[2024-01-24 13:50:25,944] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:50:25,946] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:50:25,946] [INFO] DQC Reference Directory: /var/lib/cwl/stgd034dfa6-c5d5-4f6a-acc4-b5c63f1a0166/dqc_reference
[2024-01-24 13:50:27,175] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:50:27,176] [INFO] Task started: Prodigal
[2024-01-24 13:50:27,177] [INFO] Running command: gunzip -c /var/lib/cwl/stgecaccdd4-3c0c-4171-884e-39ed35ccef4b/GCF_010730355.1_ASM1073035v1_genomic.fna.gz | prodigal -d GCF_010730355.1_ASM1073035v1_genomic.fna/cds.fna -a GCF_010730355.1_ASM1073035v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:53,530] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:53,531] [INFO] Task started: HMMsearch
[2024-01-24 13:50:53,531] [INFO] Running command: hmmsearch --tblout GCF_010730355.1_ASM1073035v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd034dfa6-c5d5-4f6a-acc4-b5c63f1a0166/dqc_reference/reference_markers.hmm GCF_010730355.1_ASM1073035v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:53,849] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:53,851] [INFO] Found 6/6 markers.
[2024-01-24 13:50:53,909] [INFO] Query marker FASTA was written to GCF_010730355.1_ASM1073035v1_genomic.fna/markers.fasta
[2024-01-24 13:50:53,909] [INFO] Task started: Blastn
[2024-01-24 13:50:53,909] [INFO] Running command: blastn -query GCF_010730355.1_ASM1073035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd034dfa6-c5d5-4f6a-acc4-b5c63f1a0166/dqc_reference/reference_markers.fasta -out GCF_010730355.1_ASM1073035v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:55,120] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:55,123] [INFO] Selected 9 target genomes.
[2024-01-24 13:50:55,123] [INFO] Target genome list was writen to GCF_010730355.1_ASM1073035v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:55,156] [INFO] Task started: fastANI
[2024-01-24 13:50:55,157] [INFO] Running command: fastANI --query /var/lib/cwl/stgecaccdd4-3c0c-4171-884e-39ed35ccef4b/GCF_010730355.1_ASM1073035v1_genomic.fna.gz --refList GCF_010730355.1_ASM1073035v1_genomic.fna/target_genomes.txt --output GCF_010730355.1_ASM1073035v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:51:08,862] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:08,863] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd034dfa6-c5d5-4f6a-acc4-b5c63f1a0166/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:51:08,863] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd034dfa6-c5d5-4f6a-acc4-b5c63f1a0166/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:51:08,875] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:51:08,875] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:51:08,875] [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	100.0	2073	2073	95	conclusive
Mycobacterium florentinum	strain=DSM 44852	GCA_002101635.1	292462	292462	type	True	99.9848	2041	2073	95	conclusive
Mycobacterium stomatepiae	strain=JCM 17783	GCA_010731715.1	470076	470076	type	True	90.3716	1695	2073	95	below_threshold
Mycobacterium triplex	strain=DSM 44626	GCA_000689255.1	47839	47839	type	True	89.4792	1762	2073	95	below_threshold
Mycobacterium triplex	strain=DSM 44626	GCA_002102415.1	47839	47839	type	True	89.463	1739	2073	95	below_threshold
Mycobacterium lentiflavum	strain=ATCC 51985	GCA_022374895.2	141349	141349	type	True	88.5593	1604	2073	95	below_threshold
Mycobacterium genavense	strain=ATCC 51234	GCA_000526915.1	36812	36812	type	True	88.2263	1423	2073	95	below_threshold
Mycobacterium ahvazicum	strain=AFP003	GCA_900176255.2	1964395	1964395	type	True	88.2138	1605	2073	95	below_threshold
Mycobacterium numidiamassiliense	strain=AB215	GCA_900157365.1	1841861	1841861	type	True	83.518	1348	2073	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:51:08,877] [INFO] DFAST Taxonomy check result was written to GCF_010730355.1_ASM1073035v1_genomic.fna/tc_result.tsv
[2024-01-24 13:51:08,878] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:51:08,878] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:51:08,878] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd034dfa6-c5d5-4f6a-acc4-b5c63f1a0166/dqc_reference/checkm_data
[2024-01-24 13:51:08,879] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:51:08,936] [INFO] Task started: CheckM
[2024-01-24 13:51:08,937] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010730355.1_ASM1073035v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010730355.1_ASM1073035v1_genomic.fna/checkm_input GCF_010730355.1_ASM1073035v1_genomic.fna/checkm_result
[2024-01-24 13:52:24,240] [INFO] Task succeeded: CheckM
[2024-01-24 13:52:24,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:52:24,266] [INFO] ===== Completeness check finished =====
[2024-01-24 13:52:24,267] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:52:24,267] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010730355.1_ASM1073035v1_genomic.fna/markers.fasta)
[2024-01-24 13:52:24,268] [INFO] Task started: Blastn
[2024-01-24 13:52:24,268] [INFO] Running command: blastn -query GCF_010730355.1_ASM1073035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd034dfa6-c5d5-4f6a-acc4-b5c63f1a0166/dqc_reference/reference_markers_gtdb.fasta -out GCF_010730355.1_ASM1073035v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:26,153] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:26,157] [INFO] Selected 11 target genomes.
[2024-01-24 13:52:26,157] [INFO] Target genome list was writen to GCF_010730355.1_ASM1073035v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:52:26,197] [INFO] Task started: fastANI
[2024-01-24 13:52:26,197] [INFO] Running command: fastANI --query /var/lib/cwl/stgecaccdd4-3c0c-4171-884e-39ed35ccef4b/GCF_010730355.1_ASM1073035v1_genomic.fna.gz --refList GCF_010730355.1_ASM1073035v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010730355.1_ASM1073035v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:42,319] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:42,334] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:42,334] [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_010730355.1	s__Mycobacterium florentinum	100.0	2073	2073	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_010731715.1	s__Mycobacterium stomatepiae	90.3716	1695	2073	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000689255.1	s__Mycobacterium triplex	89.4845	1761	2073	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	88.5967	1688	2073	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	88.2177	1605	2073	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	88.2177	1425	2073	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	85.2221	1471	2073	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900157365.1	s__Mycobacterium numidiamassiliense	83.4815	1355	2073	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667275.1	s__Mycobacterium sp001667275	82.6038	1254	2073	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.42	96.39	0.93	0.93	5	-
GCF_002102155.1	s__Mycobacterium europaeum	82.5862	1212	2073	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.26	99.26	0.97	0.97	2	-
GCF_001907675.1	s__Mycobacterium paraffinicum	82.4299	1241	2073	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 13:52:42,336] [INFO] GTDB search result was written to GCF_010730355.1_ASM1073035v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:42,336] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:42,339] [INFO] DFAST_QC result json was written to GCF_010730355.1_ASM1073035v1_genomic.fna/dqc_result.json
[2024-01-24 13:52:42,340] [INFO] DFAST_QC completed!
[2024-01-24 13:52:42,340] [INFO] Total running time: 0h2m16s