[2024-01-24 14:14:47,110] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:47,113] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:47,113] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2069a41-d468-4d00-9e5a-70b6ae1888bc/dqc_reference
[2024-01-24 14:14:49,422] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:49,422] [INFO] Task started: Prodigal
[2024-01-24 14:14:49,423] [INFO] Running command: gunzip -c /var/lib/cwl/stge11d33e5-2e1c-422c-9ed1-4c2dffe40312/GCF_025822985.1_ASM2582298v1_genomic.fna.gz | prodigal -d GCF_025822985.1_ASM2582298v1_genomic.fna/cds.fna -a GCF_025822985.1_ASM2582298v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:08,127] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:08,128] [INFO] Task started: HMMsearch
[2024-01-24 14:15:08,128] [INFO] Running command: hmmsearch --tblout GCF_025822985.1_ASM2582298v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2069a41-d468-4d00-9e5a-70b6ae1888bc/dqc_reference/reference_markers.hmm GCF_025822985.1_ASM2582298v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:08,446] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:08,447] [INFO] Found 6/6 markers.
[2024-01-24 14:15:08,497] [INFO] Query marker FASTA was written to GCF_025822985.1_ASM2582298v1_genomic.fna/markers.fasta
[2024-01-24 14:15:08,498] [INFO] Task started: Blastn
[2024-01-24 14:15:08,498] [INFO] Running command: blastn -query GCF_025822985.1_ASM2582298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2069a41-d468-4d00-9e5a-70b6ae1888bc/dqc_reference/reference_markers.fasta -out GCF_025822985.1_ASM2582298v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:09,859] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:09,862] [INFO] Selected 21 target genomes.
[2024-01-24 14:15:09,863] [INFO] Target genome list was writen to GCF_025822985.1_ASM2582298v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:09,874] [INFO] Task started: fastANI
[2024-01-24 14:15:09,874] [INFO] Running command: fastANI --query /var/lib/cwl/stge11d33e5-2e1c-422c-9ed1-4c2dffe40312/GCF_025822985.1_ASM2582298v1_genomic.fna.gz --refList GCF_025822985.1_ASM2582298v1_genomic.fna/target_genomes.txt --output GCF_025822985.1_ASM2582298v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:36,914] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:36,915] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2069a41-d468-4d00-9e5a-70b6ae1888bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:36,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2069a41-d468-4d00-9e5a-70b6ae1888bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:36,937] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:15:36,937] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:15:36,937] [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	83.6233	1422	2063	95	below_threshold
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	83.3891	1435	2063	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	80.6919	1042	2063	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	80.6058	1003	2063	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	80.5846	1132	2063	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_001044255.1	1800	1800	type	True	80.5656	1079	2063	95	below_threshold
Mycolicibacterium chubuense	strain=NCTC10819	GCA_900453455.1	1800	1800	type	True	80.5256	1119	2063	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	80.5213	1132	2063	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	80.4967	1105	2063	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	80.2013	1033	2063	95	below_threshold
Mycolicibacterium aurum	strain=NCTC10437	GCA_900637195.1	1791	1791	type	True	80.0478	1024	2063	95	below_threshold
Mycolicibacterium aurum	strain=NCTC 10437	GCA_001049355.1	1791	1791	type	True	80.0079	1029	2063	95	below_threshold
Mycolicibacterium confluentis	strain=JCM 13671	GCA_010729895.1	28047	28047	type	True	79.8001	861	2063	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	79.7228	1010	2063	95	below_threshold
Mycolicibacterium confluentis	strain=DSM 44017	GCA_002102105.1	28047	28047	type	True	79.7061	869	2063	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	79.6841	1035	2063	95	below_threshold
[Mycobacterium] fortunisiensis	strain=TNTM28	GCA_019050325.1	2600579	2600579	type	True	79.6574	884	2063	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.6381	848	2063	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.583	801	2063	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.5096	864	2063	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.3041	825	2063	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:36,939] [INFO] DFAST Taxonomy check result was written to GCF_025822985.1_ASM2582298v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:36,940] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:36,940] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:36,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2069a41-d468-4d00-9e5a-70b6ae1888bc/dqc_reference/checkm_data
[2024-01-24 14:15:36,941] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:37,001] [INFO] Task started: CheckM
[2024-01-24 14:15:37,002] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025822985.1_ASM2582298v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025822985.1_ASM2582298v1_genomic.fna/checkm_input GCF_025822985.1_ASM2582298v1_genomic.fna/checkm_result
[2024-01-24 14:16:38,102] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:38,103] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:38,126] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:38,126] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:38,127] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025822985.1_ASM2582298v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:38,127] [INFO] Task started: Blastn
[2024-01-24 14:16:38,127] [INFO] Running command: blastn -query GCF_025822985.1_ASM2582298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2069a41-d468-4d00-9e5a-70b6ae1888bc/dqc_reference/reference_markers_gtdb.fasta -out GCF_025822985.1_ASM2582298v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:40,313] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:40,317] [INFO] Selected 17 target genomes.
[2024-01-24 14:16:40,317] [INFO] Target genome list was writen to GCF_025822985.1_ASM2582298v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:40,332] [INFO] Task started: fastANI
[2024-01-24 14:16:40,332] [INFO] Running command: fastANI --query /var/lib/cwl/stge11d33e5-2e1c-422c-9ed1-4c2dffe40312/GCF_025822985.1_ASM2582298v1_genomic.fna.gz --refList GCF_025822985.1_ASM2582298v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025822985.1_ASM2582298v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:03,865] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:03,890] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:03,891] [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_010731735.1	s__Mycobacterium sediminis	99.9958	2061	2063	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_010731815.2	s__Mycobacterium arabiense	83.3669	1439	2063	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	82.8299	1332	2063	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	81.6551	1202	2063	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	81.1489	1104	2063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426545.1	s__Mycobacterium sp001426545	81.0801	1205	2063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002043095.1	s__Mycobacterium sp002043095	81.0211	1157	2063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.25	95.25	0.79	0.79	2	-
GCF_000620625.1	s__Mycobacterium sp000620625	80.9404	1155	2063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016462545.1	s__Mycobacterium sp016462545	80.65	1064	2063	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	80.6441	996	2063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_001044235.1	s__Mycobacterium chlorophenolicum	80.5927	1130	2063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	98.88	97.93	0.94	0.90	4	-
GCF_006439015.1	s__Mycobacterium hodleri_A	80.2337	993	2063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001907655.1	s__Mycobacterium diernhoferi	80.0757	934	2063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.97	99.94	1.00	1.00	3	-
GCF_005222675.1	s__Mycobacterium sp005222675	80.0201	981	2063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001954135.1	s__Mycobacterium sp001954135	79.6596	821	2063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011745145.1	s__Mycobacterium sp011745145	79.514	889	2063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243415.2	s__Mycobacterium tusciae_A	79.1605	866	2063	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 14:17:03,893] [INFO] GTDB search result was written to GCF_025822985.1_ASM2582298v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:03,893] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:03,897] [INFO] DFAST_QC result json was written to GCF_025822985.1_ASM2582298v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:03,898] [INFO] DFAST_QC completed!
[2024-01-24 14:17:03,898] [INFO] Total running time: 0h2m17s