325v1_genomic.fna.gz | prodigal -d GCF_025823255.1_ASM2582325v1_genomic.fna/cds.fna -a GCF_025823255.1_ASM2582325v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:59:23,783] [INFO] Task succeeded: Prodigal
[2024-01-25 18:59:23,783] [INFO] Task started: HMMsearch
[2024-01-25 18:59:23,784] [INFO] Running command: hmmsearch --tblout GCF_025823255.1_ASM2582325v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3be8dea8-7c4c-4f52-a8f2-4019e9baa402/dqc_reference/reference_markers.hmm GCF_025823255.1_ASM2582325v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:59:24,078] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:59:24,079] [INFO] Found 6/6 markers.
[2024-01-25 18:59:24,129] [INFO] Query marker FASTA was written to GCF_025823255.1_ASM2582325v1_genomic.fna/markers.fasta
[2024-01-25 18:59:24,129] [INFO] Task started: Blastn
[2024-01-25 18:59:24,129] [INFO] Running command: blastn -query GCF_025823255.1_ASM2582325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3be8dea8-7c4c-4f52-a8f2-4019e9baa402/dqc_reference/reference_markers.fasta -out GCF_025823255.1_ASM2582325v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:25,146] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:25,148] [INFO] Selected 13 target genomes.
[2024-01-25 18:59:25,149] [INFO] Target genome list was writen to GCF_025823255.1_ASM2582325v1_genomic.fna/target_genomes.txt
[2024-01-25 18:59:25,163] [INFO] Task started: fastANI
[2024-01-25 18:59:25,164] [INFO] Running command: fastANI --query /var/lib/cwl/stg7aa5a7b3-ff9f-40ac-9522-1aac3874e908/GCF_025823255.1_ASM2582325v1_genomic.fna.gz --refList GCF_025823255.1_ASM2582325v1_genomic.fna/target_genomes.txt --output GCF_025823255.1_ASM2582325v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:59:43,607] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:43,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3be8dea8-7c4c-4f52-a8f2-4019e9baa402/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:59:43,608] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3be8dea8-7c4c-4f52-a8f2-4019e9baa402/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:59:43,616] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:59:43,616] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:59:43,616] [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 florentinum	strain=JCM 14740	GCA_010730355.1	292462	292462	type	True	87.0638	1566	1869	95	below_threshold
Mycobacterium florentinum	strain=DSM 44852	GCA_002101635.1	292462	292462	type	True	87.0171	1570	1869	95	below_threshold
Mycobacterium triplex	strain=DSM 44626	GCA_002102415.1	47839	47839	type	True	86.7325	1521	1869	95	below_threshold
Mycobacterium triplex	strain=DSM 44626	GCA_000689255.1	47839	47839	type	True	86.7314	1537	1869	95	below_threshold
Mycobacterium lentiflavum	strain=ATCC 51985	GCA_022374895.2	141349	141349	type	True	86.2614	1466	1869	95	below_threshold
Mycobacterium ahvazicum	strain=AFP003	GCA_900176255.2	1964395	1964395	type	True	86.1059	1482	1869	95	below_threshold
Mycobacterium stomatepiae	strain=JCM 17783	GCA_010731715.1	470076	470076	type	True	86.0106	1549	1869	95	below_threshold
Mycobacterium genavense	strain=ATCC 51234	GCA_000526915.1	36812	36812	type	True	85.8261	1312	1869	95	below_threshold
Mycobacterium sherrisii	strain=ATCC BAA-832	GCA_002102355.1	243061	243061	type	True	83.3645	1351	1869	95	below_threshold
Mycobacterium simiae	strain=JCM 12377	GCA_010727605.1	1784	1784	type	True	83.1355	1378	1869	95	below_threshold
Mycobacterium numidiamassiliense	strain=AB215	GCA_900157365.1	1841861	1841861	type	True	82.6508	1294	1869	95	below_threshold
Mycobacterium nebraskense	strain=DSM 44803	GCA_002102255.1	244292	244292	type	True	82.0785	1212	1869	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	82.0768	1220	1869	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:59:43,617] [INFO] DFAST Taxonomy check result was written to GCF_025823255.1_ASM2582325v1_genomic.fna/tc_result.tsv
[2024-01-25 18:59:43,618] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:59:43,618] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:59:43,618] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3be8dea8-7c4c-4f52-a8f2-4019e9baa402/dqc_reference/checkm_data
[2024-01-25 18:59:43,619] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:59:43,671] [INFO] Task started: CheckM
[2024-01-25 18:59:43,671] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025823255.1_ASM2582325v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025823255.1_ASM2582325v1_genomic.fna/checkm_input GCF_025823255.1_ASM2582325v1_genomic.fna/checkm_result
[2024-01-25 19:00:29,350] [INFO] Task succeeded: CheckM
[2024-01-25 19:00:29,351] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:00:29,369] [INFO] ===== Completeness check finished =====
[2024-01-25 19:00:29,370] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:00:29,370] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025823255.1_ASM2582325v1_genomic.fna/markers.fasta)
[2024-01-25 19:00:29,371] [INFO] Task started: Blastn
[2024-01-25 19:00:29,371] [INFO] Running command: blastn -query GCF_025823255.1_ASM2582325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3be8dea8-7c4c-4f52-a8f2-4019e9baa402/dqc_reference/reference_markers_gtdb.fasta -out GCF_025823255.1_ASM2582325v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:30,820] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:30,823] [INFO] Selected 14 target genomes.
[2024-01-25 19:00:30,823] [INFO] Target genome list was writen to GCF_025823255.1_ASM2582325v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:00:30,836] [INFO] Task started: fastANI
[2024-01-25 19:00:30,836] [INFO] Running command: fastANI --query /var/lib/cwl/stg7aa5a7b3-ff9f-40ac-9522-1aac3874e908/GCF_025823255.1_ASM2582325v1_genomic.fna.gz --refList GCF_025823255.1_ASM2582325v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025823255.1_ASM2582325v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:00:52,468] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:52,486] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:00:52,486] [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_003112775.1	s__Mycobacterium montefiorense	97.895	1790	1869	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_010730355.1	s__Mycobacterium florentinum	87.0414	1569	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000689255.1	s__Mycobacterium triplex	86.7331	1537	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001373395.1	s__Mycobacterium lentiflavum	86.2618	1460	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176255.2	s__Mycobacterium ahvazicum	86.104	1483	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731715.1	s__Mycobacterium stomatepiae	86.0002	1551	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526915.1	s__Mycobacterium genavense	85.8194	1313	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665235.1	s__Mycobacterium sp001665235	84.6284	1474	1869	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	83.1313	1379	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	97.21	0.97	0.92	4	-
GCF_900157365.1	s__Mycobacterium numidiamassiliense	82.6636	1293	1869	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	82.2741	1179	1869	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	82.213	1168	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002102225.1	s__Mycobacterium interjectum_B	82.096	1203	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102255.1	s__Mycobacterium nebraskense	82.0774	1212	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.58	99.42	0.93	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-25 19:00:52,488] [INFO] GTDB search result was written to GCF_025823255.1_ASM2582325v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:00:52,488] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:00:52,491] [INFO] DFAST_QC result json was written to GCF_025823255.1_ASM2582325v1_genomic.fna/dqc_result.json
[2024-01-25 19:00:52,491] [INFO] DFAST_QC completed!
[2024-01-25 19:00:52,491] [INFO] Total running time: 0h1m47s