[2024-01-25 18:42:50,644] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:42:50,645] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:42:50,645] [INFO] DQC Reference Directory: /var/lib/cwl/stg70b55df4-fd97-453f-9531-088d780c4ba0/dqc_reference
[2024-01-25 18:42:51,761] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:42:51,762] [INFO] Task started: Prodigal
[2024-01-25 18:42:51,762] [INFO] Running command: gunzip -c /var/lib/cwl/stg18fe4356-1f05-45c6-881c-78babe5fcbab/GCF_900176255.2_PRJEB20293_genomic.fna.gz | prodigal -d GCF_900176255.2_PRJEB20293_genomic.fna/cds.fna -a GCF_900176255.2_PRJEB20293_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:43:10,470] [INFO] Task succeeded: Prodigal
[2024-01-25 18:43:10,470] [INFO] Task started: HMMsearch
[2024-01-25 18:43:10,470] [INFO] Running command: hmmsearch --tblout GCF_900176255.2_PRJEB20293_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70b55df4-fd97-453f-9531-088d780c4ba0/dqc_reference/reference_markers.hmm GCF_900176255.2_PRJEB20293_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:43:10,829] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:43:10,830] [INFO] Found 6/6 markers.
[2024-01-25 18:43:10,917] [INFO] Query marker FASTA was written to GCF_900176255.2_PRJEB20293_genomic.fna/markers.fasta
[2024-01-25 18:43:10,918] [INFO] Task started: Blastn
[2024-01-25 18:43:10,918] [INFO] Running command: blastn -query GCF_900176255.2_PRJEB20293_genomic.fna/markers.fasta -db /var/lib/cwl/stg70b55df4-fd97-453f-9531-088d780c4ba0/dqc_reference/reference_markers.fasta -out GCF_900176255.2_PRJEB20293_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:12,045] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:12,050] [INFO] Selected 14 target genomes.
[2024-01-25 18:43:12,050] [INFO] Target genome list was writen to GCF_900176255.2_PRJEB20293_genomic.fna/target_genomes.txt
[2024-01-25 18:43:12,057] [INFO] Task started: fastANI
[2024-01-25 18:43:12,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg18fe4356-1f05-45c6-881c-78babe5fcbab/GCF_900176255.2_PRJEB20293_genomic.fna.gz --refList GCF_900176255.2_PRJEB20293_genomic.fna/target_genomes.txt --output GCF_900176255.2_PRJEB20293_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:43:32,377] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:32,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70b55df4-fd97-453f-9531-088d780c4ba0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:43:32,378] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70b55df4-fd97-453f-9531-088d780c4ba0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:43:32,387] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:43:32,387] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:43:32,387] [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 ahvazicum	strain=AFP003	GCA_900176255.2	1964395	1964395	type	True	100.0	2025	2035	95	conclusive
Mycobacterium lentiflavum	strain=ATCC 51985	GCA_022374895.2	141349	141349	type	True	91.7139	1666	2035	95	below_threshold
Mycobacterium triplex	strain=DSM 44626	GCA_002102415.1	47839	47839	type	True	89.1312	1622	2035	95	below_threshold
Mycobacterium triplex	strain=DSM 44626	GCA_000689255.1	47839	47839	type	True	89.1254	1652	2035	95	below_threshold
Mycobacterium florentinum	strain=DSM 44852	GCA_002101635.1	292462	292462	type	True	88.3019	1578	2035	95	below_threshold
Mycobacterium florentinum	strain=JCM 14740	GCA_010730355.1	292462	292462	type	True	88.2619	1599	2035	95	below_threshold
Mycobacterium stomatepiae	strain=JCM 17783	GCA_010731715.1	470076	470076	type	True	87.4148	1621	2035	95	below_threshold
Mycobacterium genavense	strain=ATCC 51234	GCA_000526915.1	36812	36812	type	True	87.4065	1417	2035	95	below_threshold
Mycobacterium numidiamassiliense	strain=AB215	GCA_900157365.1	1841861	1841861	type	True	82.9614	1384	2035	95	below_threshold
Mycobacterium shigaense	strain=UN-152	GCA_002983495.1	722731	722731	type	True	82.9251	1323	2035	95	below_threshold
Mycobacterium shigaense	strain=JCM 32072	GCA_002356315.1	722731	722731	type	True	82.9147	1316	2035	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	82.5686	1271	2035	95	below_threshold
Mycobacterium nebraskense	strain=DSM 44803	GCA_002102255.1	244292	244292	type	True	82.5218	1279	2035	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	82.3642	1319	2035	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:43:32,389] [INFO] DFAST Taxonomy check result was written to GCF_900176255.2_PRJEB20293_genomic.fna/tc_result.tsv
[2024-01-25 18:43:32,390] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:43:32,390] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:43:32,390] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70b55df4-fd97-453f-9531-088d780c4ba0/dqc_reference/checkm_data
[2024-01-25 18:43:32,391] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:43:32,449] [INFO] Task started: CheckM
[2024-01-25 18:43:32,449] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900176255.2_PRJEB20293_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900176255.2_PRJEB20293_genomic.fna/checkm_input GCF_900176255.2_PRJEB20293_genomic.fna/checkm_result
[2024-01-25 18:44:27,649] [INFO] Task succeeded: CheckM
[2024-01-25 18:44:27,650] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:44:27,668] [INFO] ===== Completeness check finished =====
[2024-01-25 18:44:27,669] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:44:27,670] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900176255.2_PRJEB20293_genomic.fna/markers.fasta)
[2024-01-25 18:44:27,670] [INFO] Task started: Blastn
[2024-01-25 18:44:27,670] [INFO] Running command: blastn -query GCF_900176255.2_PRJEB20293_genomic.fna/markers.fasta -db /var/lib/cwl/stg70b55df4-fd97-453f-9531-088d780c4ba0/dqc_reference/reference_markers_gtdb.fasta -out GCF_900176255.2_PRJEB20293_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:29,359] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:29,363] [INFO] Selected 14 target genomes.
[2024-01-25 18:44:29,363] [INFO] Target genome list was writen to GCF_900176255.2_PRJEB20293_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:44:29,370] [INFO] Task started: fastANI
[2024-01-25 18:44:29,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg18fe4356-1f05-45c6-881c-78babe5fcbab/GCF_900176255.2_PRJEB20293_genomic.fna.gz --refList GCF_900176255.2_PRJEB20293_genomic.fna/target_genomes_gtdb.txt --output GCF_900176255.2_PRJEB20293_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:44:49,501] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:49,511] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:44:49,511] [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_900176255.2	s__Mycobacterium ahvazicum	100.0	2029	2035	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_001373395.1	s__Mycobacterium lentiflavum	91.6973	1656	2035	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	89.1166	1653	2035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_010730355.1	s__Mycobacterium florentinum	88.257	1600	2035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010731715.1	s__Mycobacterium stomatepiae	87.418	1620	2035	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	87.4059	1417	2035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112775.1	s__Mycobacterium montefiorense	86.0904	1481	2035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356315.1	s__Mycobacterium shigaense	82.9398	1313	2035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.91	99.82	1.00	1.00	3	-
GCF_003284935.1	s__Mycobacterium arosiense_A	82.5711	1170	2035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104765.1	s__Mycobacterium vulneris	82.5236	1284	2035	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	82.4984	1219	2035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672755.1	s__Mycobacterium colombiense_C	82.4511	1191	2035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284975.1	s__Mycobacterium europaeum_A	82.2109	1148	2035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.84	95.70	0.84	0.79	6	-
GCF_001666835.1	s__Mycobacterium sp001666835	82.0006	1221	2035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	99.01	0.94	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:44:49,513] [INFO] GTDB search result was written to GCF_900176255.2_PRJEB20293_genomic.fna/result_gtdb.tsv
[2024-01-25 18:44:49,513] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:44:49,516] [INFO] DFAST_QC result json was written to GCF_900176255.2_PRJEB20293_genomic.fna/dqc_result.json
[2024-01-25 18:44:49,516] [INFO] DFAST_QC completed!
[2024-01-25 18:44:49,517] [INFO] Total running time: 0h1m59s