[2024-01-24 12:15:03,481] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:03,483] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:03,483] [INFO] DQC Reference Directory: /var/lib/cwl/stg190f97a7-e87e-42c3-aa1e-5f346fb52390/dqc_reference
[2024-01-24 12:15:04,774] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:04,775] [INFO] Task started: Prodigal
[2024-01-24 12:15:04,775] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b350a7d-1a68-4232-905c-3867bb51114f/GCF_010722915.1_ASM1072291v1_genomic.fna.gz | prodigal -d GCF_010722915.1_ASM1072291v1_genomic.fna/cds.fna -a GCF_010722915.1_ASM1072291v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:30,204] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:30,205] [INFO] Task started: HMMsearch
[2024-01-24 12:15:30,205] [INFO] Running command: hmmsearch --tblout GCF_010722915.1_ASM1072291v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg190f97a7-e87e-42c3-aa1e-5f346fb52390/dqc_reference/reference_markers.hmm GCF_010722915.1_ASM1072291v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:30,519] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:30,521] [INFO] Found 6/6 markers.
[2024-01-24 12:15:30,580] [INFO] Query marker FASTA was written to GCF_010722915.1_ASM1072291v1_genomic.fna/markers.fasta
[2024-01-24 12:15:30,580] [INFO] Task started: Blastn
[2024-01-24 12:15:30,580] [INFO] Running command: blastn -query GCF_010722915.1_ASM1072291v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg190f97a7-e87e-42c3-aa1e-5f346fb52390/dqc_reference/reference_markers.fasta -out GCF_010722915.1_ASM1072291v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:31,870] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:31,875] [INFO] Selected 16 target genomes.
[2024-01-24 12:15:31,875] [INFO] Target genome list was writen to GCF_010722915.1_ASM1072291v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:31,886] [INFO] Task started: fastANI
[2024-01-24 12:15:31,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b350a7d-1a68-4232-905c-3867bb51114f/GCF_010722915.1_ASM1072291v1_genomic.fna.gz --refList GCF_010722915.1_ASM1072291v1_genomic.fna/target_genomes.txt --output GCF_010722915.1_ASM1072291v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:54,233] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:54,234] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg190f97a7-e87e-42c3-aa1e-5f346fb52390/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:54,234] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg190f97a7-e87e-42c3-aa1e-5f346fb52390/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:54,250] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:15:54,250] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:54,250] [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 agri	strain=JCM 6377	GCA_010722915.1	36811	36811	type	True	100.0	2430	2430	95	conclusive
Mycolicibacterium agri	strain=CCUG37673	GCA_002553505.1	36811	36811	type	True	99.9025	2192	2430	95	conclusive
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	82.1023	1348	2430	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	81.6235	1100	2430	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	81.6063	1110	2430	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	81.5618	1103	2430	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	81.4844	1136	2430	95	below_threshold
Mycolicibacterium pulveris	strain=JCM 6370	GCA_010725725.1	36813	36813	type	True	81.0606	1017	2430	95	below_threshold
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	81.0496	1012	2430	95	below_threshold
Mycolicibacterium komanii	strain=GPK 1020	GCA_001050035.1	1566885	1566885	type	True	80.8965	1056	2430	95	below_threshold
Mycolicibacterium celeriflavum	strain=DSM 46765	GCA_002086175.1	1249101	1249101	type	True	80.7814	969	2430	95	below_threshold
Mycolicibacterium moriokaense	strain=CIP105393	GCA_002086395.1	39691	39691	type	True	80.3543	1050	2430	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	79.858	832	2430	95	below_threshold
Mycolicibacterium alvei	strain=JCM 12272	GCA_010727325.1	67081	67081	type	True	79.4658	862	2430	95	below_threshold
Mycobacterium seoulense	strain=JCM 16018	GCA_010731595.1	386911	386911	type	True	79.2248	802	2430	95	below_threshold
Mycolicibacter hiberniae	strain=ATCC 49874	GCA_002101655.1	29314	29314	type	True	78.9621	625	2430	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:54,252] [INFO] DFAST Taxonomy check result was written to GCF_010722915.1_ASM1072291v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:54,253] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:54,253] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:54,253] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg190f97a7-e87e-42c3-aa1e-5f346fb52390/dqc_reference/checkm_data
[2024-01-24 12:15:54,254] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:54,324] [INFO] Task started: CheckM
[2024-01-24 12:15:54,324] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010722915.1_ASM1072291v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010722915.1_ASM1072291v1_genomic.fna/checkm_input GCF_010722915.1_ASM1072291v1_genomic.fna/checkm_result
[2024-01-24 12:17:07,467] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:07,469] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-24 12:17:07,498] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:07,498] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:07,499] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010722915.1_ASM1072291v1_genomic.fna/markers.fasta)
[2024-01-24 12:17:07,499] [INFO] Task started: Blastn
[2024-01-24 12:17:07,499] [INFO] Running command: blastn -query GCF_010722915.1_ASM1072291v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg190f97a7-e87e-42c3-aa1e-5f346fb52390/dqc_reference/reference_markers_gtdb.fasta -out GCF_010722915.1_ASM1072291v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:09,385] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:09,391] [INFO] Selected 17 target genomes.
[2024-01-24 12:17:09,391] [INFO] Target genome list was writen to GCF_010722915.1_ASM1072291v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:09,407] [INFO] Task started: fastANI
[2024-01-24 12:17:09,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b350a7d-1a68-4232-905c-3867bb51114f/GCF_010722915.1_ASM1072291v1_genomic.fna.gz --refList GCF_010722915.1_ASM1072291v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010722915.1_ASM1072291v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:32,142] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:32,159] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:32,160] [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_002553505.1	s__Mycobacterium agri	99.9025	2192	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_003347205.1	s__Mycobacterium moriokaense_B	82.6324	1348	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001665255.1	s__Mycobacterium sp001665255	82.1787	1051	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001668615.1	s__Mycobacterium sp001668615	82.1242	1129	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003719305.1	s__Mycobacterium sp003719305	82.1198	1344	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826815.1	s__Mycobacterium sp902826815	81.965	1386	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001583415.1	s__Mycobacterium phlei	81.5751	1109	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_900108565.1	s__Mycobacterium rutilum	81.5158	1129	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010725725.1	s__Mycobacterium pulveris	81.0761	1014	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050015.1	s__Mycobacterium malmesburyense	81.0339	1015	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050035.1	s__Mycobacterium komanii	80.9068	1054	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665535.1	s__Mycobacterium sp001665535	80.8906	1021	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.97	96.97	0.90	0.90	2	-
GCF_001668575.1	s__Mycobacterium sp001668575	80.7259	1020	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667505.1	s__Mycobacterium sp001667505	80.6831	1158	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001500025.1	s__Mycobacterium sp001500025	80.6462	1007	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873705.1	s__Mycobacterium sp014873705	80.4685	1088	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.28	98.28	0.92	0.92	2	-
GCF_002086455.1	s__Mycobacterium algericum	79.3403	691	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.66	97.92	0.93	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:32,162] [INFO] GTDB search result was written to GCF_010722915.1_ASM1072291v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:32,162] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:32,166] [INFO] DFAST_QC result json was written to GCF_010722915.1_ASM1072291v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:32,166] [INFO] DFAST_QC completed!
[2024-01-24 12:17:32,166] [INFO] Total running time: 0h2m29s