[2024-01-24 13:48:43,072] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:43,074] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:43,074] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bc762d5-4791-40f7-98a6-f2f44e2d9b9a/dqc_reference
[2024-01-24 13:48:44,383] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:44,384] [INFO] Task started: Prodigal
[2024-01-24 13:48:44,384] [INFO] Running command: gunzip -c /var/lib/cwl/stgc734eb00-e0ac-46e1-a70e-360c98c1c37c/GCF_010729665.1_ASM1072966v1_genomic.fna.gz | prodigal -d GCF_010729665.1_ASM1072966v1_genomic.fna/cds.fna -a GCF_010729665.1_ASM1072966v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:02,465] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:02,465] [INFO] Task started: HMMsearch
[2024-01-24 13:49:02,465] [INFO] Running command: hmmsearch --tblout GCF_010729665.1_ASM1072966v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bc762d5-4791-40f7-98a6-f2f44e2d9b9a/dqc_reference/reference_markers.hmm GCF_010729665.1_ASM1072966v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:02,804] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:02,805] [INFO] Found 6/6 markers.
[2024-01-24 13:49:02,857] [INFO] Query marker FASTA was written to GCF_010729665.1_ASM1072966v1_genomic.fna/markers.fasta
[2024-01-24 13:49:02,858] [INFO] Task started: Blastn
[2024-01-24 13:49:02,858] [INFO] Running command: blastn -query GCF_010729665.1_ASM1072966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bc762d5-4791-40f7-98a6-f2f44e2d9b9a/dqc_reference/reference_markers.fasta -out GCF_010729665.1_ASM1072966v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:04,156] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:04,160] [INFO] Selected 28 target genomes.
[2024-01-24 13:49:04,160] [INFO] Target genome list was writen to GCF_010729665.1_ASM1072966v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:04,172] [INFO] Task started: fastANI
[2024-01-24 13:49:04,172] [INFO] Running command: fastANI --query /var/lib/cwl/stgc734eb00-e0ac-46e1-a70e-360c98c1c37c/GCF_010729665.1_ASM1072966v1_genomic.fna.gz --refList GCF_010729665.1_ASM1072966v1_genomic.fna/target_genomes.txt --output GCF_010729665.1_ASM1072966v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:36,555] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:36,556] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bc762d5-4791-40f7-98a6-f2f44e2d9b9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:36,556] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bc762d5-4791-40f7-98a6-f2f44e2d9b9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:36,581] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:49:36,581] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:49:36,581] [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 arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	81.1771	1102	1980	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	81.0918	1089	1980	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	80.6321	992	1980	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	80.5641	968	1980	95	below_threshold
Mycolicibacterium chubuense	strain=NCTC10819	GCA_900453455.1	1800	1800	type	True	80.5565	987	1980	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	80.5188	942	1980	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	80.5044	996	1980	95	below_threshold
Mycolicibacterium litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	80.4456	958	1980	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	80.4322	939	1980	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	80.2283	957	1980	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	80.0423	912	1980	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	79.9738	914	1980	95	below_threshold
Mycolicibacterium phocaicum	strain=DSM 45104	GCA_005670655.1	319706	319706	type	True	79.8808	815	1980	95	below_threshold
Mycolicibacterium aurum	strain=NCTC 10437	GCA_001049355.1	1791	1791	type	True	79.8408	892	1980	95	below_threshold
Mycolicibacterium phocaicum	strain=JCM 15301	GCA_010731115.1	319706	319706	type	True	79.8251	820	1980	95	below_threshold
Mycolicibacterium houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	79.7967	863	1980	95	below_threshold
Mycolicibacterium aurum	strain=NCTC10437	GCA_900637195.1	1791	1791	type	True	79.7944	907	1980	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	79.7931	917	1980	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	79.7675	925	1980	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	79.7318	828	1980	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.631	807	1980	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.5712	808	1980	95	below_threshold
Mycolicibacterium confluentis	strain=JCM 13671	GCA_010729895.1	28047	28047	type	True	79.5495	811	1980	95	below_threshold
Mycolicibacterium tokaiense	strain=JCM 6373	GCA_010725885.1	39695	39695	suspected-type	True	79.4742	831	1980	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.3498	795	1980	95	below_threshold
Mycobacterium branderi	strain=JCM 12687	GCA_010728725.1	43348	43348	type	True	79.2156	695	1980	95	below_threshold
Mycobacterium celatum	strain=DSM 44243	GCA_002101595.1	28045	28045	type	True	79.2077	662	1980	95	below_threshold
Mycobacterium branderi	strain=DSM 44624	GCA_002086575.1	43348	43348	type	True	79.1594	696	1980	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:36,583] [INFO] DFAST Taxonomy check result was written to GCF_010729665.1_ASM1072966v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:36,583] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:36,584] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:36,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bc762d5-4791-40f7-98a6-f2f44e2d9b9a/dqc_reference/checkm_data
[2024-01-24 13:49:36,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:36,639] [INFO] Task started: CheckM
[2024-01-24 13:49:36,639] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010729665.1_ASM1072966v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010729665.1_ASM1072966v1_genomic.fna/checkm_input GCF_010729665.1_ASM1072966v1_genomic.fna/checkm_result
[2024-01-24 13:50:47,895] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:47,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:47,920] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:47,920] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:47,921] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010729665.1_ASM1072966v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:47,921] [INFO] Task started: Blastn
[2024-01-24 13:50:47,921] [INFO] Running command: blastn -query GCF_010729665.1_ASM1072966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bc762d5-4791-40f7-98a6-f2f44e2d9b9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_010729665.1_ASM1072966v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:50,092] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:50,096] [INFO] Selected 14 target genomes.
[2024-01-24 13:50:50,097] [INFO] Target genome list was writen to GCF_010729665.1_ASM1072966v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:50,115] [INFO] Task started: fastANI
[2024-01-24 13:50:50,116] [INFO] Running command: fastANI --query /var/lib/cwl/stgc734eb00-e0ac-46e1-a70e-360c98c1c37c/GCF_010729665.1_ASM1072966v1_genomic.fna.gz --refList GCF_010729665.1_ASM1072966v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010729665.1_ASM1072966v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:10,795] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:10,812] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:10,813] [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_010729665.1	s__Mycobacterium madagascariense	100.0	1978	1980	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_008329535.1	s__Mycobacterium sp008329535	82.9278	1208	1980	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	82.5619	1194	1980	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.25	95.25	0.79	0.79	2	-
GCA_016462545.1	s__Mycobacterium sp016462545	82.3791	1179	1980	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	82.3614	1214	1980	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	81.7273	1138	1980	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	81.5732	1141	1980	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.93	99.93	0.94	0.94	2	-
GCF_010731815.2	s__Mycobacterium arabiense	81.1948	1098	1980	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	81.1927	1118	1980	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	80.976	1095	1980	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202335.1	s__Mycobacterium sp014202335	80.8083	1077	1980	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001044255.1	s__Mycobacterium chubuense	80.5808	954	1980	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	99.98	99.97	0.99	0.98	3	-
GCF_004570325.1	s__Mycobacterium sp004570325	80.5652	956	1980	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002863225.1	s__Mycobacterium sp002863225	78.8202	653	1980	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 13:51:10,814] [INFO] GTDB search result was written to GCF_010729665.1_ASM1072966v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:10,815] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:10,820] [INFO] DFAST_QC result json was written to GCF_010729665.1_ASM1072966v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:10,820] [INFO] DFAST_QC completed!
[2024-01-24 13:51:10,820] [INFO] Total running time: 0h2m28s