[2024-01-24 12:13:28,868] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:28,872] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:28,872] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2ba22e2-d724-419c-bd1f-240f84c08413/dqc_reference
[2024-01-24 12:13:30,316] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:30,319] [INFO] Task started: Prodigal
[2024-01-24 12:13:30,319] [INFO] Running command: gunzip -c /var/lib/cwl/stgf573dfb7-b190-44c4-aac0-7b5dd182709b/GCF_021916785.1_ASM2191678v1_genomic.fna.gz | prodigal -d GCF_021916785.1_ASM2191678v1_genomic.fna/cds.fna -a GCF_021916785.1_ASM2191678v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:49,346] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:49,346] [INFO] Task started: HMMsearch
[2024-01-24 12:13:49,346] [INFO] Running command: hmmsearch --tblout GCF_021916785.1_ASM2191678v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2ba22e2-d724-419c-bd1f-240f84c08413/dqc_reference/reference_markers.hmm GCF_021916785.1_ASM2191678v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:49,734] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:49,735] [INFO] Found 6/6 markers.
[2024-01-24 12:13:49,789] [INFO] Query marker FASTA was written to GCF_021916785.1_ASM2191678v1_genomic.fna/markers.fasta
[2024-01-24 12:13:49,790] [INFO] Task started: Blastn
[2024-01-24 12:13:49,790] [INFO] Running command: blastn -query GCF_021916785.1_ASM2191678v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2ba22e2-d724-419c-bd1f-240f84c08413/dqc_reference/reference_markers.fasta -out GCF_021916785.1_ASM2191678v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:51,195] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:51,198] [INFO] Selected 22 target genomes.
[2024-01-24 12:13:51,199] [INFO] Target genome list was writen to GCF_021916785.1_ASM2191678v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:51,206] [INFO] Task started: fastANI
[2024-01-24 12:13:51,206] [INFO] Running command: fastANI --query /var/lib/cwl/stgf573dfb7-b190-44c4-aac0-7b5dd182709b/GCF_021916785.1_ASM2191678v1_genomic.fna.gz --refList GCF_021916785.1_ASM2191678v1_genomic.fna/target_genomes.txt --output GCF_021916785.1_ASM2191678v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:19,504] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:19,505] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2ba22e2-d724-419c-bd1f-240f84c08413/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:19,505] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2ba22e2-d724-419c-bd1f-240f84c08413/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:19,521] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:19,521] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:19,522] [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 lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	100.0	2033	2035	95	conclusive
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	93.5258	1784	2035	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	80.5636	1034	2035	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	80.5595	1028	2035	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	80.5327	1043	2035	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	80.4853	1100	2035	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	80.3167	1039	2035	95	below_threshold
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	80.1445	917	2035	95	below_threshold
Mycolicibacterium chitae	strain=JCM 12403	GCA_010727725.1	1792	1792	type	True	79.9893	892	2035	95	below_threshold
Mycolicibacterium chitae	strain=NCTC10485	GCA_900637205.1	1792	1792	type	True	79.9075	904	2035	95	below_threshold
Mycolicibacterium elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	79.8771	879	2035	95	below_threshold
Mycolicibacterium aurum	strain=NCTC10437	GCA_900637195.1	1791	1791	type	True	79.7726	1054	2035	95	below_threshold
Mycolicibacterium confluentis	strain=JCM 13671	GCA_010729895.1	28047	28047	type	True	79.7484	895	2035	95	below_threshold
Mycolicibacterium pulveris	strain=JCM 6370	GCA_010725725.1	36813	36813	type	True	79.7325	909	2035	95	below_threshold
Mycolicibacterium confluentis	strain=DSM 44017	GCA_002102105.1	28047	28047	type	True	79.7306	891	2035	95	below_threshold
Mycolicibacterium aurum	strain=NCTC 10437	GCA_001049355.1	1791	1791	type	True	79.7225	1045	2035	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	79.7119	1039	2035	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	79.7023	1035	2035	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.4433	797	2035	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.4032	872	2035	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.3966	875	2035	95	below_threshold
Mycobacterium noviomagense	strain=DSM 45145	GCA_002086415.1	459858	459858	type	True	78.3231	570	2035	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:19,523] [INFO] DFAST Taxonomy check result was written to GCF_021916785.1_ASM2191678v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:19,524] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:19,524] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:19,525] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2ba22e2-d724-419c-bd1f-240f84c08413/dqc_reference/checkm_data
[2024-01-24 12:14:19,526] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:19,583] [INFO] Task started: CheckM
[2024-01-24 12:14:19,583] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021916785.1_ASM2191678v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021916785.1_ASM2191678v1_genomic.fna/checkm_input GCF_021916785.1_ASM2191678v1_genomic.fna/checkm_result
[2024-01-24 12:15:21,580] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:21,581] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:21,607] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:21,608] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:21,608] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021916785.1_ASM2191678v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:21,608] [INFO] Task started: Blastn
[2024-01-24 12:15:21,609] [INFO] Running command: blastn -query GCF_021916785.1_ASM2191678v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2ba22e2-d724-419c-bd1f-240f84c08413/dqc_reference/reference_markers_gtdb.fasta -out GCF_021916785.1_ASM2191678v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:23,862] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:23,865] [INFO] Selected 14 target genomes.
[2024-01-24 12:15:23,866] [INFO] Target genome list was writen to GCF_021916785.1_ASM2191678v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:23,882] [INFO] Task started: fastANI
[2024-01-24 12:15:23,882] [INFO] Running command: fastANI --query /var/lib/cwl/stgf573dfb7-b190-44c4-aac0-7b5dd182709b/GCF_021916785.1_ASM2191678v1_genomic.fna.gz --refList GCF_021916785.1_ASM2191678v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021916785.1_ASM2191678v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:43,523] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:43,539] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:15:43,539] [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_010731815.2	s__Mycobacterium arabiense	93.5258	1784	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_010731735.1	s__Mycobacterium sediminis	83.5722	1424	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_008329645.1	s__Mycobacterium grossiae	82.7524	1335	2035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.93	99.93	0.94	0.94	2	-
GCF_008329535.1	s__Mycobacterium sp008329535	81.3303	1183	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_010729665.1	s__Mycobacterium madagascariense	81.0276	1078	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_000620625.1	s__Mycobacterium sp000620625	80.9696	1204	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_008329605.1	s__Mycobacterium sp008329605	80.7373	1109	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_001583415.1	s__Mycobacterium phlei	80.5233	1045	2035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCA_016462545.1	s__Mycobacterium sp016462545	80.4908	1064	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_001665575.1	s__Mycobacterium sp001665575	80.166	937	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_013390125.1	s__Mycobacterium hippocampi_A	80.1075	1036	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_005222675.1	s__Mycobacterium sp005222675	79.9633	1034	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_006439015.1	s__Mycobacterium hodleri_A	79.9341	1015	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_010725725.1	s__Mycobacterium pulveris	79.7412	907	2035	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 12:15:43,540] [INFO] GTDB search result was written to GCF_021916785.1_ASM2191678v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:43,541] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:43,545] [INFO] DFAST_QC result json was written to GCF_021916785.1_ASM2191678v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:43,545] [INFO] DFAST_QC completed!
[2024-01-24 12:15:43,545] [INFO] Total running time: 0h2m15s