[2024-01-25 18:54:05,525] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:54:05,526] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:54:05,526] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f601e72-9f31-4042-b6b4-5a472074105e/dqc_reference
[2024-01-25 18:54:06,650] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:54:06,651] [INFO] Task started: Prodigal
[2024-01-25 18:54:06,651] [INFO] Running command: gunzip -c /var/lib/cwl/stg53e32558-6742-49de-8fe4-062299e671cc/GCF_025821385.1_ASM2582138v1_genomic.fna.gz | prodigal -d GCF_025821385.1_ASM2582138v1_genomic.fna/cds.fna -a GCF_025821385.1_ASM2582138v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:54:29,744] [INFO] Task succeeded: Prodigal
[2024-01-25 18:54:29,744] [INFO] Task started: HMMsearch
[2024-01-25 18:54:29,744] [INFO] Running command: hmmsearch --tblout GCF_025821385.1_ASM2582138v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f601e72-9f31-4042-b6b4-5a472074105e/dqc_reference/reference_markers.hmm GCF_025821385.1_ASM2582138v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:54:30,044] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:54:30,045] [INFO] Found 6/6 markers.
[2024-01-25 18:54:30,100] [INFO] Query marker FASTA was written to GCF_025821385.1_ASM2582138v1_genomic.fna/markers.fasta
[2024-01-25 18:54:30,100] [INFO] Task started: Blastn
[2024-01-25 18:54:30,101] [INFO] Running command: blastn -query GCF_025821385.1_ASM2582138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f601e72-9f31-4042-b6b4-5a472074105e/dqc_reference/reference_markers.fasta -out GCF_025821385.1_ASM2582138v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:31,120] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:31,122] [INFO] Selected 17 target genomes.
[2024-01-25 18:54:31,122] [INFO] Target genome list was writen to GCF_025821385.1_ASM2582138v1_genomic.fna/target_genomes.txt
[2024-01-25 18:54:31,132] [INFO] Task started: fastANI
[2024-01-25 18:54:31,132] [INFO] Running command: fastANI --query /var/lib/cwl/stg53e32558-6742-49de-8fe4-062299e671cc/GCF_025821385.1_ASM2582138v1_genomic.fna.gz --refList GCF_025821385.1_ASM2582138v1_genomic.fna/target_genomes.txt --output GCF_025821385.1_ASM2582138v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:54:54,170] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:54,171] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f601e72-9f31-4042-b6b4-5a472074105e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:54:54,171] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f601e72-9f31-4042-b6b4-5a472074105e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:54:54,181] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:54:54,181] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:54:54,181] [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 szulgai	strain=DSM 44166	GCA_002116635.1	1787	1787	type	True	99.9265	1970	2085	95	conclusive
Mycobacterium angelicum	strain=DSM 45057	GCA_002086155.1	470074	470074	type	True	93.0851	1816	2085	95	below_threshold
Mycobacterium lacus	strain=DSM 44577	GCA_002102215.1	169765	169765	type	True	81.6538	1117	2085	95	below_threshold
Mycobacterium lacus	strain=JCM 15657	GCA_010731535.1	169765	169765	type	True	81.5926	1131	2085	95	below_threshold
Mycobacterium pseudokansasii	strain=MK142	GCA_900566075.1	2341080	2341080	type	True	81.2411	1209	2085	95	below_threshold
Mycobacterium ostraviense	strain=241/15	GCA_002705925.1	2738409	2738409	type	True	81.0636	1207	2085	95	below_threshold
Mycobacterium persicum	strain=AFPC-000227	GCA_002086675.1	1487726	1487726	type	True	81.0152	1141	2085	95	below_threshold
Mycobacterium kubicae	strain=CIP 106428	GCA_002101745.1	120959	120959	type	True	80.9024	1064	2085	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_010723135.1	120959	120959	type	True	80.8719	1062	2085	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_015689175.1	120959	120959	type	True	80.8206	1092	2085	95	below_threshold
Mycobacterium attenuatum	strain=MK41	GCA_900566085.1	2341086	2341086	type	True	80.6979	1137	2085	95	below_threshold
Mycobacterium gordonae	strain=DSM 44160	GCA_002101675.1	1778	1778	type	True	80.6958	1189	2085	95	below_threshold
Mycobacterium marseillense	strain=DSM 45437	GCA_002086345.1	701042	701042	type	True	80.635	1019	2085	95	below_threshold
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	80.6039	1033	2085	95	below_threshold
Mycobacterium vicinigordonae	strain=24	GCA_013466425.1	1719132	1719132	type	True	80.2116	1046	2085	95	below_threshold
Mycobacterium pseudoshottsii	strain=JCM 15466	GCA_001515365.1	265949	265949	suspected-type	True	80.056	1019	2085	95	below_threshold
Mycobacterium pseudoshottsii	strain=JCM 15466	GCA_003584745.1	265949	265949	suspected-type	True	79.9533	1045	2085	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:54:54,183] [INFO] DFAST Taxonomy check result was written to GCF_025821385.1_ASM2582138v1_genomic.fna/tc_result.tsv
[2024-01-25 18:54:54,183] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:54:54,183] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:54:54,183] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f601e72-9f31-4042-b6b4-5a472074105e/dqc_reference/checkm_data
[2024-01-25 18:54:54,184] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:54:54,247] [INFO] Task started: CheckM
[2024-01-25 18:54:54,248] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821385.1_ASM2582138v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821385.1_ASM2582138v1_genomic.fna/checkm_input GCF_025821385.1_ASM2582138v1_genomic.fna/checkm_result
[2024-01-25 18:55:59,949] [INFO] Task succeeded: CheckM
[2024-01-25 18:55:59,952] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 13.54%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 18:55:59,973] [INFO] ===== Completeness check finished =====
[2024-01-25 18:55:59,973] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:55:59,974] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821385.1_ASM2582138v1_genomic.fna/markers.fasta)
[2024-01-25 18:55:59,974] [INFO] Task started: Blastn
[2024-01-25 18:55:59,974] [INFO] Running command: blastn -query GCF_025821385.1_ASM2582138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f601e72-9f31-4042-b6b4-5a472074105e/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821385.1_ASM2582138v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:01,495] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:01,497] [INFO] Selected 20 target genomes.
[2024-01-25 18:56:01,497] [INFO] Target genome list was writen to GCF_025821385.1_ASM2582138v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:56:01,507] [INFO] Task started: fastANI
[2024-01-25 18:56:01,508] [INFO] Running command: fastANI --query /var/lib/cwl/stg53e32558-6742-49de-8fe4-062299e671cc/GCF_025821385.1_ASM2582138v1_genomic.fna.gz --refList GCF_025821385.1_ASM2582138v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821385.1_ASM2582138v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:56:30,690] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:30,702] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:56:30,702] [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_002116635.1	s__Mycobacterium szulgai	99.9136	1971	2085	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_002086155.1	s__Mycobacterium angelicum	93.1038	1814	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731535.1	s__Mycobacterium lacus	81.5926	1132	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900078675.2	s__Mycobacterium interjectum	81.2014	1064	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900566075.1	s__Mycobacterium pseudokansasii	81.1992	1218	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.48	0.96	0.94	7	-
GCF_001667015.1	s__Mycobacterium sp001667015	81.0805	1098	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002705925.1	s__Mycobacterium ostraviense	81.0792	1201	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.87	99.87	0.99	0.99	2	-
GCF_002086675.1	s__Mycobacterium persicum	81.0286	1138	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.71	99.58	0.97	0.95	12	-
GCF_002104675.1	s__Mycobacterium decipiens	80.9349	1093	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015689175.1	s__Mycobacterium kubicae	80.8445	1089	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.05	97.98	0.96	0.92	7	-
GCA_019247635.1	s__Mycobacterium sp019247635	80.7541	923	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101675.1	s__Mycobacterium gordonae	80.7357	1181	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.22	98.97	0.90	0.87	6	-
GCF_900566085.1	s__Mycobacterium attenuatum	80.7197	1134	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.59	99.54	0.94	0.93	4	-
GCF_001673155.1	s__Mycobacterium sp001673155	80.7152	937	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673635.1	s__Mycobacterium asiaticum_C	80.6711	1124	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.07	99.07	0.94	0.94	2	-
GCF_001053185.1	s__Mycobacterium bohemicum	80.6214	989	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_001417955.2	s__Mycobacterium gordonae_B	80.6152	1164	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731675.1	s__Mycobacterium marseillense	80.6097	1030	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.64	95.51	0.95	0.90	6	-
GCF_017086405.1	s__Mycobacterium gordonae_D	80.4072	1166	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013466425.1	s__Mycobacterium vicinigordonae	80.2089	1046	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:56:30,703] [INFO] GTDB search result was written to GCF_025821385.1_ASM2582138v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:56:30,704] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:56:30,707] [INFO] DFAST_QC result json was written to GCF_025821385.1_ASM2582138v1_genomic.fna/dqc_result.json
[2024-01-25 18:56:30,707] [INFO] DFAST_QC completed!
[2024-01-25 18:56:30,707] [INFO] Total running time: 0h2m25s