[2024-01-24 12:23:03,494] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,496] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,496] [INFO] DQC Reference Directory: /var/lib/cwl/stge70f3a5d-c9a6-4cd2-83cf-e011766c00ed/dqc_reference
[2024-01-24 12:23:04,859] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:04,860] [INFO] Task started: Prodigal
[2024-01-24 12:23:04,860] [INFO] Running command: gunzip -c /var/lib/cwl/stg4e004c41-5b9c-4bdb-95b9-88098033390a/GCF_002086345.1_ASM208634v1_genomic.fna.gz | prodigal -d GCF_002086345.1_ASM208634v1_genomic.fna/cds.fna -a GCF_002086345.1_ASM208634v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:24,730] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:24,731] [INFO] Task started: HMMsearch
[2024-01-24 12:23:24,731] [INFO] Running command: hmmsearch --tblout GCF_002086345.1_ASM208634v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge70f3a5d-c9a6-4cd2-83cf-e011766c00ed/dqc_reference/reference_markers.hmm GCF_002086345.1_ASM208634v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:25,019] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:25,021] [INFO] Found 6/6 markers.
[2024-01-24 12:23:25,067] [INFO] Query marker FASTA was written to GCF_002086345.1_ASM208634v1_genomic.fna/markers.fasta
[2024-01-24 12:23:25,068] [INFO] Task started: Blastn
[2024-01-24 12:23:25,068] [INFO] Running command: blastn -query GCF_002086345.1_ASM208634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge70f3a5d-c9a6-4cd2-83cf-e011766c00ed/dqc_reference/reference_markers.fasta -out GCF_002086345.1_ASM208634v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:26,250] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:26,257] [INFO] Selected 13 target genomes.
[2024-01-24 12:23:26,258] [INFO] Target genome list was writen to GCF_002086345.1_ASM208634v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:26,266] [INFO] Task started: fastANI
[2024-01-24 12:23:26,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e004c41-5b9c-4bdb-95b9-88098033390a/GCF_002086345.1_ASM208634v1_genomic.fna.gz --refList GCF_002086345.1_ASM208634v1_genomic.fna/target_genomes.txt --output GCF_002086345.1_ASM208634v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:44,692] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:44,692] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge70f3a5d-c9a6-4cd2-83cf-e011766c00ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:44,693] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge70f3a5d-c9a6-4cd2-83cf-e011766c00ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:44,708] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:23:44,709] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:44,709] [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 marseillense	strain=DSM 45437	GCA_002086345.1	701042	701042	type	True	100.0	1773	1777	95	conclusive
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	99.9954	1776	1777	95	conclusive
Mycobacterium paraintracellulare	strain=KCTC 29084	GCA_002104735.1	1138383	1138383	suspected-type	True	92.5195	1515	1777	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	92.5092	1552	1777	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000277125.1	1767	1767	suspected-type	True	92.508	1555	1777	95	below_threshold
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	92.4911	1564	1777	95	below_threshold
Mycobacterium intracellulare subsp. yongonense	strain=05-1390	GCA_000418535.2	1203599	1767	type	True	92.488	1599	1777	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	92.4714	1562	1777	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000172115.1	1767	1767	suspected-type	True	92.4338	1386	1777	95	below_threshold
Mycobacterium intracellulare subsp. chimaera	strain=DSM 44623	GCA_002219285.1	222805	1767	type	True	92.2957	1587	1777	95	below_threshold
Mycobacterium intracellulare subsp. chimaera	strain=JCM_14737	GCA_001938095.1	222805	1767	type	True	92.2952	1580	1777	95	below_threshold
Mycobacterium mantenii	strain=DSM 45255	GCA_002086335.1	560555	560555	type	True	86.8585	1414	1777	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	86.7921	1450	1777	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:44,711] [INFO] DFAST Taxonomy check result was written to GCF_002086345.1_ASM208634v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:44,711] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:44,711] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:44,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge70f3a5d-c9a6-4cd2-83cf-e011766c00ed/dqc_reference/checkm_data
[2024-01-24 12:23:44,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:44,766] [INFO] Task started: CheckM
[2024-01-24 12:23:44,766] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002086345.1_ASM208634v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002086345.1_ASM208634v1_genomic.fna/checkm_input GCF_002086345.1_ASM208634v1_genomic.fna/checkm_result
[2024-01-24 12:24:41,715] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:41,717] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:41,740] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:41,740] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:41,741] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002086345.1_ASM208634v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:41,741] [INFO] Task started: Blastn
[2024-01-24 12:24:41,741] [INFO] Running command: blastn -query GCF_002086345.1_ASM208634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge70f3a5d-c9a6-4cd2-83cf-e011766c00ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_002086345.1_ASM208634v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:43,409] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:43,413] [INFO] Selected 13 target genomes.
[2024-01-24 12:24:43,413] [INFO] Target genome list was writen to GCF_002086345.1_ASM208634v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:43,424] [INFO] Task started: fastANI
[2024-01-24 12:24:43,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e004c41-5b9c-4bdb-95b9-88098033390a/GCF_002086345.1_ASM208634v1_genomic.fna.gz --refList GCF_002086345.1_ASM208634v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002086345.1_ASM208634v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:01,630] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:01,641] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:01,641] [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_010731675.1	s__Mycobacterium marseillense	99.9954	1776	1777	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.64	95.51	0.95	0.90	6	conclusive
GCF_000277125.1	s__Mycobacterium intracellulare	92.508	1555	1777	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.48	95.71	0.93	0.84	82	-
GCF_001667315.1	s__Mycobacterium sp001667315	90.864	1509	1777	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004298145.1	s__Mycobacterium sp004298145	89.7641	1404	1777	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105755.1	s__Mycobacterium colombiense	87.1768	1480	1777	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.60	97.75	0.94	0.91	4	-
GCF_001953985.1	s__Mycobacterium colombiense_B	87.1467	1461	1777	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.54	96.91	0.93	0.88	12	-
GCF_001672755.1	s__Mycobacterium colombiense_C	87.0681	1371	1777	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	86.9756	1373	1777	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731775.1	s__Mycobacterium mantenii	86.7899	1451	1777	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.19	95.22	0.92	0.90	6	-
GCF_003284975.1	s__Mycobacterium europaeum_A	86.6285	1342	1777	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.84	95.70	0.84	0.79	6	-
GCF_001667145.1	s__Mycobacterium sp001667145	86.1502	1338	1777	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	84.1812	1298	1777	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.58	99.42	0.93	0.92	4	-
GCF_001907675.1	s__Mycobacterium paraffinicum	83.7594	1287	1777	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 12:25:01,644] [INFO] GTDB search result was written to GCF_002086345.1_ASM208634v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:01,645] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:01,649] [INFO] DFAST_QC result json was written to GCF_002086345.1_ASM208634v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:01,650] [INFO] DFAST_QC completed!
[2024-01-24 12:25:01,650] [INFO] Total running time: 0h1m58s